relatório de actividades 2008

RELATÓRIO DE ACTIVIDADES
2008
ÍNDICE
PÁG.
1.
INTRODUÇÃO
3
2. INVESTIGAÇÃO CIENTÍFICA
2a. Cancer Biology
7
2b. Cancer Genetics
13
2c. Carcinogenesis
29
2d. Population Genetics
38
2e. Genetics, Evolution and Pathology
48
2f. Tumour Evolution and Development
56
2g. Genetic Diversity
59
2h. Public Health and Cancer
64
2i. Tumour Molecular Models
68
3. EDUCAÇÃO CONTÍNUA E DIFUSÃO CIENTÍFICA
72
4. SERVIÇO À COMUNIDADE
4a. UPS
75
4b. UPSi
82
4c. UPSs
87
5. RECÉM-DOUTORADOS
90
6. RESUMO DOS PROJECTOS
91
7. TRABALHOS PUBLICADOS
100
8. REVISTAS CIENTÍFICAS INTERNACIONAIS COM MEMBROS
DO IPATIMUP NOS SEUS EDITORIAL BOARDS
108
9. NÚCLEO DE AMIGOS DO IPATIMUP
109
10. ANEXOS - PROGRAMAS DOS EVENTOS
110
10.1 DIA DO IPATIMUP
10.2 PORTO CANCER MEETING
10.3 PORTUGALIAE GENETICA
10.4 CONFERÊNCIA DO EQUINÓCIO
2
1. INTRODUÇÃO
No primeiro parágrafo do Plano de Actividades para 2008 referimos que:
“Desde finais de 2005 que temos vindo a escrever nos Planos de Actividades o seguinte “As
actividades do IPATIMUP em 2006, assim como nos anos seguintes, serão condicionadas
fortemente pelas características do Contrato Programa (2006-2010) que vier a ser assinado com o
Ministério da Ciência, Tecnologia e Ensino Superior. Se for possível cumprir o acordado
anteriormente, de modo informal, com a Fundação para a Ciência e Tecnologia, o IPATIMUP terá
possibilidade de reforçar o seu quadro de pessoal investigador e técnico, consolidando as
actividades de alguns grupos/áreas e criando condições para o estabelecimento de novas
competências e de novas áreas de intervenção fundamentais para o crescimento do Instituto, tanto
em termos nacionais como internacionais.
Infelizmente e tal como referimos no Relatório de Gestão, não só ainda não foi possível assinar o
novo Contrato Programa, como o financiamento que nos tem vindo a ser atribuído nos últimos anos
representa uma diminuição de cerca de 350.000 EUROS/ano em relação ao financiamento de 2005.
Com as limitações atrás referidas – a que se tem de somar a interrupção do subsídio da Reitoria e o
intervalo de mais de dois anos sem abertura de concursos de projectos por parte da FCT – o
IPATIMUP procurará atingir, no ano de 2008, os seguintes objectivos” (fim de citação do Plano de
Actividades para 2008).
Antes de passar à avaliação do que conseguimos, ou não, concretizar em 2008 em relação ao que
nos havíamos proposto, é de referir que continuamos sem convencer a FCT e a Reitoria a reverem a
sua posição. Isto é, em 2008, o IPATIMUP recebeu da FCT, a título de Financiamento Plurianual, o
valor correspondente a 2005, isto é, menos cerca de 350 000 EUROS do que em 2006, e continuou
sem receber os 225 000 EUROS correspondentes ao subsídio da Reitoria da Universidade do Porto.
Apesar desta seríssima limitação o IPATIMUP conseguiu atingir, em 2008, a maioria dos objectivos a
que se havia proposto
a) Mantivemos a investigação científica no nível alcançado nos últimos anos.
Os investigadores do IPATIMUP publicaram, em 2008, 110 artigos científicos, 96 dos quais em
revistas internacionais indexadas com Factor de Impacto (FI). 94 (98%) desses artigos foram
publicados em revistas com FI igual ou superior a 1, e 43 (45%)em revistas com FI entre 3 e 26,4.
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No quadro seguinte documenta-se a evolução da qualidade e quantidade da produção científica no
IPATIMUP (2000-2008).
A WEB of KNOWLEDGE (ISI) tem uma lista dos artigos de todas as áreas cientificas mais citados no
mundo. Portugal tinha, em Janeiro de 2009, 399 artigos nesta lista e a Universidade do Porto, 63.
Os investigadores do IPATIMUP foram autores, ou co-autores, de 11 desses artigos.
Os investigadores do IPATIMUP continuam a integrar Corpo Editoriais de revistas científicas de
Patologia Humana, Oncologia, Oncobiologia, Genética, Medicina Molecular, Gastroenterologia e
Endocrinologia. Nesta altura são 27 as Revistas Cientificas Internacionais que contam com membros
do IPATIMUP nos seus Corpos Editoriais (Ver Lista das Revistas no fim do Relatório).
No fim do Relatório encontra-se a lista da totalidade dos artigos publicados em 2008 com os
Factores de Impacto das respectivas revistas.
b) Finalizámos a contratação dos 11 novos investigadores seniores cujas “posições” haviam sido
abertas, no âmbito do Programa CIENCIA 2007, para “pós-docs” com três anos de experiência.
Sete dos 11 investigadores foram recrutados “fora” do IPATIMUP (cinco portugueses, um brasileiro
e um dinamarquês) e os quatro restantes eram já bolseiros pós-doutoramento do IPATIMUP.
c) Reforçou-se a participação em Programas Doutorais em articulação com a Faculdade de
Medicina, ICBAS, Faculdade de Ciências e Faculdade de Engenharia, assim como com o Hospital S.
João, o IPO-Porto e o IBMC/INEB. Para além do Programa GABBA, iniciámos o Programa Doutoral
em Medicina e Oncologia Molecular, o Programa Doutoral em Patologia e Genética Molecular e o
Programa Doutoral para médicos da Fundação Calouste Gulbenkian e da Fundação Champalimaud.
Em 2008 terminaram os seus doutoramentos 8 “estudantes” do IPATIMUP (os últimos 4 realizaram
4
as suas Provas já no 1º trimestre deste ano). As actividades de Divulgação Científica e da Educação
Continua tiveram, entretanto, um desenvolvimento notável.
d) Continuámos a reestruturação do IPATIMUP no sentido de separar a componente de prestação
de serviços das actividades de investigação e de divulgação científica. O processo de criação de uma
empresa – IPATIMUP Diagnósticos – não avançou, no entanto, tanto como gostaríamos, em parte
devido à nossa inexperiência no chamado mundo empresarial. As actividades de prestação de
serviços por parte das três Unidades vocacionadas para isso (UPS, UPSi e UPSs) mantiveram-se no
nível anterior ou tiveram mesmo, no caso da Genética Molecular (UPSs), uma subida substancial.
e) O novo site do IPATIMUP foi construído e está em pleno funcionamento.
f) Dificuldades na empresa encarregada da instalação do sistema informático do INFOCANCER não
nos permitiu concretizar o objectivo de ter o Programa a funcionar em 2008.
g) A construção do I3S, cuja criação oficial teve lugar em Fevereiro de 2008, continuou a ser
concretizada a vários níveis: pessoas, serviços e logística. O Consórcio I3S recebeu, em Novembro
de 2008, o Prémio Corino de Andrade da Ordem dos Médicos.
h) Consolidou-se o Consórcio com o IPO-Porto e assinou-se um Protocolo de Colaboração com o
H.S.João com incidência particular na optimização da utilização dos Bancos de Tecidos e Tumores
de ambas as instituições.
i) Não foi possível agregar, em 2008, nenhum Centro de Investigação da U.Porto ao IPATIMUP (O
candidato melhor colocado viu a sua classificação baixar para Bom).
j) O IPATIMUP tem-se involvido seriamente na construção do Health Cluster Portugal. A criação do
Cluster foi formalizada oficialmente em Abril de 2008 e o Governo oficializou a criação do
Respectivo Polo de Competitividade em Saúde em Fevereiro de 2009.
k) Comemorou-se a 21 de Abril de 2008 o Dia do IPATIMUP que, desta vez, homenageou
especialmente os Amigos do IPATIMUP na pessoa do Doutor Luis Portela.
l) O IPATIMUP realizou, em 2008, como nos anos anteriores, três reuniões internacionais – uma
sobre Genética Populacional e Genética Forense (Portugaliae Genetica, 11ª edição), outra sobre
5
Cancro (Porto Cancer Meeting – 17ª edição) e a terceira sobre Ciência e Cultura (Conferências do
Equinócio – 12ª edição).
6
2. INVESTIGAÇÃO CIENTIFICA
2 a. CANCER BIOLOGY
TEAM:
Coordinator: Paula Soares (PS), BSc, MSc, PhD.
Scientific Consultant: Manuel Sobrinho-Simões (MSS), MD, PhD
Principal Investigators: Clara Sambade (CS) MD, PhD; Gabriela Almeida (GA), Helena
Vasconcelos(HV), BSc, PhD José Manuel Lopes (JML) MD, PhD, Valdemar Máximo (VM) BSc, PhD;.
Investigators/collaborators: Ana Preto(AP), BSc, PhD; Ana Sofia Rocha(ASR), BSc, PhD,
Post-Docs: Paula Boaventura (PB) BSc, PhD; Patrícia Castro(PC), BSc, PhD; Jorge Lima(JL), BSc, PhD.
PhD Students: Andreia Palmeira (AP), André Silva (AS), Catarina Eloy MD (CE), Helena Popúlo (HP),
Hugo Prazeres (HugoP), Joana Silva (JS), Jonh Preto (JP), Raquel Lima(RL), Ricardo Celestino (RC),
Vitor Trovisco(VT)*.
MSc Students: Eva Barbosa (EB)*, Inês Alvelos (IA), Joana Santos(JS), Joana Torres (JT), Raquel
Portugal (RP)*, Sara Carvalho (SC).
BI’s: Alexandra Faustino (AF)Catarina Gonçalves(JG), João Vinagre (JV).
Undergraduate students: Sara Carvalho (SC), Maria Inês Castro (MIC), Inês Gonçalves (IG), Liliana
Santos (LS).
Pathologists: Isabel Amendoeira, MD, Elsa Fonseca MD, PhD, João Magalhães, MD.
+ Clinicians: Manuel Cardoso de Oliveira (MCO), MD, PhD, Endocrine Surgeon; Duarte Pignatelli (DP),
MD, PhD, Endocrinologist; José Teixeira Gomes (JTG) , MD, PhD, Endocrine Surgeon.
Visiting researchers: Margriet De Vries (MdV), Medical student.
* - Concluded their theses in 2008.
** - Investigator who is in charge of starting a joint project with the IBMC, ICBAS and INSRA-Porto.
ASR Moved to Jacques Dumont Lab during 2007 but maintains a project with CB group.
AP will stay in part-time since she has got a job as Professor in UM.
PC is doing her Post –Doc under the supervision of Eugénio Santos (University of Salamanca) and
PS.
Main Objectives
1. The main objective of the group is to progress in the understanding of the etiopathogenesis of
some types of human cancer, with an emphasis on thyroid and neuroendocrine tumours. Within this
frame, a particular attention is paid to: a) genetic alterations in tyrosine kinase receptors and signal
transducing molecules involved in the mitogen-activated protein kinases (MAPK) pathway; and b)
mitochondrial alterations secondary to mitochondrial DNA mutations/deletions or to mutations in
nuclear genes encoding mitochondrial enzymes. In addition to these basic/translational research
component, the group has a more basic, scientific interest in some aspects of cell cycle, apoptosis
and motility/invasiveness processes in cancer development.
2. Some members of the group are also involved in clinical-pathological studies in other types of
human tumours(e.g. lymphoma/leukemia), and in projects aiming to validate and/or identify
molecular targets for cancer treatment, namely via the utilization of cell signalling inhibitors and the
down regulation of gene expression using siRNAs.
Main research topics
1 - Oncobiology of familial and sporadic thyroid tumours with an emphasis on papillary carcinoma.
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2 - Role of mitochondrial alterations in the etiopathogenesis of sporadic, irradiation-induced and
familial tumours (the study of post-Chernobyl tumours is made under this frame).
Additional topics subheadings:
•
Oncobiology of neuroendocrine tumours with an emphasis on those of the digestive system
•
Validation of molecular targets in cancer treatment and/or chemo-resistance
Main Achievements
In the beginning of 2003, RET rearrangements , RAS mutations and PAX8/PPARG translocations
were thought to be the major genetic alterations associated with papillary thyroid carcinoma (PTC)
and follicular carcinomas (FTC). In 2003 we have identified BRAFV600E mutation as a major
oncogenic event in PTC (in about 50% of the cases) which does not coexist with RET/PTC or RAS
mutation. We showed that the BRAFV600E mutation was specifically associated with the
conventional type of PTC, as well as with some variants of PTC displaying a prominent papillary
growth pattern. We also showed that BRAF mutation is associated with PTC that progress to
undifferentiated carcinoma, and that is rarely involved in pediatric and post-Chernobyl PTC. We
detected a new type of BRAF mutation (BRAFVK6001E) in a solid variant of PTC. We have shown
that the follicular variant of PTC which is known to behave differently from conventional PTC,
namely regarding its tendency to give rise to lung and bone metastases displays a different BRAF
mutation (BRAFK601E in about 7-9% of the cases and no BRAFV600E) and that it shares some of the
molecular features of FTC: frequent occurrence of PAX8/PPARtranslocation and N-RAS mutations.
We have also demonstrated that the FTC are clearly aneuploid whereas almost every PTC is diploid
or quasi–diploid. We found an association between the presence of a polymorphism in H-RAS and
the occurrence of aneuploidy in thyroid tumours. We also detected an association between the
presence of H-RAS 81-C allele and significantly higher amounts of H-RAS p21 mRNA isoform. These
findings support the hypothesis that H-RAS 81 T-C polymorphism may induce aneuploidy through
the overexpression of p21 isoform of H-RAS.
Regarding the role of the mtDNA mutations/variants and of nuclear genes that codify for
mitochondrial proteins in the etiopathogenesis of thyroid tumours we identified, for the first time,
somatic and germline mutations in the GRIM-19 gene in sporadic and familial Hurthle cell tumours of
the thyroid and described the mtDNA alterations in these settings.
Future workplan
-Clinicopathological studies
We intend to go further in the basic/translational studies in thyroid oncobiology field, in an attempt
to identify thyroid cancer patients who have a guarded prognosis. We have initiated a collaborative
project involving pathologists, scientists and clinicians from IPATIMUP, IPO-Porto and H S João; we
propose to perform a thorough clinico-pathological re-evaluation of the thyroid cancer cases
diagnosed and treated in the three institutions that showed an aggressive (metastatic and/or
recurrent) behavior, including an in depth immunohistochemical and molecular analysis using for
comparison a control group of matched cases without any signs of persistent or recurrent disease
at follow-up. Two MD, MSc will develop PhD thesis in this area.
-Dissecting molecular pathways (MAPK and RET)
To progress in the understanding of the role played by genetic alterations in the ethiopathogenesis
of thyroid carcinoma, we have established in vitro systems in which we can evaluate the functional
role and the signaling pathways activated by different oncogenic mutations. Using transfection cell
8
models, we have been comparing the transcription activation patterns of BRAF mutants with those
of RET/PTC; the results obtained show that STAT1/STAT3 appears to be differentially activated by
RET/PTC and by BRAF; in order to progress in this study we are performing luciferase-reporter
assays using the IRE-LUC (for STAT3) and GAS-LUC (for STAT1) constructs. Another part of the
project consists in the “construction” of conditional clones of thyroid cell lines harbouring both
mutated B-RAF and RET/PTC-1; to pursue this study we are now engineering TPC-1 and 8505C cell
lines with a tetracycline-regulated expression system (T-REx System).
In a previous study we have characterized RET mutational spectrum in a series of Portuguese
hereditary and sporadic Medullary Thyroid Carcinoma. We detected 3 novel RET variants
(Arg886Trp, Ser649Leu and Glu511Lys), all of which were absent in normal controls, and will be the
focus of further studies. Functional studies of novel RET mutations were started in 2007.
-Melanoma vs PTC
Given the genetic and biologic similarities between PTC and melanoma (BRAF and N-RAS mutations,
and c-MET overexpression), we decided, in 2007, to start studying melanomas from this standpoint.
For that, 97 human melanoma samples were collected and classified according to their histotypes.
An exhaustive clinic-pathological database was organized and tissue microarrays (TMA) blocks were
constructed from the melanoma samples. We have started the study of mTOR pathway (by
immunohistochemistry) and the genetic characterization of the tumours.
-Mitochondria and cancer
To address the issue of the relationship between mitochondria(mt) and cancer, we have recently
started a project centred on cybrid cell lines, in order to verify the functional effects induced by
mtDNA alterations. These cybrids cell lines were obtained by fusing of a mtDNA-free cell line with an
enucleated cell line.We are focusing at present on XTC.UC1,a thyroid cancer-derived cell line which
presents two mtDNA mutations – 3571insC in ND1 gene and G15557A in CytB gene.
The role of GRIM-19 in the etiopathogenesis of oncocytic tumours will be followed-up by checking
for gene expression and mutations in other types of mitochondrion-rich human tumors. We have
already studied renal oncocytomas and Warthin’s tumours of the salivary glands. We have recently
observed an association between low levels of GRIM-19 expression and STAT3 phosphorylation and
nuclear localization,in renal cell carcinomas, suggesting that GRIM-19 plays a role through STAT3
pathway; we are checking now for the expression of STAT3 downstream genes in a series of renal
tumours in order to clarify our hypothesis.
MSc Theses concluded:
Eva Barbosa. Hiperparatiroidismo Primário – da clínica ao gene. MSc Course on Molecular Medicine
and Molecular Oncology, Medical Faculty of the University of Porto,2008.
Raquel Portugal. Mutações e delecções do ADN mitocondrial (mtDNA) em oncocitomas renais. MSc
Course on Molecular Medicine and Molecular Oncology, Medical Faculty of the University of Porto,
2008.
PhD Theses concluded:
Victor Trovisco. “Role of BRAF gene alterations in the natural history of papillary thyroid
carcinoma”. Supervisor Manuel Sobrinho-Simões (Porto, Portugal).Thesis defended at the Medical
Faculty of University of Porto, February 2008. Papers:
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Soares P, Trovisco V, Lima J, Rocha A, Castro P, Preto A, Máximo V, Botelho T, Seruca R and
Sobrinho-Simões M. “BRAF mutations and RET/PTC rearrangements are alternative events in the
etiopathogenesis of PTC”. Oncogene, 2003; 22:4578-4580.
Trovisco V, Soares P, Preto A, Vieira de Castro I, Lima I, Castro P, Máximo V, Botelho T, Moreira S,
Meireles AM, Magalhães J, Abrosimov A, Cameselle-Teijeiro J and Sobrinho-Simões M. “Type and
prevalence of BRAF mutations are closely associated to papillary thyroid carcinoma histotype and
patients’ age but not with tumour aggressiveness”. Virchows Archiv, 2005; 446:589-595.
Trovisco V, Vieira de Castro I, Soares P, Máximo V, Silva P, Magalhães J, Abrosimov A, Guiu XM and
Sobrinho-Simões M. “BRAF mutations are associated with some histological types of papillary
thyroid carcinoma”. The Journal of Pathology, 2004; 202:247-251.
Trovisco V, Soares P, Soares R, Magalhães J, Sá-Couto P and Sobrinho-Simões M. “A new BRAF gene
mutation detected in a case of a solid variant of papillary thyroid carcinoma”. Human Pathology,
2005; 36:694-7.
Trovisco V, Couto JP, Cameselle-Teijeiro J, Vieira de Castro I, Fonseca E, Soares P and SobrinhoSimões M. “Acquisition of BRAF gene mutation is not a requirement for nodal metastization of
PTC”. Submitted for publication to ‘Clinical Endocrinology’.
Soares P, Trovisco V, Rocha AS, Feijao T, Rebocho AP, Fonseca E, Vieira de Castro I, CameselleTeijeiro J, Cardoso-Oliveira M, Sobrinho-Simões M. “BRAF mutations typical of papillary thyroid
carcinoma are more frequently detected in undifferentiated than in insular and insular-like poorly
differentiated carcinomas”. Virchows Archiv, 2004; 444:572-576.
Publications
A.Within the main research topics
1.
Prazeres HJ, Rodrigues F, Soares P, Naidenov P, Figueiredo P, Campos B, Lacerda M, Martins
TC. Loss of heterozygosity at 19p13.2 and 2q21 in tumours from familial clusters of non-medullary
thyroid carcinoma. Fam Cancer 7:141-149, 2008
2.
Máximo V, Lima J, Soares P, Silva A, Bento I, Sobrinho-Simões M. GRIM-19 in Health and
Disease. Adv Anat Pathol 15:46-53, 2008.
3.
Sobrinho-Simões M, Máximo V, Rocha AS, Trovisco V, Castro P, Preto A, Lima J, Soares P.
Intragenic mutations in thyroid cancer.Endocrinol Metab Clin North Am 37:333-362, 2008
4.
Cameselle-Teijeiro J, Pardal F, Eloy C, Ruiz-Ponte C, Celestino R, Castro P, Soares P, SobrinhoSimões M. Follicular thyroid carcinoma with an unusual glomeruloid pattern of growth. Hum Pathol.
39:1540-1547, 2008.
5.
Trovisco V, Couto JP, Cameselle-Teijeiro J, de Castro IV, Fonseca E, Soares P, SobrinhoSimões M. Acquisition of BRAF gene mutations is not a requirement for nodal metastasis of papillary
thyroid carcinoma. Clin Endocrinol (Oxf). 69:683-685, 2008.
6.
Rocha AS, Paternot S, Coulonval K, Dumont JE, Soares P, Roger PP.Cyclic AMP inhibits the
proliferation of thyroid carcinoma cell lines through regulation of CDK4 phosphorylation. Mol Biol
Cell.19:4814-4825, 2008.
7.
Bertagnolli AC, Soares P, van Asch B, Amorim A, Cirnes L, Máximo V, Cassali GD. An
assessment of the clonality of the components of canine mixed mammary tumours by
mitochondrial DNA analysis. Vet J. 2008 Aug 25. [Epub ahead of print]
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B.Related with the main or acessory research topics
1.
Steinmuller T, Kianmanesh R, Falconi M, Scarpa A, Taal B, Kwekkeboom DJ, Lopes JM,
Perren A, Nikou G, Yao J, Delle Fave GF, O'Toole D: Consensus guidelines for the management of
patients with liver metastases from digestive (neuro)endocrine tumors: Foregut, Midgut, Hindgut,
and Unknown Primary. Neuroendocrinology 87:47-62, 2008.
2.
Eriksson B, Kloppel G, Krenning E, Ahlman H, Plockinger U, Wiedenmann B, Arnold R,
Auernhammer C, korner M, Rindi G, Wildi S all other Frascati Consensus Conference participants,
including Lopes JM: Consensus guidelines for the management of patients with digestive
neuroendocrine tumors- well differentiated jejuna-ileal tumor/carcinoma. Neuroendocrinology 87: 819, 2008.
3.
Ramage J, Goretzki PE, Manfredi R, Komminoth P, Ferone D, Hyrdel R, Kaltsas G, Kelestimur
F, Kvols L, Scoazec JY, Garcia MIS, Caplin ME, all other Frascati Consensus Conference participants,
including Lopes JM: Consensus guidelines for the management of patients with digestive
neuroendocrine tumors- well differentiated colon and rectum tumor/carcinoma.
Neuroendocrinology 87: 31-39, 2008.
4.
Plockinger U, Couvelard A, Falconi M, Sundin A, Salazar R, Christ E, Herder WW, Gross D,
Knapp WH, Knigge UP, Kulke MH, Pape UF all other Frascati Consensus Conference participants,
including Lopes JM: Consensus guidelines for the management of patients with digestive
neuroendocrine tumors- well differentiated appendix and
goblet cell carcinoma.
Neuroendocrinology 87: 20-30, 2008.
5.
Preto A, Figueiredo J, Velho S, Ribeiro A, Soares P, Oliveira C, Seruca R. BRAF provides
proliferation and survival signals in MSI colorectal carcinoma cells displaying BRAF(V600E) but not
KRAS mutations. J Pathol. 214:320-327, 2008.
6.
Ferreira AC, Gomes L, Máximo V, Amil J, Carneiro F, Machado JC, Tavarela-Veloso F. GRIM-19
mutations are not associated with Crohn's disease. Inflamm Bowel Dis, 14:434-435, 2008.
C.Other topics
1.
Eloy C, Lopes JM, Faria G, Moreira H, Brandão A, Silva T, Carneiro F: Clear Cell Change in
Colon Polyps. Int J Surgical Pathol 2008 Jul 8. [Epub ahead of print].
2.
Gouveia AM, Pimenta AP, Capelinha AF, Cruz D, Silva P, Lopes JM: Surgical margin status and
prognosis of gastrointestinal stromal tumor. World J Surgery 32:2375-2382, 2008.
3.
Lima-Ramos V, Pacheco-Figueiredo L, Costa S, Pardal F, Silva A, Amorim J, Lopes JM, Reis
RM. Role of TP53 codon 72 polymorphism in susceptibility, overall survival and adjuvant therapy
response in gliomas. Cancer Genetics and Cytogenetics 180:14-19, 2008.
4.
Gomes AL, Gouveia A, Capelinha AF, Cruz D, Silva P, Reis RM, Pimenta A, Lopes JM.
Molecular alterations of c-Kit and PDGFRA in GISTs. An evaluation study of a Portuguese series. J
Clin Pathol 61:203-208, 2008.
5.
Horta R, Barreto F, Marques M, Rebelo M, Reis JC, Lopes JM, Amarante J: Epithelialmyoepithelial parotid carcinoma after kidney transplantation. ecancermedicalscience 82, 2008. doi:
10.3332/ecancer.2008.92.
6.
Morais P, Magina S, Ribeiro MD, Rodrigues M, Lopes JM, Thanh HL, Wehnert M, Guimarães
H: Restrictive dermopathy-a lethal congenital laminopathy. Case report and review of the literature.
European Journal of Pediatrics 2008 Nov 20. [Epub ahead of print]. 7.
Soares H, Maia A,
Campos M, Dória S, Lopes JM, Fontoura M: Clinicopathological features of 45,X/46,Xidic(Y)
mosaicism and therapeutic implications:case report. São Paulo Medical Journal 126: 297-299, 2008.
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8.
Timonera E, Eloy C, Paiva ME, Lopes JM, Asa S, van der Kwast: Composite adenomatoid
tumor and myelolipoma of adrenal gland: report of two cases. Arch Pathol Lab Med 132:265-267,
2008.
9.
Viana-Pereira M, Lopes JM, Little S, Milanezi F, Basto D, Pardal F, Jones C, Reis RM: Analysis
of EGFR overexpression, EGFR gene amplification and the EGFRvIII mutation in Portuguese highgrade gliomas. Anticancer Res 28:913-920, 2008.
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2b. CANCER GENETICS
Coordinator: Raquel Seruca
Principal Investigators: Carla Oliveira, Céu Figueiredo, Fátima Carneiro, Fernando Schmitt,
Gianpaolo Suriano, Joana Paredes, José Carlos Machado
Post-Docs: Adeline Grellier, Cecília Durães, José Luis Costa, Marina Leite, Sofia Fernandes
PhD students: Ana Costa, Ana Machado, Ana Mateus, Ana Ribeiro, André Albergaria, André Vieira
Angela Costa, António Ferreira, Carlos Resende, Fernanda Milanezi, Hugo Pinheiro, Joana Carvalho,
Joana Correia, Joana Fernandes, Joana Figueiredo, Maria Melo, Nair Lopes, Nuno Guimarães,
Patrícia Oliveira, Paulo Canedo, Renata Carriço, Rui Ferreira, Sérgia Velho, Sílvia Carvalho
The research of our group focuses on the molecular genetics of three common types of epithelial
cancer (gastric, breast, and colorectal carcinoma). We aim at 1) identifying individuals at risk for the
various forms of these tumours; 2) identifying pathological features and molecular markers
occurring in the setting of familial and sporadic carcinoma; and 3) identifying signalling pathways
mediated by genetic and environmental factors in order to identify new molecular targets for
therapeutic intervention, in order to find molecular biomarkers associated to tumour progression or
to predict therapy response in cancer patients.
1. Identifying individuals at risk for gastric carcinoma
1. a) Bacterial factors for sporadic gastric carcinoma
Gastric cancer is the second most common cause of cancer-related death. Patients infected with H.
pylori are at increased risk of gastric cancer. Our group has previously shown that gastric cancer
seems to depend on the combined effects of bacterial pathogenicity and host susceptibility. It is
currently suggested that H. pylori infection induces DNA damage, and/or inhibits DNA repair, both in
vivo and in vitro, induces a decrease in repair activity and a transient mutator phenotype,
contributing to epithelial gastric genomic instability and to its neoplastic transformation.
In 2008, we investigated a possible link between bacterial infection and genetic instability of the
host genome, we examined the effect of H. pylori infection on known cellular repair pathways in
vitro and in vivo. Moreover, various types of genetic instabilities in the nuclear and mitochondrial
DNA were examined.We observed the effects of H. pylori infection on a gastric cell line (AGS), on
C57BL/6 mice and on individuals with chronic gastritis. Following H. pylori infection, the activity and
expression of BER and MMR are downregulated both in vitro and in vivo. Moreover, H. pylori
induces genomic instability in nuclear CA repeats in mice and in mitochondrial DNA of AGS cells and
chronic gastritis tissue, and this effect in mitochondrial DNA is associated with bacterial virulence.
Our results suggest that H. pylori impairs central DNA repair mechanisms, inducing a transient
mutator phenotype, rendering gastric epithelial cells vulnerable to the accumulation of genetic
instability and thus contributing to gastric carcinogenesis in infected individuals (Machado A, in
press in Clinical Cancer Research) .
1. b) Host factors for sporadic gastric carcinoma
The tumor necrosis factor alpha (TNFA)-308*A allele has been found to confer an increased risk of
gastric carcinoma. Inconsistency in risk estimates across populations lead us to hypothesize about
the presence of an alternative causal locus in the same chromosomal region. A suitable approach is
to determine the tumor necrosis factor haplotypic structure in order to clarify whether the
association between the *A allele and the increased risk of gastric carcinoma is etiologic or
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secondary to linkage disequilibrium. Firstly, we assessed the association between the TNFA-308G>A
polymorphism and the risk of gastric carcinoma in a population from Northern Portugal (508 gastric
carcinoma patients, 713 controls); secondly, we genotyped five microsatellite loci (TNFa, b, c, d, e)
flanking the TNFA-308G>A locus to establish the haplotypic structure associated with this singlenucleotide polymorphism in cases (122 patients) and controls (169 individuals). We found a
significant association between the *A allele and increased risk of gastric carcinoma (odds ratio, 1.7;
95% confidence interval, 1.3-2.2) confirming previous results in our population. Regarding the *A
allele-associated haplotypes, the most relevant difference was found for the H1A haplotype present
in 33.1% of the cases and 12.5% of the controls. We also observed haplotypes associated with the *A
allele that were found only in cases or controls. A population differentiation test showed that the
gastric carcinoma and the control groups were significantly different for the *A allele haplotypic
structure. This suggests that the association between the TNFA-308G>A polymorphism and
increased risk of gastric carcinoma is dependent on linkage disequilibrium with an as yet
unidentified locus.
Further, it has been demonstrated that polymorphisms within inflammation-related genes are
associated with the risk of gastric carcinoma (GC) in people infected with Helicobacter pylori.
Recently, polymorphisms in the gene encoding the interferon gamma receptor 1 (IFNGR1) were
found to be associated with increased susceptibility to H pylori infection. We aimed to determine
the association between polymorphisms in the IFNGR1 gene and development of chronic gastritis
and GC. METHODS: In a case-control study including 733 controls, 213 patients with chronic gastritis
and 393 patients with GC, the IFNGR1 -611*G/*A, -56*C/*T, +1004*A/*C and +1400*T/*C
polymorphisms were genotyped. A second independent case-control study including 100 controls
and 65 patients with GC was used for confirmation of the original results. The effect of the -56*C/*T
promoter polymorphism in the level of expression of the IFNGR1 gene was evaluated by an IFNGR1 56*C/*T allele specific luciferase reporter assay. In patients with early onset GC (defined as being
less than 40 years of age at the time of diagnosis) we found a significant over-representation of the
IFNGR1 -56*T/*T homozygous genotype with an odds ratio (OR) of 4.1 (95% confidence interval (CI)
1.6 to 10.6). This result was confirmed in a second independent case-control study. In the luciferase
reporter assay we observed a 10-fold increase (p<0.001) in luciferase expression associated with the
IFNGR1-56*T allele. Our results indicate that the IFNGR1 -56C/T polymorphism is a relevant host
susceptibility factor for GC development. Our data also indicate that this genetic polymorphism is
functionally relevant and may be related to the early development of GC.
1. c) Genetic factors for familial forms of gastric cancer
Hereditary diffuse gastric cancer (HDGC) families carry CDH1 heterozygous germline point or small
frameshift CDH1 mutations in 30% of the cases described to date. HDGC tumors acquire complete
CDH1 inactivation through CDH1 promoter hypermethylation in 50% of the cases. We hypothesized
that CDH1 genomic rearrangements would be found in the germline of CDH1 negative HDGC families
and somatically as the ‘second-hit’ in DGC of CDH1 mutation carriers. The germline of 93 CDH1
mutation negative families was screened for large genomic rearrangements by MLPA and validated
by RT-PCR. Breakpoints were cloned with oligo-CGH-arrays and long-range-PCR. In-silico analysis was
used to determine a potential mechanism for rearrangements. Samples collected from 28 DGC (17
patients among 15 HDGC families) were analyzed for somatic CDH1 mutations, LOH and promoter
hypermethylation. Seven percent of previously described mutation negative HDGC probands carried
genomic deletions caused by mechanisms involving mainly non-allelic homologous recombination in
Alu-sequences. Two families carried an identical deletion encompassing the full CDH3 sequence and
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CDH1 exons 1 and 2, most probably derived from a common ancestor. Other deletions affecting
exons 1, 2, 15 and/or 16 were identified. CDH1 somatic deletions (LOH) were found in 42.9% of 28
neoplastic lesions analyzed, adding LOH as a major ‘second-hit’ mechanism in HDGC tumors. CDH1
large deletions increase the susceptibility to HDGC when occurring in patients’s germline; and
determine DGC development when targeting the wild-type allele in CDH1 germline mutation carriers’
stomachs. These results are pivotal for HDGC management and treatment.
Our team focuses on the role of E-cadherin germline mutations of the missense type found in the
setting of both hereditary diffuse gastric cancer and early onset diffuse gastric cancer. As reference
laboratory of the International Gastric Cancer Linkage Consortium, we have been involved in the
functional characterization of 5 new HDGC-associated E-cadherin germline missense mutations,
aiming at unrevealing their pathogeneicity, using in vitro assays. These HDGC-associated E-cadherin
germiline missense mutations found: one in German family, one found in a Dutch family, one from
an Italian family, and two from Portuguese families.
Further, we explored the hypothesis that mutations affecting different E-cadherin protein domains
have distinct effects on cell motility. To accomplish our objective we characterized the effect of
eleven HDGC CDH1 germline missense mutations (T118R, L214P, G239R, A298T, T340A, P373L,
R749W, E757K, E781D, P799R and V832M) on cell motility. Our results allowed the identification of
the E-cadherin domains pivotal for cell motility, further demonstrated a genotype-phenotype
correlation, and defined a subset of HDGC cases which may benefit from EGFR inhibitors.
2. Identifying molecular markers occurring in the setting of familial and sporadic cancer
2. a) Gastric cancer
We determined the second-hit mechanism leading to tumour development on the context of HDGC.
Seventeen patients belonging to 15 HDGC families carrying distinct CDH1 germline mutations and
meeting the IGCLC criteria were analysed. The mean age of the patients was 39.5±12.6 years old
ranging from 23 to 67. We independently analyzed a total of 28 neoplastic lesions, collected from 17
patients for CDH1 promoter hypermethylation, LOH and, mutations within the hotspot exons 7-10,
where CDH1 somatic mutations cluster. We did not extend the mutation analyses to all CDH1 exons
due to lack of material. In order to dilute contamination with DNA from normal cells, DNA was
extracted from macrodissected areas enriched in neoplastic cells. This approach allowed us to
specifically analyze molecular alterations occurring in neoplastic cells that are easily masked when a
large population of normal cells contaminates tumor samples. Frequency of 2nd-hit inactivation
mechanisms in HDGC families and neoplastic lesions. We found somatic epi/genetic alterations in
one or more neoplastic lesions from 80.0% of the families analyzed (12/15 probands). These somatic
epi/genetic alterations were present in 75% of the neoplastic lesions analyzed (21/28 lesions): 81.3% in
primary carcinomas (13/16) and 66.7% in metastases (8/12). In three primary tumors and four
metastases, no 2nd-hit mechanism was identified. All alterations found in HDGC neoplastic lesions
were absent from constitutional DNA, representing the 2nd-hit inactivation mechanism. Epigenetic
and genetic CDH1 alterations occur either alone or simultaneously in HDGC neoplastic lesions. From
the 28 HDGC lesion analyzed, CDH1 promoter hypermethylation was found in nine (32.1%) cases, LOH
in seven (25.0%), and both alterations in five cases (17.9%), most probably reflecting tumor
population heterogeneity. We did not find somatic mutations, in the regions analyzed, in any of the
neoplastic lesions. In HDGC primary tumors (n=16), we found CDH1 promoter hypermethylation in
eight (50%) cases, LOH in two (12.5%), and both alterations in three (18.8%). CDH1 epigenetic
alterations alone were present in 50% of the cases, while LOH, concomitantly or not with epigenetic
alterations, was present in 31.3% of the cases. The eight neoplastic lesions harboring CDH1 promoter
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hypermethylation only, retained both alleles and did not show somatic mutations. In metastatic
lesions (n=12) we found CDH1 promoter hypermethylation in one (8.3%) case, LOH in five (41.7%), and
both alterations in two (16.7%). In metastases, 8.3% of the lesions displayed CDH1 epigenetic
alterations only, while 58.3% displayed LOH concomitantly or not with CDH1 hypermethylation.
The comparison of 2nd-hit mechanisms in primary tumors and metastatic lesions showed that
primary tumors displayed preferentially epigenetic alterations (50%) as single events, while
metastatic lesions displayed preferentially genetic (LOH) concomitantly or not with epigenetic
alterations (58.3%) (p=0.0274). The tumor associated methylation observed in our series of HDGC
patients is very unlikely agerelated, since the majority of patients were younger than 50 years old at
diagnosis. Sixty-nine percent of patients younger than 50 years old (n=9/13) displayed CDH1
promoter hypermethylation in their tumors while 50% (n=2/4) of patients older than 50 years old had
hypermethylation in their tumors. Different lesions from the same patient display distinct patterns
of 2nd-hit mechanisms
In three families multiple lesions from the same patient were analyzed. In one family, we analyzed
one primary tumor foci and two metastases and found that while the primary tumor displayed LOH,
both metastases displayed methylation concomitant with distal LOH. Moreover, the LOH pattern
displayed by the primary tumor foci showed loss of the complete CDH1 coding region while in both
metastases only the distal 3’ LOH marker (D16S3067) showed loss.
In another family, we studied two patients: two primary tumor foci and one metastasis from patient
1 and, two primary tumor foci and two metastases from patient 2. Primary tumors from patient 1
displayed different 2nd-hit mechanisms, one displayed methylation and the other LOH at least at
two intragenic markers (germline mutation and rs1801552). The metastasis displayed LOH at a single
intragenic marker (germline mutation). As for patient 2, primary tumor foci displayed also different
2nd-hit mechanisms, one displayed methylation only and the other displayed methylation
concomitantly with distal LOH (D16S3067). The two metastases from patient 2 displayed LOH only,
but with different patterns of loss. The results in these two families are likely to indicate that the
different lesions analyzed in each patient’s stomach/metastases arose as a result of independent
2nd-hit mechanisms, acting somatically at the CDH1 locus.
In the last family several lesions were analyzed from a single patient and a different scenario was
observed: the two primary tumor foci analyzed showed methylation only, but in the three ovarian
metastasis no methylation, LOH or somatic mutation in any of the 16 CDH1 exons (exceptionally in
this case enough DNA was available for CDH1 complete mutation screening)
was found as a 2nd-hit mechanism. We validated all 2nd-hit results by confirming the common origin
of all neoplastic lesions and matched normal tissue, from each patient, with a large set of
insertion/deletion markers in twenty different chromosomes. This analysis allowed us to infer
whether each lesion arose independently in each patient’s stomach/metastases or whether all
lesions were likely to arise as a result of a common trigger mechanism. Moreover, we used the
insertion/deletion patterning to exclude allele dropout as a potential reason for loss at single CDH1
LOH markers. LOH was commonly observed in HDGC tumors at the CDH1 locus while no allele
dropout occurred in the PCR amplification of the 32 insertion/deletion markers. The E-cadherin
immunoexpression in HDGC tumors is generally consistent with the combination of germline and/or
somatic defects.
We performed E-cadherin immunohistochemistry in 26 of 28 lesions using an antibody that
recognizes the cytoplasmic domain of the protein and therefore is expected to stain E-cadherin fulllength or near full-length proteins only. We assessed the percentage of positive and negative cells
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for E-cadherin immuno-reactivity as well as the cellular localization of the protein. For all cases, we
had as internal control normal E-cadherin expression either at the foveolar zone or in non-disrupted
glands, adjacent to all tumor areas. All lesions analyzed contained neoplastic cells displaying
abnormal or absent E-cadherin protein expression and localization, with the exception of neoplastic
cells belonging to tumor from one family, which displayed only homogeneous membrane
expression.
In most cases we observed consistency of immuno-histochemistry results and the combination of
germline and somatic defects . Both the percentage of expressing cells and the cellular localization
of the protein were independent of type and site of CDH1 germline mutation as well as from type of
CDH1 somatic inactivation mechanism and type of lesion analyzed (primary tumor or metastasis).
The type of 2nd-hit mechanism is not dependent on the type and site of CDH1 germline mutation.
We performed association studies in order to understand whether the type of 2nd-hit in HDGC
tumors was dependent on the CDH1 germline mutation type. We analyzed whether individuals
carrying either truncating or missense mutations displayed any specific type of 2nd-hit inactivation
mechanism and verified that no association exists between these two parameters.
In addition, no association was found between the site of CDH1 germline mutation and the type of
CDH1 somatic inactivation mechanism. Somatic promoter hypermethylation alone and LOH alone or
with concurrent promoter hypermethylation occurred in tumors from carriers harbouring germline
mutations dispersed throughout the CDH1 gene.
2. b) Colorectal cancer
Little was known about the frequency of KRAS and BRAF mutations in pre-malignant lesions and in
CRCs at different stages of progression. In order to determine the oncogenic importance and the
timing of occurrence of KRAS and BRAF mutations in the process of colorectal tumorigenesis, we
recently analyzed a series of mixed hyperplastic and adenomatous colorectal polyps. We found that
mutations in KRAS or BRAF in these pre-malignant lesions occur in a mutually exclusive manner, as
earlier verified for MSI CRC. Moreover, KRAS and BRAFV600E mutations occur in 35% and 30% of the
polyps, respectively. When comparing the frequency of KRAS and BRAF mutations found in our
series of colorectal polyps with that observed in MSI CRC, no difference is observed. These
observations highlight the role of both KRAS and BRAF activation as primary genetic events and
their role in the initiation of this subset of sporadic CRC.
In addition, these polyps were also studied for molecular phenotypes previously associated to
sporadic MSI CRC. In MSI sporadic CRC, BRAF mutations were preferentially found in CRC associated
with hMLH1 promoter hypermethylation. In our series of polyps, none of the cases, including those
with BRAF mutations, harbored methylation at the hMLH1 promoter and all were microsatellite
stable. These results demonstrate that KRAS or BRAF mutations precede hMLH1 promoter
methylation and MSI phenotype. This data challenges the current assumption that MMR deficiency
in sporadic CRC induces not only an accumulation of mutations in non-coding and coding repetitive
tracts but also an increased rate of missense mutations, namely in proto-oncogenes. Instead, it
suggests that in sporadic MSI CRC, KRAS and BRAF oncogenic mutations are triggers of malignancy
rather than gene targets of MMR deficiency. Moreover, it is likely that in sporadic MSI CRC pathway,
the late acquisition of hMLH1 methylation leading to loss of MMR repair occurs mostly in the
transition from a premalignant to a malignant stage.
Interestingly, in the same study, we verified that CIMP phenotype occurred in 25% of the polyps and
all were mutated for BRAF. These results are in accordance with what was previously found in CRC
for the association of BRAF mutations with the CIMP phenotype. Furthermore, both results (in
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polyps and in CRCs) suggest that BRAF mutant colorectal cancer cells need to accumulate extra
epi/genetic alterations in order to acquire full transformation.
2. c) Breast cancer
The expression of additional genes, others than oestrogen receptor, may be important to the
hormone-responsive phenotype of breast cancer. Microarrays analysis have revealed that FOXA1
and GATA-3 are expressed in close association with ER-α, both encoding for transcription factors
with a potential involvement in the ER α-mediated action in breast cancer. The purpose of this study
was to explore if the concomitant expression of ER α, FOXA1 and GATA-3 may provide an
opportunity to identify specific subsets of patients that could have a good prognosis, as well as
would benefit from endocrine treatment.
We evaluate FOXA1 and GATA-3 expression in 249 breast carcinomas by immunohistochemistry,
associating it with breast cancer molecular markers, clinico-pathological features and patient’s
survival. FOXA1 expression was demonstrated in 42% invasive carcinomas, while GATA-3 was
detected in 48% of the cases. FOXA1 expression was inversely associated with tumour size,
Nottingham prognostic index, histological grade, vascular invasion, lymph node stage and HER-2
overexpression, while GATA-3 expression showed inverse association with histological grade and
HER-2. Both FOXA1 and GATA-3 were directly associated with ERα and PR. Among FOXA1 positive
tumours, 83.1% are comprised in the luminal A subtype, similarly to GATA-3, where 87.7% of positive
tumours were classified within this molecular subtype. Cases that were ER-/FOXA1+/GATA-3+, ER/FOXA1-/GATA-3- and ER+/FOXA1-/GATA-3- showed an association with an increased tumour size
compared with tumours expressing the three markers. Cox proportional hazard analysis showed
FOXA1 and the cluster ER±/FOXA1+/GATA-3+ as significant predictors for disease-free survival.
FOXA1 was an independent predictor of good outcome in breast cancer, whereas GATA-3 was an
important luminal marker. Patients whose carcinomas lack FOXA1 and GATA-3 expression present a
5-fold increased risk for recurrence compared with the ones that are positive for these two markers.
3. Identifying signaling pathways mediated by genetic factors in the distinct cancer models
3. a) Signaling pathways mediated by P-cadherin in breast cancer
Cell-cell adhesion is an elementary process in normal epithelial cellular architecture. Several studies
have demonstrated the role mediated by cadherins in this process, besides their role in the
maintenance of cell polarity, differentiation and cell growth. In tumor progression, these molecules
are frequently altered. In breast cancer, tumors that express P-cadherin are of high histological
grade, decreased cell polarity, show an aggressive behavior and a worse patient survival. However,
little is known how this protein influences the very aggressive behavior of these tumors. To achieve
this goal, we set up a breast cancer cell model, where P-cadherin was overexpressed in MCF-7/AZ
cell line, and we analyze its role in migration, motility and invasion. We showed that P-cadherin
overexpression, in breast cancer cells with wild-type E-cadherin, promotes cell migration, motility
and invasion. Moreover, we found that the presence of P-cadherin induces the secretion of matrix
metalloproteases, specifically MMP-1 and MMP-2, which lead to P-cadherin ectodomain cleavage.
Further, we show that soluble P-cadherin fragment is a key mechanism to induce in vitro invasion of
breast cancer cells. Overall, our results contribute to elucidate the mechanism underlying the
invasive behaviour and the poor prognosis of P-cadherin expressing breast tumors.
Changes in junctional catenin expression may compromise cadherin-mediated adhesion, increasing
cell malignant properties such as invasive and metastatic abilities. Altered expression of a-, b-, c- and
p120-catenin has been reported to be associated with E-cadherin loss or decreased expression, in
both breast carcinomas and breast cancer cell lines.
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To investigate the expression and subcellular localisation of p120- and b-catenin in a series of human
invasive breast carcinomas, and correlate it with biological markers and clinicopathological
parameters. Both catenins frequently exhibited a reduced membranous or cytoplasmic staining
pattern. These alterations were significantly correlated with lack of both
E-cadherin and oestrogen receptor-a expression. It was possible to associate the expression of bcatenin with histological grade, tumour size and nodal status, suggesting a relevant role for this
catenin as a prognostic factor. The majority of E- and P-cadherin co-expressing tumours were
related to cytoplasmic expression of p120- catenin; in this group of breast carcinomas, patient
survival was poor. Results indicate that p120-catenin cytoplasmic accumulation may play an
important role in mediating the oncogenic effects derived from P-cadherin aberrant expression,
including enhanced motility and invasion, particularly in tumours which maintain E-cadherin
expression.
3. b) Signaling pathways mediated by E-cadherin
We used a panel of eleven gastric cancer cells lines associated E-cadherin germline missense
mutations, all of them harbouring functional consequences, impairing in vitro the ability of Ecadherin to mediate cell-cell adhesion and to suppress invasion.
It has been previously described that wild-type E-cadherin binds to EGFR via the extracellular
domain of both proteins, and as such inhibits its activation and consequent cell motility. To confirm
that the increased migratory behaviour observed for some of the E-cadherin mutations under study
is associated to EGFR activation, we performed immunofluorescence analysis using a phosphospecific antibody against the tyrosine residue 1086 of the cytoplasmic domain of EGFR.
All cell lines expressing extracellular mutant forms of E-cadherin, (T118R, L214P, G239R, A298T and
P373L), displayed higher EGFR activation than cells expressing wild-type E-cadherin. A clear
membranous staining with a punctuate pattern was observed, as well as staining of what we
believe is the cell surface. This phenotype is similar to what we observed for cells negative for Ecadherin, which also displayed increased EGFR phosphorylation in comparison to the wild-type
expressing cells. The same pattern was observed for the cells expressing the intracellular mutations
within the juxtamembrane region, R749W and E757K, which is in accordance with the motility
analysis results. The activation pattern of EGFR for the other intracellular mutations E781D, P799R
and V832M resembled the one observed for wild-type E-cadherin expressing cells]. In these cases,
the staining was weaker and had a more diffuse pattern, being the cell-cell contacts not so
pronounced .
Altogether, all cell lines displaying high migratory behaviour also exhibited high EGFR activation.
An inverse correlation between the susceptibility of EGFR activation by EGF and the ability of the Ecadherin mutants to form a stable complex with EGFR has been previously reported. To verify if the
increase in EGFR activation would correlate with reduced stability of E-cadherin/EGFR heterodimers,
we characterised the interaction between EGFR and E-cadherin for the cells expressing mutations in
either the extracellular or the juxtamembrane domain. A reduced affinity of EGFR to the
extracellular mutant forms of E-cadherin T118R, L214P, G239R, A298T and P373L was observed,
when compared to the wild-type E-cadherin protein. As predicted, immunoprecipitation was also
weaker for mutants R749W and E757K, since lower amounts of E-cadherin are expressed. We next
raised the question whether mutations in the intracellular juxtamembrane domain of E-cadherin
would also affect the stability of the EGFR/E-cadherin complexes, or if this result was due solely to
reduced expression. To this end, we repeated the immunoprecipitation using lysates of cells treated
with DMSO, and therefore with restored E-cadherin expression. Under these conditions, strong
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immunocomplexes were obtained, suggesting that the juxtamembrane region of E-cadherin is not
involved in complex formation with EGFR.
Since cell motility of mutants R749W and E757K could be restored to levels similar to wild-type Ecadherin expressing cells upon DMSO treatment, we questioned whether the EGFR activation
observed for these mutants would play a direct role in cell motility. Motility assay was repeated in
the presence of the EGFR inhibitor Tyrphostin AG 1478, and we observed a significant decrease in
cell motility, pointing to a direct involvement of EGFR in the motility of these cells.
Extracellular E-cadherin mutations lead to EGFR independent activation of p38 MAPK and Src
kinase.
Cell migration depends on the highly dynamic cycle of three processes – cell-substrate adhesion,
remodelling of the actin cytoskeleton and cell-substrate detachment. Tyrosine kinases and MAPK
work together to modulate the actin cytoskeleton. To understand whether MAPKs and Src kinase
are involved in the motile phenotype observed in E-cadherin extracellular and juxtamembrane
mutant cells, we assessed the activation profile of ERK1/2, p38 MAPK and Src kinase in our stable cell
lines, by using phospho-specific antibodies.
Phosphorylation levels of ERK1/2 did not show marked differences amongst the different cell lines.
p38 MAPK and Src kinase active levels were more pronounced for the cells expressing the
extracellular E-cadherin mutants T118R, L214P, G239R, A298T, T340A and P373L when compared to
juxtamembrane mutations (R749W, and E757K) and cells expressing wild-type E-cadherin or the
empty vector, despite the higher EGFR activation and migration phenotype observed for mock and
the juxtamembrane mutants.. These results suggest that the increase in the phosphorylation levels
of p38 MAPK and Src kinase is independent of EGFR activity. To confirm this hypothesis, cells were
treated with the EGFR inhibitor Tyrphostin AG 1478 prior to lysis and the activation levels of p38
MAPK and Src kinase analysed by western-blot analysis. Surprisingly, in the presence of the EGFR
inhibitor, the levels of active p38 MAPK and Src kinase markedly increased for the extracellular
mutant expressing cells, pointing to independent signalling pathways, and potentially a
compensatory mechanism. For mock cells and cells expressing wild-type E-cadherin or the
intracellular mutants, no marked differences were obtained upon EGFR inhibition, and the results
were not very consistently clear, perhaps because of the very low basal level of activation observed.
Immunoblotting for the total forms of these kinases revealed comparable amounts of total p38
MAPK and Src kinase for all cell lines.
Collaborative Projects between Cancer Genetics and other Groups at IPATIMUP
As example we describe a collaboration programme between Cancer Genetics and Carcinogenesis
It is a long last interest of our group to identify molecular mechanisms underlying E-cadherin
dysfunction in cancer development and progression. Most studies mainly focus on the role of
epi/genetic alterations in its promoter region and in its coding sequence or in its transcriptional
repressors. Since E-cadherin is a glycoprotein it can be post-transcriptional modified (PTM) by
phosphorylation, O-glycosylation and N-glycosylation. In fact, N-glycans has been shown to be
essential for E-cadherin folding and to assure its biological functions. In this collaborative project we
aim to elucidate the role of GnT-III and GnT-V glycosyltransferases and its products, in E-cadherin
expression. We found that GnT-III knockdown resulted in a remarkable modification of cell
morphology accompanied by a membranar de-localization of E-cadherin with an increase of
cytoplasmic expression. Further, we verified that E-cadherin regulates the transcription levels of
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GnT-III which through competition with GnT-V glycosylate E-cadherin molecule. In primary gastric
carcinoma, this mutual regulatory mechanism between E-cadherin and GnT-III/GnT-V was also
observed.
Funded Projects
"Vitamina D como terapia dos carcinomas mamários de tipo basal: ficção ou realidade?"
PI: Fernando Schmitt, Sponsor: SPO, From: 2008-04-14 To: 2010-04-14
"Evaluation and Control of Neglected Mucosal Enteric Infections in Childhood"
PI: José Carlos Machado , Sponsor: EU, From: 2006-01-01 To: 2011-10-01
"Global RNAi approaches to unravel eukaryotic host functions that modulate bacterial infections"
PI: Céu Figueiredo, Sponsor: Era Net PathoGenoMics, From: 2007-02-01 To: 2010-02-01
"Parasite and host genetic diversity in Helicobacter infections"
PI: José Carlos Machado, Sponsor: Era Net PathoGenoMics, From: 2007-02-01 To: 2010-02-01
"The role of chronic infections in the development of cancer"
PI: José Carlos Machado, Sponsor: EU, From: 2006-01-01 To: 2010-01-01
"Archives Tissues: Improving Molecular Medicine Research and Clinical Pratice"
PI: Fátima Carneiro, Sponsor: EU, From: 2007-11-01 To: 2010-02-28
“Exploring the role of E-cadherin trafficking deregulation in epithelial cancer progression”
PI: Gianpaolo Suriano, Sponsor: FCT, From: 2008-02-01 To: 2011-02-01
“Role of novel regulatory mechanisms in the loss of E-cadherin expression”
PI: Carla Oliveira, Sponsor: FCT, From: 2007-08-01 To: 2010-08-01
“MLK3, a new gene in MSI gastrointestinal cancer”
PI: Raquel Seruca, Sponsor: FCT, From: 2008-07-01 To: 2011-07-01
“P-cadherin Expression: its effect in breast cancer metastasis and angiogenesis using in vivo animal
models”
PI: Fernando Schmitt, Sponsor: SANOFI-AVENTIS FRANÇA, From: 2007-09-01 To: 2010-09-01
"Basal-like Breast Cancer: are mammary stem cells new targets for cancer therapy?"
PI: Joana Paredes , Sponsor: FCG, From: 2008-12-15 To: 2011-12-15
"Mutated suppressor tRNAs as a therapeutic tool for cancer associated syndromes: HDGC as a
model"
PI: Carla Oliveira, Sponsor: FCG, From: 2008-12-01 To: 2011-12-01
"Criação de um Banco de DNA e RNA acoplado ao Banco de Tecidos e Tumores do H. S. João"
PI: Fátima Carneiro, Sponsor: IPATIMUP, From: 2008-10-01 To: 2009-10-01
"The role of protein quality control in cancer"
PI: Joana Correia, Sponsor: IPATIMUP, From: 2008-11-01 To: 2009-05-01
"Clinical and functional relevance of Helicobacter pylori vacA intermediate region and CagA tyrosine
phosphorylation motifs"
PI: Céu Figueiredo, Sponsor: IPATIMUP, From: 2008-10-01 To: 2009-10-01
"The involvement of microRNAs in gastric cancer"
PI: Carla Oliveira, Sponsor: IPATIMUP, From: 2008-11-01 To: 2009-11-01
"Regulation of P-cadherin Expression in Breast Cancer"
PI: Joana Paredes, Sponsor: IPATIMUP, From: 2008-10-08 To: 2009-10-08
“Does P-cadherin expression interfere with E-cadherin function in invasive breast cancer cells?”
PI: Joana Paredes, Sponsor: IPATIMUP, From: 2008-10-28 To: 2010-10-28
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Inter-Groups (IPATIMUP)
Raquel Seruca; Paula Soares, The role of BRAF in neoplasia
Raquel Seruca; Celso Reis, The role of E-cadherin in glycosyltranferase expression and glycosylation
in cancer
Gianpaolo Suriano; Jorge Rocha, The pathogenic role of E-cadherin germline missense mutations in
HDGC
José Carlos Machado; Jorge Rocha, Inflammation-related genetic polymorphisms associated with
risk of development of GC
Céu Figueiredo; Leonor David, Characterization of Helicobacter pylori virulence factors in strains
from a population in Mozambique.
Céu Figueiredo; Celso Reis, Identification of glycosylation-associated genes induced by Helicobacter
pylori in gastric cells: a glycomic approach.
Céu Figueiredo; Luís F. S. Silva, Clarification of the relevance of Muc1 polymorphism in the
Helicobacter pylori infection
National Collaborations
Raquel Seruca; Peter Jordan (Instituto Nacional Ricardo Jorge), The role of BRAF and RAC1B in
colorectal cancer
Raquel Seruca; Miguel Soares (IGC -Instituto Gulbenkian de Ciência), The role of Heme oxygenase-1
and MLK3 in colorectal cancer
Carla Oliveira; Manuel Santos (Department of Biology and CESAM, Universidade de Aveiro); Ana
Paula Pego (INEB- Instituto de Engenharia Biomédica), Mutated suppressor tRNAs as a therapeutic
tool for cancer associated syndromes: HDGC as a model
Gianpaolo Suriano; Paulo Pereira; Fernando Casares (IBMC- Instituto de Biologia Molecular e
Celular), In vivo consequences of germline E-cadherin missense mutations
Raquel Seruca; Pedro Granja (INEB- Instituto de Engenharia Biomédica), Targeting nanoprobes for
early detection of invasive cancer cells using Hereditary Diffuse Gastric Cancer as a model
Céu Figueiredo; Maria J. Vieira and Nuno Azevedo (Dept. Biological Engeneering, Universidade do
Minho, Braga), Evaluation of Helicobacter pylori transmission routes; PNA probes for Helicobacter
pylori detection
Céu Figueiredo; Lurdes Monteiro (Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisboa),
Characterization major outer membrane proteins family in Helicobacter pylori strains isolated from
Portuguese patients
Céu Figueiredo; Manuel A. Coimbra (Dept. Chemistry University of Aveiro, Aveiro), PYLORI L&EPS:
Structural Characterisation of Lipo- and Exopolysaccharides from Helicobacter pylori - Establishment
of the chemical and biochemical basis for the development of vaccines and for the understanding of
the adhesion processes
Fernando Schmitt; Fátima Baltazar (ICVS – Minho University), Expression of MCT’s
(monocarboxilate transporters) in cancer
Fernando Schmitt; Rui Reis (ICVS – Minho University), Expression of c-kit and PDGFR in breast
cancer
Fernando Schmitt; Adhemar Longatto (ICVS – Minho University), Cancer Pathology
Joana Paredes; Fátima Baltazar; Adhemar Longatto (ICVS – Minho University), Cadherins and
catenins expression in gastric cancer
22
Joana Paredes; Perpétua Pinto do Ó (INEB- Instituto de Engenharia Biomédica), Stem Cell
Mammospheres
International Collaborations
Belgium
• VIB Department for Molecular Biomedical Research, University of Ghent (Frans Van Roy),
Ghent, Belgium,” E-cadherin signalling”, Gianpaolo Suriano
• Ghent University Hospital (Marc Mareel), Ghent, Belgium, “Host responses to Helicobacter
pylori infection”, Céu Figueiredo, Joana Paredes
• Jules Bordet Intitute (martine Piccart), Brussels, Belgium, “European MINDACT Project”,
Fernando Schmitt
Brazil
• Faculdade de Medicina (Dulciene Queiroz), Belo Horizonte, Brazil, “Helicobacter pylori and
other Helicobacter species”, Céu Figueiredo
• Department of Genetics, FFFCMPA (Carla Graziadio), Porto Alegre, Brazil, “Hereditary
gastric câncer”, Carla Oliveira, Raquel Seruca
• São Paulo University (Venâncio Alves), São Paulo, Brazil, “Lymphangiogenesis”, Fernando
Schmitt
Canada
• Genetic Pathology Evaluation Centre, University of British Columbia (David G Huntsman),
Vancouver, Canada, “Hereditary Diffuse Gastric Cancer”, Carla Oliveira, Gianpaolo Suriano,
Raquel Seruca, Fátima Carneiro
• Department of Obstetrics and Gynecology, University of British Columbia (Auersperg Nelly),
Vancouver, Canada, “Borderline ovarian cancer”, Carla Oliveira
Costa Rica
• Institute of Health Research (INISA) (Vanessa Ramirez), University of Costa Rica, San José,
Costa Rica, “Genetic susceptibility to sporadic gastric carcinoma”, José Carlos Machado
Denmark
• Roskilde University (Lene J Rasmussen), Roskilde, Denmark, “MMR related cancer”, Raquel
Seruca
Finland
• University of Helsinki (Ari Ristimaki), Helsinki, Finland, “The role of C/EBP transcription
factors in gastric carcinogenesis”, José Carlos Machado
• University of Helsinki (Lauri A Aaltonen, Paivi Peltomaki), Helsinki, Finland, “MMR related
cancer”, Raquel Seruca
France
• Institut Pasteur (Eliette Touati), Paris, France, “Inhibition of Helicobacter pylori growth by
fatty acids”, José Carlos Machado
• INSERM U762 CEPH, INSERM (Richard Hamelin, Alex Duval), Paris, France, “MMR related
cancer genes”, Raquel Seruca
• Institut Pasteur (Eliette Touati), Paris, France, “Mouse model of Helicobacter pylori
infection”, Céu Figueiredo, Raquel Seruca
Germany
• Department of Virology, Hannover Medical School (Thomas Schulz), Hannover, Germany,
José Carlos Machado
• Technische Universität München (Birgit Luber, Gisela Keller, Karl Becker), Germany, “Ecadherin related cancer”, Raquel Seruca, Fátima Caneiro
• Max Planck Institute for Infection Biology (Thomas Meyer), Berlin, Germany, “Host cell
responses to Helicobacter pylori”, Céu Figueiredo
23
•
•
Italy
•
•
•
University of Heidelberg (Federico Canzian), Heidelberg, Germany, “Genetic susceptibility”,
José Carlos Machado
University of Tuebingen (Nikolaus Blin), Heidelberg, Germany, “Gastric cancer”, José Carlos
Machado
Division of Surgical Oncology, University of Siena (Franco Roviello), Siena, Italy, “Hereditary
Diffuse Gastric Cancer”, Carla Oliveira, Gianpaolo Suriano, Raquel Seruca
CBM S.c.r.l. AREA SCIENCE PARK (Elia Stupka), Trieste, Italy, “Non-coding sequences”, Carla
Oliveira
Consorzio per l’AREA di Ricerca Scientifica e Tecnologica di Trieste (Giorgio Stanta), Trieste,
Italy, IMPACTS project, Fátima Carneiro
Publications in 2008
1. Allum WH, Meyer HJ, Garofalo A, Schuhmacher C, de Manzoni G, Degiuli M, Kulig J, van de Velde
C, Roukos D, Barr H, Nowak W, Wittekind C, Sendler A, Park K, Hartgrink H, Haringsma J, Seruca R.
European Union Network of Excellence (EUNE) for Gastric Cancer Steering Group. Gastric cancer in
Europe. Br J Surg 95(4):406-8, 2008. IF - 4,3
2. Azevedo M, Eriksson S, Mendes N, Serpa J, Figueiredo C, Resende LP, Ruvoën-Clouet N, Haas R,
Borén T, Le Pendu J, David L: Infection by Helicobacter pylori expressing the BabA adhesin is
influenced by the secretor phenotype. J Pathol 215: 308-316, 2008. IF – 5,4
3. Bajpai S, Correia J, Feng Y, Figueiredo J, Sun SX, Longmore GD, Suriano G, Wirtz D. {alpha}Catenin mediates initial E-cadherin-dependent cell-cell recognition and subsequent bond
strengthening. Proc Natl Acad Sci U S A, 105(47):18331-6, 2008 IF – 9,59
4. Barber M, Murrell A, Ito Y, Maia AT, Hyland S, Oliveira C, Save V, Carneiro F, Paterson A, Grehan
N, Dwerryhouse S, Lao-Sirieix P, Caldas C, Fitzgerald R: Mechanisms and sequelae of E-cadherin
silencing in hereditary diffuse gastric cancer. J Pathol 216:295-306, 2008. IF – 5,4
5. Barber M, Save V, Carneiro F, Dwerryhouse S, Lao-Sirieix P, Hardwick R, Caldas C, Fitzgerald R:
Histopathological and molecular analysis of gastrectomy specimens from hereditary diffuse gastric
cancer patients has implications for endoscopic surveillance of individuals at risk. J Pathol 216:286294, 2008. IF – 5,4
6.
Canedo P, Castanheira-Vale AJ, Lunet N, Pereira F, Figueiredo C, Gioia-Patricola L, Canzian F,
Moreira H, Suriano G, Barros H, Carneiro F, Seruca R, Machado JC: The interleukin-8-251*T/*A
polymorphism is not associated with risk for gastric carcinoma development in a Portuguese
population. Eur J Cancer Prev 17:28-32, 2008. IF – 4,45
7.
Canedo P, Corso G, Pereira F, Lunet N, Suriano G, Figueiredo C, Pedrazzani C, Moreira H,
Barros H, Carneiro F, Seruca R, Roviello F, Machado JC. The interferon gamma receptor 1 (IFNGR1) 56C/T gene polymorphism is associated with increased risk of early gastric carcinoma. Gut 57:15041508, 2008. IF – 10,0
8. Canedo P, Durães C, Pereira F, Regalo G, Lunet N, Barros H, Carneiro F, Seruca R, Rocha J,
Machado JC. Tumour necrosis factor alpha Extended Haplotypes and Risk of Gastric Carcinoma.
Cancer Epidemiol Biomarkers Prev 2008 17:2416-2420, 2008. IF – 4,6
9.
Capellá G, Pera G, Sala N, Agudo A, Rico F, Del Giudicce G, Plebani M, Palli D, Boeing H, Bas
Bueno-de-Mesquita H, Carneiro F, Berrino F, Vineis P, Tumino R, Panico S, Berglund G, Simán H,
Nyrén O, Hallmans G, Martinez C, Dorronsoro M, Barricarte A, Navarro C, Quirós JR, Allen N, Key T,
Bingham S, Caldas C, Linseisen J, Nagel G, Overvad K, Tjonneland A, Boshuizen HC, Peeters PHM,
NumansME, Clavel-Chapelon F, Trichopoulou A, Lund E, Jenab M, Kaaks R, Riboli E, Gonzalez CA:
24
DNA repair polymorphisms and the risk of stomach adenocarcinoma and severe chronic gastritis in
the EPIC-EURGAST study. Int J Epidemiol 37:1316-1325, 2008. IF – 5,15
10.
Carneiro F, Oliveira C, Leite M, Seruca R: Molecular targets and biological modifiers in gastric
cancer. Semin Diagn Pathol 25:274-287, 2008. IF – 1,66
11.
Carneiro F, Oliveira C, Suriano G, Seruca R: Molecular pathology of familial gastric cancer,
with an emphasis on Hereditary Diffuse Gastric Cancer (HDGC). J Clin Pathol 61:25-30, 2008. IF – 2,4
12.
Carneiro F; Seruca R: Editorial sobre “Importância e caracterização do carcinoma gástrico
em famílias com diagnóstico ou suspeita de síndroma de Lynch”. J Port Gastrenterol 15(2):54-55,
2008. –
13.
Costa JL, Meijer G, Ylstra B, Caldas C. Array comparative genomic hybridization copy number
profiling: a new tool for translational research in solid malignancies. Seminars in Radiation Oncology
18: 98-104, 2008. IF – 3,78
14.
Costa S, Pinto D, Pereira D, Rodrigues H, Cameselle-Teijeiro J, Medeiros R, Schmitt F.
Importance of TP53 codon 72 and intron 3 duplication 16bp polymorphisms in prediction of
susceptibility on breast cancer. BMC Cancer 8: 32, 2008 IF – 2,7
15.
Costa S, Pinto D, Pereira D, Rodrigues H, Cameselle-Teijeiro J, Medeiros R, Schmitt F. XRCC1
Arg399Gln and RAD51 5’UTR G135C polymorphisms and their outcome in tumor aggressiveness and
survival of Portuguese breast cancer patients. Breast Cancer Res Treat 109: 183-185, 2008. IF – 4,45
16.
Crusius JBA, Canzian F, Capellá G, Penã AS, Pera G, Sala N, Agudo A, Rico F, Del Giudice G,
Palli D, Plebani M, Boeing H, Bueno-de-Mesquita HB, Carneiro F, Pala V, Save VE, Vineis P, Tumino R,
Panico S, Berglund G, Manjar J, Stenling R, Hallmans G, Martinez C, Dorronsoro M, Barricarte A,
Navarro C, Quirós JR, Allen N, Key TJ, Binghan S, Caldas C, Linseisen J, Kaak R, Overvad K,
Tjønneland A, Büchner FC, Peeters PHM, Numans ME, Clavel-Chapelon F, Trichopoulou A, Lund E,
Jenab M, Rinaldi S, Ferrari P, Riboli E, González CA: Cytokine gene polymorphisms and the risk of
adenocarcinoma of the stomach in the European prospective investigation into cancer and nutrition
(EPIC-EURGAST). Ann Oncol 19:1894-1902, 2008. IF – 4,87
17.
Di Palma S, Collins N, Bilous M, Sapino A, Mottolese M, Kapranos N, Schmitt F, Isola J. A
quality assurance exercise to evaluate the accuracy and reproducibility of chromogenic in situ
hybridization for HER2 analysis in breast cancer. J Clin Pathol 61: 757-760, 2008. IF – 2,4
18.
Dufloth R, Arruda A, Heinrich JK, Schmitt F, Zeferino LC. The investigation of DNA repair
polymorphisms with histopathological characteristics and hormone receptors in a group of Brazilian
women with breast cancer. Genetics and Molecular Research 7: 574-582, 2008 –
19. Ferreira AC, Gomes L, Máximo V, Amil J, Carneiro F, Machado JC, Tavarela-Veloso F. Grim-19
mutations are not associated with Crohn’s Disease. Inflamm Bowel Dis 14:434-435, 2008. IF – 4,7
20.
Ferreira AC, Isomoto H, Moriyama M, Fujioka T, Machado JC, Yamaoka Y. Helicobacter and
Gastric Malignancies. Helicobacter 13 (Suppl 1): 28-24, 2008. IF – 2,4
21.
Gama A, Alves A, Schmitt FC. Identification of molecular phenotypes in canine mammary
carcinomas with clinical implications: application of the human classification. Virchows Arch 453: 123132, 2008. IF – 2,0
22.
Gama A, Alves A, Schmitt FC. Invasive micropapillary carcinoma in dog (letter). Vet Pathol 45:
600-601, 2008. IF – 1,37
23.
Gama A, Paredes J, Gartner F, Alves A, Schmitt F. Expression of E-cadherin, P-cadherin and Bcatenin in canine malignant mammary tumours in relation to clinicopathological parameters,
proliferation and survival. The Vet Journal 177: 45-53, 2008. IF – 1,75
25
24.
Jenab M, McKay JD, Ferrari P, Biessy C, Laing S, Capella Munar GM, Sala N, Peña S, Crusius
JB, Overvad K, Jensen MK, Olsen A, Tjonneland A, Clavel-Chapelon F, Boutron-Ruault MC, Kaaks R,
Linseisen J, Boeing H, Bergmann MM, Trichopoulou A, Georgila C, Psaltopoulou T, Mattiello A, Vineis
P, Pala V, Palli D, Tumino R, Numans ME, Peeters PH, Bueno-de-Mesquita HB, Lund E, Ardanaz E,
Sánchez MJ, Dorronsoro M, Navarro Sanchez C, Quirós JR, Hallmans G, Stenling R, Manjer J, Régner
S, Key T, Bingham S, Khaw KT, Slimani N, Rinaldi S, Boffetta P, Carneiro F, Riboli E, Gonzalez C: CDH1
gene polymorphisms, smoking, Helicobacter pylori infection and the risk of gastric cancer in the
European Prospective Investigation into Cancer and Nutrition (EPIC-EURGAST). Eur J Cancer 44:774780, 2008 IF – 4,45
25.
Karam R, Carvalho J, Bruno I, Graziadio C, Senz J, Huntsman D, Carneiro F, Seruca R,
Wilkinson MF, Oliveira C: The NMD mRNA surveillance pathway downregulates aberrant E-cadherin
transcripts in gastric cancer cells and in CDH1 mutation carriers. Oncogene. 27: 4255-4260, 2008. IF –
6,4
26.
Kocjan G, Bourgain C, Fassina A, Hagmar B, Herbert A, Kapila K, Kardum-Skelin I, KlobovesPrevodnik V, Krishnamurthy S, Koutselini H, Majak B, Olszewski W, Onal B, Pohar-Marinsek Z,
Shabalova I, Smith J, Tani E, Vielh P, Wiener H, Schenck U, Schmitt F. The role of breast FNAC in
diagnosis and clinical management: a survey of current practice. Cytopathology 19: 271-278, 2008. IF
– 1,2
27.
Lima-Rodrigues M, Valle-Fernandes A, Lamas N, Cruz A, Baltazar F, Milanezi F, Nunes R, Reis
RM, Pedrosa J, Castro AG, Almeida A. A new model of laryngitis: neuropeptide, cyclooxygenase, and
cytokine profile, Laryngoscope. 118(1):78-86, 2008 . IF – 2,0
28.
Longatto-Filho A, Duarte M, Schmitt FC. Lymphangiogenesis: from the pig embryos to
cancer. J Bras Patol Med Lab 44: 215-220, 2008.—
29.
Longatto-Filho A, Pinheiro C, Ferreira L, Scapulatempo C, Alves VA, Baltazar F, Schmitt F.
Peritumoural, but not intratumoural, lymphatic vessel density and invasion correlate with colorectal
carcinoma poor-outcome markers. Virchows Arch 452: 133-138, 2008. IF – 2,0
30.
Macedo FYB, Baltazar F, Almeida PR, Távora F, Ferreira FV, Schmitt FC, Brito GA, Ribeiro R.
Cyclooxygenase-2 expression on ifosfamide-induced hemorrhagic cystitis in rats. J Cancer Res Clin
Oncol 134: 19-27, 2008. IF – 2,36
31.
Macedo FYB, Baltazar F, Mourão LC, Almeida PR, Mota JM, Schmitt FC, Ribeiro RA. Induction
of COX-2 expression by acrolein in the rat model of hemorrhagic cystitis. Exp Toxicol Pathol 59: 425430, 2008. IF – 1,3
32.
Maia CJ, Santos CR, Schmitt F, Socorro S. Regucalcin is expressed in rat mammary gland and
prostate and down-regulate by 17B-estradiol. Mol Cell Biochem 311: 81-86, 2008. IF – 1,7
33.
Maia CJ, Socorro S, Schmitt F, Santos CR. STEAP1 is over-expressed in breast cancer and
down-regulated by 17B-estradiol in MCF-7 cells and in the rat mammary gland. Endocrine 34(1-3):10816, 2008. IF – 2,57
34.
Maia CJB, Socorro S, Schmitt F, Santos CRA. Characterization of oligoadenylate synthetase-1
expression in rat mammary gland and prostate: effects of 17-estradiol on the regulation of OAS1g in
both tissues. Mol Cell Biochem 314: 113-121, 2008. IF – 1,76
35.
Marchio C, Iravani M, Natrajan R, Lambros MB, Savage K, Tamber N, Fenwick K, Mackay A,
Senetta R, Di Palma S, Schmitt FC, Bussolati G, Ellis IO, Ashworth A, Sapino A, Reis-Filho JS. Genomic
and immunophenotypical characterization of pure micropapillary carcinomas of the breast. J Pathol
215: 398-410, 2008. IF – 5,4
26
36.
Marcos NT, Magalhães A, Ferreira B, Oliveira MJ, Carvalho AS, Mendes N, Gilmartin T, Head
SR, Figueiredo C, David L, Santos-Silva F, and Reis CA: Helicobacter pylori induces b3GnT5 in human
gastric cell lines, modulating expression of the SabA adhesin ligand sialyl-Lewis x. J Clin Invest 118:
2325-2336, 2008. IF – 2,88
37.
Marques M, Magro F, Cardoso H, Carneiro F, Portugal R, Lopes J, Costa Santos C: Infliximabinduced lupus-like syndrome associated with autoimmune hepatitis. Inflamm Bowel Dis 14:723-725,
2008. 5- Ferreira AC, Gomes L, Máximo V, Amil J, Carneiro F, Machado JC, Tavarela-Veloso F: GRIM-19
mutations are not associated with Crohn's disease. Inflamm Bowel Dis 14:434-435, 2008. IF – 4,7
38.
Martinho O, Gonçalves A, Moreira MA, Ribeiro LFJ, Queiroz GS, Schmitt FC, Reis RM,
Longatto-Filho A. KIT activation in uterine cervix adenosquamous carcinomas by KIT/SCF
autocrine/paracrine stimulation loops. Gynecol Oncol 111: 350-355, 2008.IF – 2,6
39.
Martins P, Schmitt F, Almeida H, Frazao JM. Evaluation of parathyroid gland angiogenesis in
chronic kidney disease associated with secondary hyperparathyroidism. Nephrol Dial Transplant
23(9):2889-94, 2008 IF – 3,16
40.
Matos P, Oliveira C, Velho S, Gonçalves V, da Costa LT, Moyer MP, Seruca R, Jordan P. BRaf(V600E) cooperates with alternative spliced Rac1b to sustain colorectal cancer cell survival.
Gastroenterology 135(3):899-906, 2008 IF – 11,67
41.
Milanezi F, Carvalho S, Schmitt FC. EGFR/HER2 in breast cancer: a biological approach for
molecular diagnosis and therapy. Expert Rev Mol Diagn 8: 417-434, 2008. IF – 3, 1
42.
Moutinho C, Mateus A R, Milanezi F, Carneiro F, Seruca R, Suriano G: EGFR structural
alterations in gastric cancer. BMC Cancer 8: 10, 2008 IF – 2,7
43.
Paredes J, Correia AL, Ribeiro AS, Milanezi F, Cameselle-Teijeiro J, Schmitt FC. Breast
carcinomas that co-express E- and P-cadherin are associated with p120-catenin cytoplasmic
localisation and poor patient survival. J Clin Pathol 61: 856-862, 2008.IF – 2,4
44.
Pinheiro C, Longatto-Filho A, Scapulatempo C, Ferreira L, Martins S, Pellerin L, Rodrigues M,
Alves VA, Schmitt F, Baltazar F. Increased expression of monocarboxylate transporters 1, 2 and 4 in
colorectal carcinomas. Virchows Arch 452: 139-146, 2008. IF – 2,0
45.
Pinto M, Wu Y, Mensink RG, Cirnes L, Seruca R, Hofstra RM. Somatic mutations in mismatch
repair genes in sporadic gastric carcinomas are not a cause but a consequence of the mutator
phenotype. Cancer Genet Cytogenet. 180: 110-4, 2008 IF – 1,55
46.
Preto A, Figueiredo J, Velho S, Ribeiro A, Soares P, Oliveira C, Seruca R. BRAF provides
proliferation and survival signals in MSI colorectal carcinoma cells displaying BRAF(V600E) but not
KRAS mutations. J Pathol. 214:320-327, 2008. IF – 5,4
47.
Rodrigues M, Vitó I, Santos R, Paiva J, Pontes P, Silva P, Carneiro F: Establishment of a
Tumour Bank: The experience of the Department of Pathology of Hospital S.João (Porto, Portugal).
Cell and Tissue Bank 2008 Jul 2. –
48.
Schmitt FC, Longatto-Filho A, Valent A, Vielh P. Molecular techniques in cytopathology
practice. J Clin Pathol 61:258-267, 2008. IF – 2,4
49.
Silva F, Carvalho S, Milanezi F, Schmitt FC. Carcinoma da mama de tipo basal. Acta Med Port
21: 387-392, 2008.—
50.
Simões-Correia J, Figueiredo J, Oliveira C, van Hengel J, Seruca R, van Roy F, Suriano G.
Endoplasmic reticulum quality control: a new mechanism of E-cadherin regulation and its implication
in cancer. Hum Mol Genet. 17(22):3566-76, 2008 IF – 7,8
51.
Simpson PT, Reis-Filho JS, Lambros MBK, Jones C, Steele D, Mackay A, Iravani M, Fenwick K,
Dexter T, Jones A, Reid L, Da Silva L, Shin SJ, Hardisson D, Ashworth A, Schmitt FC, Palacios J,
27
Lakhani SR. Molecular profiling pleomorphic lobular carcinomas of the breast: evidence for a
common molecular genetic pathway with classic lobular carcinomas. J Pathol 215: 231-244, 2008. IF –
5,4
52.
Trindade E, Pissarra S, Carneiro F, Amil Dias J: Esofagite eosinofílica: causa de disfagia
persistente. ENDOnews 22:11-12, 2008.—
53.
Valbuena C, Carvalho E, Bustorff M, Ganhão M, Relvas S, Nogueira R, Carneiro F, Oliveira JP:
Kidney biopsy findings in heterozygous Fabry disease females with early nephropathy. Virchows
Arch 453: 329-338, 2008. IF – 2,0
54.
van Krieken JH, Jung A, Kirchner T, Carneiro F, Seruca R, Bosman FT, Quirke P, Fléjou JF,
Plato Hansen T, de Hertogh G, Jares P, Langner C, Hoefler G, Ligtenberg M, Tiniakos D, Tejpar S,
Bevilacqua G, Ensari A: KRAS mutation testing for predicting response to anti-EGFR therapy for
colorectal carcinoma: proposal for a European quality assurance program. Virchows Arch 453:417431, 2008. IF – 2,0
55.
Velho S, Moutinho C, Cirnes L, Albuquerque C, Hamelin R, Schmitt F, Carneiro F, Oliveira C,
Seruca R. BRAF, KRAS and PI3KCA mutations in colorectal serrated polyps and cancer: primary or
secondary genetic events in colorectal carcinogenesis ? BMC Cancer 8: 255, 2008 IF – 2,7
56.
Viana-Pereira M, Lopes JM, Little S, Milanezi F, Basto D, Pardal F, Jones C, Reis RM: Analysis
of EGFR overexpression, EGFR gene amplification and the EGFRvIII mutation in Portuguese highgrade gliomas. Anticancer Research 28:913-920, 2008. IF – 1,4
57.
Vieira DS, Dufloth RM, Schmitt FC, Zeferino LC. Carcinoma de mama: novos conceitos na
classificação. Rev Bras Ginecol Obstet 30: 42-47, 2008. –
58.
Woo MM, Salamanca CM, Miller M, Symowicz J, Leung PC, Oliveira C, Ehlen TG, Gilks CB,
Huntsman D, Auersperg N. Serous borderline ovarian tumors in long-term culture: phenotypic and
genotypic distinction from invasive ovarian carcinomas. Int J Gynecol Cancer 18(6):1234-47, 2008 IF
– 1,4
59.
Eloy C, Lopes JM, Faria G, Moreira H, Brandão A, Silva T, Carneiro F: Clear Cell Change in
Colon Polyps. International Journal of Surgical Pathology 2008 Jul 8 IF – 1,0
28
2c. CARCINOGENESIS
Group Leader: Leonor David, MD PhD, Full Professor of Pathology from the Medical Faculty of the
University of Porto and senior Researcher of IPATIMUP
Staff members: Fátima Gartner, PhD, Full Professor at ICBAS; Celso Reis, PhD, senior Investigator;
Raquel Almeida, PhD, senior Investigator; Hugo Osório, PhD, senior Investigator; Emerson
Bernardes, PhD, senior Investigator; Ana Carvalho, post-Doc; Luisa Silva, post-Doc; Nuno Marcos,
PhD student; Rita Barros, PhD student; Salomé Pinho, PhD student; Liliana Silva, PhD student (jointly
with the Dental Faculty); Ana Magalhães, PhD student; Joana Gomes, PhD student; Joana Oliveira,
BI; Bruno Pereira, BI; Vania Camilo, BI; Lara Marcos, BI; Sofia Santos, graduate student; Catarina
Gomes, graduate student; Nuno Mendes, technician.
Objectives/Goals of the research activity - The main objective of the group is to identify alterations
of mucins and mucin glycosylation, associated with gastric carcinoma and precancerous lesions,
that may be relevant for the development of diagnostic and therapeutic strategies. We are also
engaged in understanding the molecular mechanisms involved in the development of such
alterations, including the identification of transcription factors responsible for cancer/pre-cancer
transdifferentiation, as well as to extend our expertise on other cancer models (ex: mammary
cancer from dogs).
Major achievements during 2008 – The group continued previous studies on the clarification of the
mechanisms involved in the development of intestinal metaplasia (IM) and demonstrated that
matrix derived BMP2/4, through the Smad4 pathway, are responsible for regulation of the CDX2
homeobox transcription factor in gastric cells. We have also shown that Helicobacter pylori is capable
to induce CDX2 expression in gastric cells. Progress was made on regulation of the CDX2 by GATA
transcription factors and an inhibitory effect was demonstrated for SOX2. Progress was also made
on the characterization of the CDX2 autoregulatory mechanism and a CDX2 expression construct
with loxP sites was obtained for functional assays in living cells. In vivo studies consisting in the
transfection of siRNAs to downregulate CDX2 in a transgenic mouse model containing a construct
composed of the Beta-Galactosidase gene regulated by a 9.3 kb CDX2 promoter in the intestine,
were initiated. This experiment is expected to show whether CDX2 is autoregulated in vivo.
Optimization of the delivery conditions of the siRNAs in vivo were assayed. This work is being
performed in collaboration with Jean-Noel Freund from Strasbourg. Methylation of CDX2
expression was also analysed by treating cell lines with 5-aza-cytidine and bisulphite treatment was
performed both in cell lines and in tissue samples (normal gastric mucosa and IM), and we observed
it is not a relevant regulatory mechanism of CDX2 expression.
We continued our work on the genotype/phenotype associations in the Secretor and Lewis systems
and their relevance for gastrointestinal infectious diseases – Helicobacter pylori and Calicivirus. We
e
29
demonstrated that Secretor status, together with ABO histo-blood group phenotype for some viral
strains, is determinant for adhesion of Helicobacter pylori and Calicivirus (the work on H. pylori was
published and the work on calicivirus is being prepared by Jacques Le Pendu from Nantes). We
continued the collaboration with the group of Jorge Rocha from IPATIMUP, to elucidate the
phenotype/genotype discrepancies in the Secretor and Lewis systems. We demonstrated that FUT2
G428A is the major responsible for the non-Secretor phenotype in the Portuguese population, similarly
to the observation in most western countries. We have further confirmed that mutations previously
described by our group – G739A and T839C – greatly reduce enzyme activity towards Type 1
acceptor substrates despite that they are active in cell systems and in the gastric mucosa.
Haplotype/phenotype associations are currently under publication.
The group demonstrated a mechanism that the most virulent H. pylori strains, cagPAI+, use to induce in
the host gastric cell the biosynthesis of the Sialyl-Lex carbohydrate antigen, the ligand of H. pylori SabA
adhesin. This mechanism was first observed by performing a wide gene-expression search using a
microarray platform from the Consortium for Functional Glycomics. The results showed an
increased expression of the β3GnT5 glycosyltransferase. This mechanism was further demonstrated
using a panel of H. pylori strains with different cagPAI status. In addition, we demonstrated that
overexpression of β3GnT5 is capable of leading to de-novo/increased Sialyl-Lex expression in gastric
cells and that this expression increases adhesion of H. pylori.
We showed that virulent H. pylori strains induced a remarkable expression of Syndecan-4,
suggesting that this proteoglycan may be involved in the modulation of H. pylori-associated
gastritis. We observed that H. pylori infected individuals show increased expression of syndecan-4 in
gastric mucosa and this expression was associated with the cagPAI status of the infecting strain.
We progressed in understanding the molecular basis for the expression of the simple mucin-type
carbohydrate antigen Sialyl-Tn. Using a novel monoclonal antibody, produced in collaboration with
Dr. Ulla Mandel from the University of Copenhagen, we demonstrated that, both in intestinal
metaplasia and in gastric carcinomas, the immunodetection of enzyme ST6GalNAc-I co-localizes with
expression of Sialyl-Tn (unpublished results), confirming previous observations from the group
showing that this enzyme is responsible for Sialyl-Tn biosynthesis.
We showed that one member of the GalNAc-transferase gene family, the ppGalNAc-T6, shows an
expression in gastric carcinomas that is associated with the presence of venous invasion. This is a
further demonstration on the contribution that aberrant O-glycosylation plays in gastric cancer
development and progression.
30
The group continued the characterization of the role that Sialyl-transferases (ST3Gal-III, ST3Gal-IV,
ST3gal-VI) play in building the terminal sialylation of the carbohydrate chain, leading to the
formation of Sialyl-Lewisa and Sialyl- Lewisx antigens. We demonstrated that ST3Gal-III is involved in
the sialylation of both type-I and type-II chains, participating in the biosynthesis of Sialyl-Lewisa and
Sialyl-Lewisx, whereas ST3Gal-IV preferentially sialylates type-II chains leading to the biosynthesis of
Sialyl-Lewisx. Finally, we demonstrated that the products of the complex carbohydrate structures
also depend on the set of fucosyltrasferases and their activities in the cell lines. The cellular models
developed are currently being used in functional assays where Sialylated Lewis antigens play crucial
roles.
To continue our research on the role of sialylation in gastric tumor progression, we have recently
started investigating the interplay between sialyltransferases and galectin-3 expression. Galectin-3 is
one of the 15 known members of the galectin family of β-galactoside-binding lectins that are
overexpressed in a wide range of tumours and may promote tumour growth and metastasis
depending on its subcellular localization. Intracellular galectin-3 has been shown to protect tumor
cells against apoptosis. Paradoxally, several studies have pointed that extracellular galectin-3
induces tumor cell death. However, since galectin-3-binding to β-galactosides is sensitive to terminal
α2-6 sialylation, sialyltransferases expression may protect tumor cells against galectin-3-induced cell
death, thus counteracting the pro-apoptotic effect of galectin-3. This observation fits the increased
aggressiveness associated with higher expression of ST6Gal-I and ST6GalNAc-I sialyltransferases in
several types of cancer. Our working hypothesis is that sialylation of galectin-3 receptors in the
cancer cells may, besides conferring protection to cell death, increase galectin-3 released within
tumor microenvironment where it can modulate immune response.
The group continued the detailed characterization of the glycosylation profile of the genetically
modified mice from the Consortium for Functional Glycomics (Celso Reis is a member of this
consortium). These mice are knocked-out for one of the following glycosyltransferases - Core2GlcNAc (controlling mucin type O-glycosylation braching), FUT2 (controlling terminal H-type 1
terminal chain), ST3Gal-IV (controlling terminal sialylation forming the Sialyl-Lewis structures), and
the control wild type mice with the C57BL6 background. We demonstrated major alterations in the
glycan structures, such as lack of H-type 1 and Lewisb in the FUT2 K.O. mice. Mass spectrometry
analysis is being performed to further confirm these expression profiles. The mice models are being
used for evaluating the role of the different glycans for H. pylori adhesion. In addition, we have
started an evaluation in vitro of novel compounds for anti-adhesive treatment of H. pylori.
31
The group has progressed in the establishment of a mass spectrometry approach for identification
of cancer-associated glycoproteins in the serum of cancer patients, in the context of an European
project. Proteomics protocols for identification of low abundance proteins, namely Combinatorial
Peptide Ligand Libraries CPLL, were implemented and successful identification of low abundance
glycoproteins was achieved.
During 2008 we extended our study of gastric lesions in a Mozambican population and showed a low
prevalence of chronic atrophic gastritis and intestinal metaplasia, in line with the so-called “African
enigma” - why do Mozambicans, despite having a high rate of Helicobacter pylori infection, has a
low rate of gastric carcinoma? During 2008 the collection of material in Mozambique was completed
and studies will be continued in 2009. An initial study showed that two SNPs have a significantly
different distribution in individuals with and without IM, one in the Mozambican population (located
in the promoter region of the CDX2 gene) and the other in the Portuguese population (located
about 7 kb downstream of the CDX2 gene). We will increase the number of Mozambican individuals
included in this study in order to confirm the relevance of this SNP and perform functional promoter
assays.
Fátima Gartner leads the veterinary division of the group in close line to our main objectives. We
showed that canine mammary carcinomas overexpress MUC1 mucin and there was a significant
association between development of distant metastases and MUC1 over-expression, similarly to what
the group has previously shown in human gastric carcinomas.
The group has shown that the pattern of E-cadherin N-glycosylation in canine mammary carcinoma
is characterized by highly branched N-glycans, increase in sialylation and expression of few high
mannose structures. Detailed mass spectrometry analysis demonstrated a new N-glycosylation site
containing a potential complex type N-glycan in E-cadherin from a mammary carcinoma cell line. Our
study demonstrates the importance of E-cadherin N-glycans in the process of tumor development and
in the transformation to the malignant phenotype.
The proteomics unit headed by group members is currently serving projects from the group, as
detailed above, and also researchers from other groups at IPATIMUP and from other research
institutes in Porto – IBMC, CIMAR, Medical Faculty of Porto, and the Faculty of Engineering of Porto
and outside Porto, namely Coimbra - Centre for Neuroscience and Cell Biology (CNC) and Braga Minho University. The Proteomics Unit had a central role in our successful application to FP7
framework program and in a recently funded FCT project (see projects below).
Apart from the mainstream of the group objectives we collaborated in several publications, mainly
clinico-pathologic dscriptions (see “Other” publications).
Financing/Projects
32
The group won Royalties from monoclonal antibodies sells: 2008 – 6.285€
•
MUC5AC (MAB2011, Clone CLH2). CHEMICON INTERNATIONAL INC. 28835 Single oak
drive, Temecula, CA 92590; California, USA.
•
MUC5AC (NCL-MUC5). NOVOCASTRA LABORATORIES Ltd. Balliol Business Park
West, Benton Lane, Newcastle upon Tyne; NE12 8EW, United Kingdom.
•
MUC5AC (CLH2 sc-33667).SANTA CRUZ BIOTECHNOLOGY Inc., USA.
•
MUC6 (NCL-MUC6). NOVOCASTRA LABORATORIES Ltd. Balliol Business Park West,
Benton Lane, Newcastle upon Tyne; NE12 8EW, United Kingdom.
•
MUC6 (CLH5 sc-33668).SANTA CRUZ BIOTECHNOLOGY Inc., USA.
•
MUC5AC and MUC6. Cell Marque Corporation, USA.
The group gathered 425.401€ for funding during 2008 and has approved funding for 2009
(300.780€). The funding for 2008, after deduction of 20% overheads (85.080€), and salaries: 86.340€:
one technician – 14.700€/year; two pos-docs – 35.880€/year and 35.760€ for the 4BIs/year, leaves
253.981€ for Lab running costs.
1.
“Molecular mechanisms of biosynthesis of cancer associated mucin carbohydrate antigens
in gastric carcinoma”. Association for International Cancer Research (AICR grant Ref: 05088). PI: Celso Reis. Total budget for 2005 – 2008 - 112.320€ (2008 -9.360€).
2. “A strategy for preventing H. pylori-associated gastric cancer based on materials with
specific receptors to the bacteria – from SAM´s to Gly-R chitosan microspheres” (Project
PTDC/CTM/65330/2006). P.I. Cristina Martins (INEB). Total budget for the group 2008-2010:
71.948€ (2008 – 20.000€; 2009 - 30.600€)).
3. “Genes associated to intestinal metaplasia of the gastric mucosa (MUC2 mucin and
fucosyltransferase FUT3): transcriptional regulation and relevance for Helicobacter pylori
adhesion” (Project POCI/SAU-OBS/55549/2004). PI: Leonor David. Total budget for 20052008: 96.680€ (2008 – 12.000€).
4. “Lesions of the gastric mucosa in Mozambique and Portugal: the “African enigma”. Study of
biologic factors and lifestyle that contribute to understand the differences in incidence of
gastric carcinoma in two countries with a high prevalence of Helicobacter pylori infection:
Mozambique and Portugal”. Fundação Calouste Gulbenkian (Project FC-68697). PI: Leonor
David. Total budget for 2005-2008: 100.000€ (2008 - 15.000€).
5. “Identification of signalling pathways involved in Cdx2 regulation in two human models of
altered intestinal differentiation: intestinal metaplasia and juvenile polyposis”. Fundação
33
para a Ciência e a Tecnologia (Project POCTI/SAU-OBS/55840/2004). PI: Raquel Almeida.
Total budget for 2005-2008: 98.500€ (2008 – 10.000€).
6. “CDX2 autoregulation in the reversibility/irreversibility of gastric intestinal metaplasia”.
Fundação para a Ciência e a Tecnologia (Project PTDC/SAU-OBD/64490/2006). PI: Raquel
Almeida. Total budget for 2008-2011: 148.500€ (2008 – 48.560€; 2009 – 50.900€).
7.
“Biological characterization of canine mammary mixed tumours: histogenesis, tumour
progression and genetic alterations”. Fundação para a Ciência e a Tecnologia
(POCI/CVT/57795/2004). PI: Fátima Gartner. Total budget for 2005-2008: 92.225€ (2008 –
12.000€).
8.
“Cat mammary tumours-Pathologic, Molecular and Cytogenetic approaches”. Fundação
para a Ciência e a Tecnologia (POCI/CVT/62940/2004). PI: Fátima Gartner. Total budget for
2005-2008: 82.927€ (2008 – 17.508€).
9. “In vitro and in vivo manipulation of the expression of Sialyl lexisx and E-cadherin in canine
malignant
mammary
tumours”.
Fundação
para
a
Ciência
e
a
Tecnologia
(PTDC/CVT/65537/2006). PI: Fátima Gartner. Total budget for 2007-2009: 156.178€ (2008 –
57.533€; 2009 - 48.440,00€).
10. “Secretor and Lewis phenotypes/genotypes in Helicobacter pylori and calicivirus infection”.
Fundação para a Ciência e a Tecnologia (PTDC/SAU-MII/64153/2006). PI: Leonor David. Total
budget for 2007-2007-2010: 130.000€ (2008 – 47.440€; 2009 - 47.440€).
11. “Discovery of novel cancer serum biomarkers based on aberrant post-translational
modifications of O-glycoproteins, O-PTM-Biomarkers, and their application to early
detection of cancer”. Seventh Framework Program – Health (Grant agreement nº: 201381).
PI: Joyce-Taylor Papadimitriou, King’s College London. Total budget for the group 2008 2010: 264.000€ (2008 – 88.000€; 2009 - 88.000€).
12. “Early detection of cancer using serum biomarkers based on aberrant post-translational
modifications
of
O-glycoproteins”.
Fundação
para
a
Ciência
e
a
Tecnologia
(PIC/IC/82716/2007). P.I. Celso A. Reis. Total budget for 2009 – 2011: 111.400€ (2009 –
35.400€).
International collaborations
•
Faculty of Health Sciences of the University of Copenhagen – Ulla Mandel and Henrik
Clausen. This collaboration has been fundamental for characterization of carbohydrate
34
antigens and glycosyltransferases using unique monoclonal antibodies. We will collaborate
with this group for building glycopeptides arrays with the context of the European project.
•
INSERM, Nantes – Jacques Le Pendu. This collaboration has been critical for the prosecution
of the study of Secretor and Lewis phenotypes/genotypes, due to the unique expertise of
Jacques Le Pendu in such complex field.
•
INSERM, Strasbourg – Jean-Noel Freund. This collaboration started in 2006 with the
acceptance of Jean-Noel Freund to be co-supervisor of the PhD thesis of Rita Barros. Raquel
Almeida and Jean-Noel Freund successfully applied for travel money for one year at the
CRUP. This collaboration will be essential for the study of CDX2 regulation in intestinal
metaplasia.
•
Universite des Sciences et Technologies de Lille – Anne Harduin-Lepers. This collaboration
has been useful in the cloning and recombinant expression of sialyltransferases.
•
Umea University, Sweden – Thomas Borén. This collaboration has contributed for the
establishing of H.pylori adhesion assays. Thomas Borén acceptance to be co-supervisor of
the PhD thesis of Ana Magalhães.
•
Consortium for Functional Glycomics – The Scripps Research Institute, CA, USA - James
Paulson. This collaboration has provided the use of resources of the Consortium (funded by
the NIH), including the Microarray analysis and the knock-out mice.
•
University of Uppsala - Ola Soderberg. This collaboration has allowed the successful
establishment of Proximity-Ligation assays for identification of glycopeptides structures in
situ.
•
University of Cologne - Tilo Schwientek. This collaboration is essential for the identification
of the cancer serum glycoproteome in the context of the European project. Celso Reis and
Tilo Schwientek successfully applied for travel money for 2 years at the FCT/DAAD program,
which will allow crucial technological exchange in the glycoproteomics field between the
groups.
Master Thesis
In 2008 one Master student of the group, Nuno Mendes, defended his thesis at the Medical Faculty
of Porto, entitled “Study of polymorphisms in the CDX2 locus in Portugal and Mozambique.
Relationship with the development of intestinal metaplasia in the stomach.” The aim of the work
was to study the allelic distribution of 8 SNPs in the CDX2 locus in two populations, Portuguese and
35
Mozambican, in subjects with and without intestinal metaplasia. We identified one SNP, located
about 7 Kb downstream of the CDX2 gene, in the Portuguese population which is associated
(P<0.05) with IM and a different SNP, located in the promoter region of the CDX2 gene, in the
Mozambican population with suggestion of a negative association with the IM phenotype.
Functional studies and a higher number of Mozambican subjects with IM are essential to confirm
the hypothesis that CDX2 polymorphims can have a “facilitating” or “inhibitory” effect in the
metaplastic process.
Selected publications:
1. Azevedo M, Eriksson S, Mendes N, Serpa J, Figueiredo C, Resende LP, Ruvoën-Clouet N, Haas R,
Borén T, Le Pendu J, David L: Infection by Helicobacter pylori expressing the BabA adhesin is
influenced by the secretor phenotype. J Pathol 215: 308-316, 2008.
2. Barros R, Pereira B, Duluc I, Azevedo M, Mendes N, Camilo V, Jácobs RJ, Paulo P, Santos-Silva F,
van Seuningen I, van den Brink GR, David L, Freund J-N, Almeida R: Key elements of the BMP/SMAD
pathway co-localize with CDX2 in intestinal metaplasia and regulate CDX2 expression in human
gastric cell lines. J Pathol 215: 411-420, 2008.
3. Marcos NT, Magalhães A, Ferreira B, Oliveira MJ, Carvalho AS, Mendes N, Gilmartin T, Head SR,
Figueiredo C, David L, Santos-Silva F, and Reis CA: Helicobacter pylori induces b3GnT5 in human
gastric cell lines, modulating expression of the SabA adhesin ligand sialyl-Lewis x. J Clin Invest 118:
2325-2336, 2008.
4. Barros R, Marcos N, Reis CA, De Luca A, David L, Almeida R: Letter to the Editor - CDX2 expression
is induced by Helicobacter pylori in AGS cells. Scand J Gastroenterol 44:124-125, 2009 (accepted
2008).
5. Carrilho C, Modcoicar P, Cunha L, Ismail M, Guisseve A, Lorenzoni C, Fernandes F, Peleteiro B,
Almeida R, Figueiredo C, David L, Lunet N: Prevalence of Helicobacter pylori infection, chronic
gastritis and intestinal metaplasia in Mozambican dyspeptic patients. Virchows Arch (in press)
2009.
6. de Oliveira JT, Pinho SS, de Matos AJ, Hespanhol V, Reis CA, Gartned F: MUC1 expression in
canine malignant mammary tumours and relationshio to clinicopathological features. Vet J (Epub
ahead of print) 2008.
7. Pinho SS, Osório H, Nita-Lazar M, Gomes J, Lopes C, Gartner F, Reis CA: Role of E-cadherin N-
36
glycosylation profile in a mammary tumor model. Biochem Biophys Res Commun 379(4):1091-1096,
2009. Epub 2009 Jan 19.
8. Gomes J, Marcos NT, Berois N, Osinaga E, Magalhães A, Pinto-de-Sousa J, Almeida R, Gartner F,
Reis
CA:
Expression
of
UDP-N-acetyl-D-galactosamine:polypeptide
N-
acetylgalactosaminyltransferase-6 in gastric mucosa, intestinal metaplasia, and gastric carcinoma.
J Histochem Cytochem 57(1):79-86, 2009. Epub 2008 Oct 14.
“Other” publications:
1. Silva L, David L, Ribeiro D, Felino A: Odontomas: A clinicopathologic study in a Portuguese
population. Quintessence Int (in press) 2009.
2. Santos S, Sá D, Bastos E, Guedes-Pinto H, Gut I, Gartner F, Chaves R: An efficient protocol for
genomic DNA extraction from formalin-fixed paraffin-embedded tissues. Res Vet Sci (Epub ahead
of print) 2008.
3. Dias-Pereira P, Lopes CC, Matos AJ, Pinto D, Gartner F, Lopes C, Medeiros R: Estrogens
metabolism associated with polymorphisms: influence of COMT G482A genotype on age of onset
of canine mammary tumors. Vet Pathol 45: 124-130, 2008.
4. Monteiro R, Calhau C, Silva AO, Pinheiro-Silva S, Guerreiro S, Gartner F, Azevedo I, Soares P:
Xanthohumol inhibits inflammatory factor production and angiogenesis in breast câncer
xenografts. J Cell Biochem 104: 1699-1707, 2008.
5. Saraiva AL, Gartner F, Pires MA: Expression of p63 in normal canine skin and primary cutaneous
glandular carcinomas. Vet J 177: 136-140, 2008.
6. Gama A, Paredes J, Gartner F, Alves A, Schmitt F: Expression of E-cadherin, P-cadherin and betacatenin in canine malignant mammary tumours in relation to clinicopathological parameters,
proliferation and survival. Vet J 177: 45-53, 2008.
7. Costa NR, Mendes N, Marcos NT, Reis CA, Caffrey T, Hollingsworth MA, Santos-Silva F: Relevance
of MUC1 mucin variable number of tandem repeats polymorphism in H pylori adhesion to gastric
epithelial cells. World J Gastroenterol 14: 1411-1414, 2008.
37
2d. POPULATION GENETICS
Group Leader: António Amorim, PhD
Staff members: Maria João Prata, PhD; Leonor Gusmão, PhD; Luísa Azevedo, PhD; Alexandra Lopes,
PhD (post-Doc); Sandra Martins, PhD (post-Doc); Ricardo Araújo PhD (post-Doc); Ana Goios, PhD
student; Barbara van Asch, PhD student; Elisabete Oliveira, PhD student; Filipe Pereira, PhD student;
Iva Gomes, PhD student; Rita Quental, PhD student; Sofia Quental, PhD student; Rui Pereira, PhD
student; Verónica Gomes, PhD student, Inês Soares PhD student; Nádia Pinto, PhD student; Cíntia
Alves, chief technician; João Carneiro, MSc student; Sergio Costa, MSc student; Vânia Pereira MSc
student; Alfredo Gusmão, research grantee (BIC); Ana Moleirinho, research grantee (BIC).
Objectives/Goals of the research activity
The group aims at understanding the origin and evolution of (mainly) human genetic diversity and
their consequences and applications, both normal and pathological (using autosomal, X and Y
linked, as well as mtDNA markers).
This requires the development of descriptive and analytical formal tools and techniques adequate
to specific genomic segments, in order to achieve the genetic characterisation of normal
populations, their origins, phylogeny and evolution, and disease susceptibility profiles.
The applications in which we concentrate our efforts are molecular diagnostics and forensics, but
a line of research involving the history, conservation and management of domesticates and
laboratory animals as well as food quality assessment is now established. Diagnostic tools for dairy
cattle pathogens and pine wood nematode are under development.
Major achievements during 2008
According to the work plan formulated in 2007,
- We showed that close inbreeding (directly measured or evaluated through the proxy marital radius
between members of the couple) reduces human fertility, but as genetic distance increases, a
complex relationship emerges [7, 8]
- We developed a diagnostic kit based on the SNaPshot technology for lab mouse lines and their
wild and domestic relatives [4]
- A rapid method for testing the susceptibility of Aspergillus fumigatus to anti-mycotics was
developed [20] and a microsatellite based multiplex PCR for differentiation between Aspergillus
fumigatus strains was tested and validated (results already published in 2009)
- The role of erythrocyte enzymes in relation to malaria susceptibility was investigated and TPI gene
promoter variation in three sub-Saharan Africa population samples was analysed, showing no
correlation to disease severity (results already published in 2009)
38
- Timings and mechanisms of triplet repeat instability were in investigated in Machado-Joseph
disease [9] showing that 72% of expansions were associated to the worldwide spread TTACAC
lineage, whereas the GTGGCA displayed 75% of all contractions observed. The analysis of flanking
recombinant haplotypes did not suggest any further distant cis elements acting up- or
downstream the ATXN3 locus.
- Concerning the research on domesticates, we developed a PCR based assay for the identification
of male lineages in goats [11], we reviewed the state-of-the art in the species identification
through DNA [10] and we concluded the evaluation of the results of the quality control exercise
(www.gepisfg.org/ISFG/Castellano/Grupos_de_trabajo/Genetica_forense_no_humana/ejercicio2008.php)
- On the newly defined X chromosome markers, population and mutation analysis, we performed a
segregation study identifying 4 de novo mutations [13]
- The mutational spectra of Portuguese maple syrup urine disease and mucopolysaccharidosis type
IIIB were addressed in: [15] where a founder mutation in the Portuguese Gypsy community was
identified and a large deletion due to non-homologous recombination discovered [16] for the
first disease and in [21] and [22] for the second.
- The analyses of of DNA sequence variation patterns revealed the evolutionary role of mtDNA
secondary structures [12]; possible misleading results on mtDNA sequencing resulting from
nuclearly transferred sequences (NUMTS) was ruled out [5;14]
- On the issue of tracing population demographic histories through lineage and individuality
markers, we have shown: the surprising amount of Iberian male lineages into Portuguese
Gypsies gene pool [6], the complex genetic substructure of S. Tomé e Príncipe [3] and Tunisia
[23], the smallness of the founding female gene pool of Ashkenazi Jews [2], we have traced the
X-chromosome profile of a Colombian population [13], and the Y chromosome gene pools of
various populations [17, 18, 19]
- Forensic applications were specifically addressed in [1], where the quantification of genetic
evidence obtained from non recombining markers was analysed, in [4] where the described PCR
method is evaluated in terms of identification of inbred and wild mice, in [5] and [14], where the
potential error risks in forensic use of mtDNA is discussed, in [17] where a large interlaboratorial
quality control pilot study on Y chromosome STRs typing is reported and reviewed in [10] where
the pitfalls of DNA based species barcoding are addressed.
WORK PLAN FOR 2009
We intend to study
- X chromosome markers: population and mutation analysis, sequence variation and comparative
analyses between humans and other primates, optimisation of genotyping and interlaboratorial
quality control evaluation;
39
- The genetic diversity of erythrocyte enzymes in relation to malaria susceptibility
- The clonality of tumours through mtDNA typing
- The dynamics of normal and pathogenic mtDNA diversity and nuclear mtDNA insertions (NUMTs)
- The development of a PCR based method for differentiation between Aspergillus fumigatus
- The Timings and mechanisms of triplet repeat instability
- The genetic pools of domesticates (in particular and Portuguese dog, pig, sheep and goat
autochthonous breeds): history and management, control, certification and traceability
- Pharmacogenetically relevant variation
- Mutation dynamics and diagnostic improvement
- Meta-patterns of DNA sequence variation: development of detecting algorithms and comparative
genomics; generalised kinship analysis and sequence comparison not requiring alignments
- Indel (insertion/deletion) markers: development of multiplex typing assay, population analysis and
forensic applications
- Population demographic histories through lineage and individuality markers, with special emphasis
on Jewish, European and African ethnic/geographic groups
- Molecular diagnostic tools for dairy cattle pathogens
PAPERS
1. AMORIM A (2008) A cautionary note on the evaluation of genetic evidence from uniparentally
transmitted markers. Forensic Sci Int Genet. 2(4): 376-378.
2. BEHAR DM, METSPALU E, KIVISILD T, ROSSET S, TZUR S, HADID Y, YUDKOVSKY G,
ROSENGARTEN D, PEREIRA L, AMORIM A, KUTUEV I, GURWITZ D, BONNE-TAMIR B, VILLEMS R,
SKORECKI K (2008) Counting the founders: the matrilineal genetic ancestry of the Jewish
Diaspora. PLoS ONE 3(4): e2062.
3. COELHO M, ALVES C, COIA V, LUISELLI D, USELI A, HAGEMEIJER T, AMORIM A, DESTRO-BISOL G,
ROCHA J (2008) Human Microevolution and the Atlantic Slave Trade: A Case Study from São
Tomé. Current Anthropology 49: 134-143
4. GOIOS A, GUSMÃO L, ROCHA AM, FONSECA A, PEREIRA L, BOGUE M, AMORIM A (2008)
Identification of mouse inbred strains through mitochondrial DNA single-nucleotide extension.
Electrophoresis 29(23): 4795-4802.
5. GOIOS A, PRIETO L, AMORIM A, PEREIRA L (2008) Specificity of mtDNA-directed PCR-influence
of NUclear MTDNA insertion (NUMT) contamination in routine samples and techniques. Int J
Legal Med. 122: 341 – 345
40
6. GUSMÃO A, GUSMÃO L, GOMES V, ALVES C, CALAFELL F, AMORIM A, PRATA MJ (2008) A
Perspective on the History of the Iberian Gypsies Provided by Phylogeographic Analysis of YChromosome Lineages. Ann Hum Genet. 72: 215-27
7. LABOURIAU R, AMORIM A (2008) Comment on "An association between the kinship and fertility
of human couples" Science 322(5908): 1634.
8. LABOURIAU R, AMORIM A (2008) Human fertility increases with marital radius. Genetics 178:
601-603
9. MARTINS S, COUTINHO P, SILVEIRA I, GIUNTI P, JARDIM LB, CALAFELL F, SEQUEIROS J,
AMORIM A (2008) Cis-acting factors promoting the CAG intergenerational instability in MachadoJoseph disease. Am J Med Genet B Neuropsychiatr Genet. 147B: 439-446
10. PEREIRA F, CARNEIRO J, AMORIM A. Identification of Species with DNA-Based Technology:
Current Progress and Challenges. Recent Pat DNA Gene Seq. 2(3):187-200.
11. PEREIRA F, CARNEIRO J, SOARES P, MACIEL S, NEJMEDDINE F, LENSTRA JA, GUSMÃO L,
AMORIM A (2008) A multiplex primer extension assay for the rapid identification of paternal
lineages in domestic goat (Capra hircus): Laying the foundations for a detailed caprine Y
chromosome phylogeny. Mol Phylogenet Evol. 49(2): 663-8.
12. PEREIRA F, SOARES P, CARNEIRO J, PEREIRA L, RICHARDS MB, SAMUELS DC, AMORIM A (2008)
Evidence for variable selective pressures at a large secondary structure of the human
mitochondrial DNA control region. Mol Biol Evol. 25(12): 2759-70.
13. PICO A, CASTILLO A, VARGAS C, AMORIM A, GUSMÃO L (2008) Genetic profile characterization
and segregation analysis of 10 X-STRs in a sample from Santander, Colombia. Int J Legal Med. 122:
347–351
14. PRIETO L, ALONSO A, ALVES C, CRESPILLO M, MONTESINO M, PICORNELL A, BREHM A,
RAMÍREZ JL, WHITTLE MR, ANJOS MJ, BOSCHI I, BUJ J, CEREZO M, CARDOSO S, CICARELLI R,
COMAS D, CORACH D, DOUTREMEPUICH C, ESPINHEIRA RM, FERNÁNDEZ-FERNÁNDEZ I,
FILIPPINI S, GARCIA-HIRSCHFELD J, GONZÁLEZ A, HEINRICHS B, HERNÁNDEZ A, LEITE FP,
LIZARAZO RP, LÓPEZ-PARRA AM, LÓPEZ-SOTO M, LORENTE JA, MECHOSO B, NAVARRO I,
PAGANO S, PESTANO JJ, PUENTE J, RAIMONDI E, RODRÍGUEZ-QUESADA A, TERRA-PINHEIRO
MF, VIDAL-RIOJA L, VULLO C, SALAS A (2008) 2006 GEP-ISFG collaborative exercise on mtDNA:
reflections about interpretation, artefacts, and DNA mixtures. Forensic Sci Int Genet 2(2):126-33.
15. QUENTAL S, MACEDO-RIBEIRO S, MATOS R, VILARINHO L, MARTINS E, TELES EL, RODRIGUES E,
DIOGO L, GARCIA P, EUSÉBIO F, GASPAR A, SEQUEIRA S, FURTADO F, LANÇA I, AMORIM A,
PRATA MJ (2008) Molecular and structural analyses of maple syrup urine disease and
identification of a founder mutation in a Portuguese Gypsy community. Mol Genet Metab.
94(2):148-56.
16. QUENTAL S, MARTINS E, VILARINHO L, AMORIM A, JOÃO PRATA M (2008) Maple syrup urine
disease due to a new large deletion at BCKDHA caused by non-homologous recombination. J
Inherit Metab Dis. 2008 Dec 16. [Epub ahead of print]
17. SÁNCHEZ-DIZ P, ALVES C, CARVALHO E, CARVALHO M, ESPINHEIRA R, GARCÍA O, PINHEIRO MF,
PONTES L, PORTO MJ, SANTAPA O, SILVA C, SUMITA D, VALENTE S, WHITTLE M, YURREBASO I,
CARRACEDO A, AMORIM A, GUSMÃO L; GEP-ISFG (The Spanish and Portuguese Working Group
of the International Society for Forensic Genetics) (2008) Population and segregation data on 17
Y-STRs: results of a GEP-ISFG collaborative study. Int J Legal Med. 122(6):529-33.
41
18. SOARES-VIEIRA JÁ, BILLERBECK AEC, IWAMURA ESM, MENDONÇA BB, GUSMÃO L, OTTO P
(2008) Population and mutation analysis of Y-STR loci in a sample from the city of São Paulo
(Brazil). Genet Mol Biol 31:651-656.
19. TOSCANINI U, GUSMÃO L, BERARDI G, AMORIM A, CARRACEDO A, SALAS A, RAIMONDI E (2008)
Y chromosome microsatellite genetic variation in two Native American populations from
Argentina: Population stratification and mutation data. Forensic Sci Int Genet. 2(4):274-280.
20.ARAUJO R, COUTINHO I, ESPINEL-INGROFF A (2008)
Rapid method for testing the
susceptibility of Aspergillus fumigatus to amphotericin B, itraconazole, voriconazole and
posaconazole by assessment of oxygen consumption. J Antimicrob Chemother. 62(6):1277-80.
21. MANGAS M, NOGUEIRA C, PRATA MJ, LACERDA L, COLL MJ, SOARES G, RIBEIRO G, AMARAL O,
FERREIRA C, ALVES C, COUTINHO F, ALVES S (2008) Molecular analysis of mucopolysaccharidosis
type IIIB in Portugal: evidence of a single origin for a common mutation (p.R234C) in the Iberian
Peninsula. Clin Genet 73:251-6.
22. COUTINHO MF, LACERDA L, PRATA MJ, RIBEIRO H, LOPES L, FERREIRA C, ALVES S (2008)
Molecular characterization of the Portuguese patients with mucopolysaccharidosis IIIC: two
novel mutations in the HGSNAT gene. Clin Genet 74:194-5.
23. KHODJET-EL-KHIL H, FADHLAOUI-ZID K, GUSMÃO L, ALVES C, BENAMMAR-ELGAAIED A,
AMORIM A (2008) Substructure of a Tunisian Berber Population as Inferred from 15 Autosomal
Short Tandem Repeat Loci. Hum Biol 80: 435–448
Without IPATIMUP affiliation (resulting from work performed in previous host institutions)
Silva RM, Paredes JA, Moura GR, Manadas B, Lima-Costa T, Rocha R, Miranda I, Gomes AC,
Koerkamp MJG, Perrot M, Holstege FCP, Boucherie H, Santos MAS (2008). Genetic Code
Alteration Plays a Critical Role in the Evolution of Candida Genes - Quantitative Analysis of Single
Amino Acid Changes using a 4000 QTRAP® system. Applied Biosystems Technical note 115TN10-01.
Conde-Vancells J, Rodriguez-Suarez E, Embade N, Gil D, Matthiesen R, Valle M, Elortza F, Lu SC, Mato
JM, Falcon-Perez JM (2008) Characterization and Comprehensive Proteome Profiling of
Exosomes Secreted by Hepatocytes. J Proteome Res 7 (12), 5157–5166
Matthiesen R, Jensen ON (2008) Analysis of mass spectrometry data in proteomics. Methods Mol
Biol. 453: 105-22.
Molina H, Matthiesen R, Kandasamy K, Pandey A (2008) Comprehensive comparison of collision
induced dissociation and electron transfer dissociation. Anal Chem 80(13): 4825-35
Hackenberg M, Matthiesen R (2008) Annotation-Modules: a tool for finding significant
combinations of multisource annotations for gene lists. Bioinformatics 24(11): 1386-93
Martínez-Chantar ML, Vázquez-Chantada M, Ariz U, Martínez N, Varela M, Luka Z, Capdevila A,
Rodríguez J, Aransay AM, Matthiesen R, Yang H, Calvisi DF, Esteller M, Fraga M, Lu SC, Wagner C,
Mato JM (2008) Loss of the glycine N-methyltransferase gene leads to steatosis and
hepatocellular carcinoma in mice. Hepatology 47(4): 1191-9.
Costa-de-Oliveira S, Araujo R, Silva-Dias A, Pina-Vaz C, Rodrigues AG (2008) Propofol lipidic infusion
promotes resistance to antifungals by reducing drug input into the fungal cell. BMC Microbiol.
2008 Jan 17;8:9.
42
Araujo R, Cabral JP, Rodrigues AG (2008) Air filtration systems and restrictive access conditions
improve indoor air quality in clinical units: Penicillium as a general indicator of hospital indoor
fungal levels. Am J Infect Control. 2008 Mar;36(2):129-34.
Araujo R, Carneiro A, Costa-Oliveira S, Pina-Vaz C, Rodrigues AG, Guimaraes JE (2008) Fungal
infections after haematology unit renovation: evidence of clinical, environmental and economical
impact. Eur J Haematol. 2008 May;80(5):436-43.
PhDs
Finished
- Pereira F. “Development of uniparentally transmitted genetic markers for the characterization
of male and female gene pools of Portuguese small ruminants autochthonous breeds” Faculty
of Sciences, University of Porto, IPATIMUP, and Department of Genetics, Smurfit Institute,
Trinity College, Dublin 2, Ireland. Fundação para a Ciência e Tecnologia (SFRH/BD/19585/2004);
approved Jan 6th, 2009
- Oliveira E. “Study of Genetic Polimorphisms in Pediatric Acute Lymphoblastic Leukemia Pharmacogenetic Role in the Treatment and Relationship with susceptibility to the
leukemogenic process”. Faculty of Sciences, University of Porto, IPATIMUP, and School of
Medicine , Washington University in St. Louis. Fundação para a Ciência e Tecnologia
(SFRH/BD/17124/2004); approved Feb 13th, 2009
- Goios A “Dynamics of the mitochondrial genome – the moving boundary between normal and
pathogenic diversity” Faculty of Sciences, University of Porto, IPATIMUP and Department of
Statistics, University of Glasgow. Fundação para a Ciência e Tecnologia (SFRH/BD/16518/2004);
approved Jan 16th, 2009
Ongoing
- Gomes I “X chromosome markers: genetic characterization, population analysis and forensic
applications” University Santiago de Compostela, IPATIMUP and CEGEN (National Genotyping
Center of Spain). Fundação para a Ciência e Tecnologia (SFRH/BD/21647/2005). Since November
2004.
- Quental R “Congenital Disorders of Glycosylation (CDG): Enzymatic, Biochemical and Molecular
Features” Faculty of Sciences, University of Porto, IPATIMUP and Department of Human
Genetics, Catholic University of Leuven, Belgium. Fundação para a Ciência e Tecnologia
(SFRH/BD/23657/2005). Since February 2006.
- Quental S “Functional, Expression and Structural investigation of the mutational spectrum of
Portuguese Maple Syrup Urine Disease patients” Faculty of Sciences, University of Porto,
IPATIMUP and Department of Human Genetics, School of Medicine, Emory University, Atlanta,
USA. Fundação para a Ciência e Tecnologia (SFRH/BD/22685/2005). Since January 2006.
- Van Asch B “Development of uniparentally transmitted genetic markers for the characterization
of male and female gene pools of Portuguese pig (Sus scrofa) autochthonous breeds:
applications for the control, certification and traceability of meat products” Faculty of Sciences,
University of Porto, IPATIMUP and Modelo Continente Hipermercados SA. Fundação para a
Ciência e Tecnologia (SFRH/BDE/15581/2006). Since July 2006.
- Pereira R “Bridging the gap between Short Tandem Repeats (STRs) and Single Nucleotide
Polymorphisms (SNPs)” Institute of Legal Medicine of the University of Santiago de Compostela
43
-
and IPATIMUP. Fundação para a Ciência e Tecnologia (SFRH/BD/30039/2006). Since January
2007.
Gomes V “Ethnicity and genetics in sub-Saharan Africa” Institute of Legal Medicine of the
University of Santiago de Compostela and IPATIMUP. Fundação para a Ciência e Tecnologia
(SFRH/BD/36045/2007). Since December 2008.
MScs
Finished
- Vânia Pereira “Deciphering the origin of foci of high prevalence of hereditary anemias in
Portugal: epidemiological and evolutionary study”, FC University of Porto and IPATIMUP
- João Carneiro: “Forensic applications of mtDNA”, FC University of Porto and IPATIMUP
- Sérgio Costa: “Portuguese autochthonous dog breeds - mtDNA diversity”, University of Porto
and IPATIMUP
- Ivone
- Inês Nogueiro
Ongoing
- S Botão
- D Teixeira
NATIONAL AND INTERNATIONAL COOPERATIONS
The group is currently engaged in various collaborative projects with
-
Dep. Statistics, Univ. Glasgow (mtDNA), Vincent Macaulay
Department of Pathology, Cambridge University (sex chromosomes biology), Nabeel A Affara
Faculdade de Medicina, UP (Aspergillus genotyping), Cidália Pina-Vaz
Hôpital Nôtre Dame, Montreal, Canada (Machado-Joseph disease), Guy Rouleau
Inst. Med. Legal, Univ. Santiago Compostela (forensic genetics), Angel Carracedo
Centro de Genética Médica Jacinto de Magalhães / INSA (human genetic diseases), Laura
Vilarinho
Instituto Nacional de Medicina Legal (forensic genetics and databases), Francisco Corte-Real
Laboratorio Biología-ADN, Servicio Central de Analítica, Comisaría General Policía Científica,
Madrid (forensic genetics), Lourdes Prieto
Instituto Português de Arqueologia, Lisboa, Portugal (domesticates), Simon J.M. Davis
Rambam Medical Center, Haifa, Israel (Jewish populations) Doron Behar
UniGene, IBMC Porto (genetic diseases), Jorge Sequeiros
Univ Pompeu Fabra (population genetics modelling), Francesc Callafel
Univ. Tunis (population genetics), Houssein Khodjet, Lotfi Cherni
Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg,
USA (mtDNA), David C. Samuels
Jackson Laboratory, Bar Harbor, USA (lab mouse genetics), Molly Bogue
44
-
PRICAI-Fundacion Favaloro, Buenos Aires, Argentina (population genetics), Eduardo Raimondi
Inst. Higiene e Medicina Tropical, Lisboa (malaria and PKLR polymorphisms), Virgílio do Rosário,
Ana Paula Arez
Institute of Integrative and Comparative Biology, Univ. Leeds (mtDNA), Martin Richards, Pedro
Soares
Institute of Comparative Medicine, University of Glasgow Veterinary School, Glasgow, Scotland
(domesticates), Massimo Palmarini.
Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of
Aarhus, DK-8830 Tjele, Denmark (population models and fertility) Rodrigo Labouriau
Institute for Pharmacogenomics and Individualized Therapy – University of North Carolina,
Chapel Hill NC, USA – Howard McLeod
IPO – Porto, Serviço de Pediatria; Lucília Norton; Department of Genetics; Ana Peixoto, MR
Teixeira
IPO – Lisboa, Serviço de Pediatria; Mário Chagas
Hospital Pediátrico de Coimbra – Serviço de Hematologia; Maria Manuela Benedito e Maria
Lurdes Maricato
Hospital S.João Porto – Serviço de Pediatria; Fátima Ferreira
Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Brazil (population
genetics), Sidney Santos
Laboratory of Comparative Pathology, Department of General Pathology, Institute of Biological
Science, Federal University of Minas Gerais, Brazil (canine tumors clonality), AC Bertagnolli
Department of Zoology, University of Oxford, UK, C Capelli
Cherni L, Fernandes V, Pereira JB, Costa MD, Goios A, Frigi S, Yacoubi-Loueslati B, Amor MB,
Slama A, Amorim A, El Gaaied AB, Pereira L.
Laboratory of Genetics Immunology and Human Pathology, Faculty of Sciences of Tunis, Tunisia,
L Cherni
Division of Blood Group Serology, Medical University of Vienna, 1090 Vienna, Austria; W Mayr
Department of Forensic Biology, Office of the Chief Medical Examiner, New York, NY, USA; M
Prinz
Laboratório de Genética Humana e Médica, Departamento de Patologia, Universidade Federal
do Pará, Belém, PA, Brazil; EM Rodrigues
Faculty of Veterinary Medicine, Utrecht University, The Netherlands (domesticates) Johannes A.
Lenstra.
Agriculture Research Institute of Mozambique, Department of Animal Sciences, Artificial
Insemination Centre, Maputo, Mozambique (domesticates), Sónia Maciel
Departamento de Toxicología y Legislación Sanitaria, Facultad de Medicina, Universidad
Complutense de Madrid, Spain; E Arroyo-Pardo
Departamento de Antropologia, Universidade de Coimbra, Coimbra, Portugal; Licínio Manco
Genetic Laboratory, UIS-Industrial University of Santander, Bucaramanga, Colombia; Adriana
Pico
45
Visiting researchers at IPATIMUP
Sidney Emanuel Batista dos Santos
Ândrea Kely Campos Ribeiro dos Santos
Laboratório de Genética Humana e Médica, Departamento de Patologia, Universidade Federal do
Pará, Belém, Pará , Brazil
Elizeu Fagundes de Carvalho, do Laboratório de Diagnostico por DNA da Universidade do Estado do
Rio de Janeiro, Brasil
Rosa Fregel, Departamento de genética, Universidade de La Laguna, Tenerife, Canarias, Espanha
Patrícia
Inês Nogueiro
Martha Lucia Hincapie López, Universidad Industrial de Santander. Bucaramanga, Colombia.
Mónica Carvalho - Forensic Genetic Service, Central Region Department, National Institute of Legal
Medicine, Coimbra, Portugal
Organization of Scientific Meetings
• Portugaliae Genetica 11th. edition, 27-28 March
Coordination of QC/QA cooperative exercises
• Colaborative exercise on canine mtDNA, Non-human Forensic Genetics Workgroup, António
Amorim and José Pestano Brito, with Barbara Van Asch; GEP- ISFG
Editorial Boards
Open Forensic Science Journal (A Amorim)
Forensic Science International: Genetics (L Gusmão)
Invited talks
A Amorim - Quantificação da prova genética. II Congresso Nacional de Genética Forense, 5-7/11,
Brasília
A Amorim, Guilherme Jaques - Mesa Redonda I – Genética Forense não Humana. II Congresso
Nacional de Genética Forense, 5-7/11, Brasília
A Amorim - A Identificação Humana por DNA: Perspectiva Histórica, Aplicações e Desenvolvimento Conferência Inaugural, III Simpósio Internacional de Identificação Humana por DNA, 24-26/6,
Escola de Magistratura do Estado do Rio de Janeiro
A Amorim - Tracing human migrations through genetics: using markers or finding enhancers? XV
Cursos Internacionais de Verão de Cascais, 3/7
L Gusmão – A Gypsy Tale. Kolloquium Berlin 6 June 2008. Institut fur Pathologie. Charité
Universitatsmedizin Berlin.
L Gusmão – Estrutura e objectivos do Grupo Espanhol e Português da Sociedade Internacional de
Genética Forense (GEP-ISFG). III Simpósio Internacional de Identificação Humana por DNA. Rio
de Janeiro, Brazil, 24 e 26 de Junho de 2008.
L Gusmão – Utilização de marcadores dos cromossomas X e Y em investigação de vínculos genéticos
e criminais. III Simpósio Internacional de Identificação Humana por DNA. Rio de Janeiro, Brazil, 24
e 26 de Junho de 2008.
46
L Gusmão – Utilidad de los distintos marcadores de ADN en genética de poblaciones. I Congreso
Latinoamericano de Genética Humana y IX Congreso Colombiano de Genética. Cartagena de
Indias, Colombia, 8-10 de Outubro de 2008.
Science diffusion
A Amorim - Genética, reproduções e evoluções, ES Aurélia de Sousa, 16/01, Ermesinde
A Amorim – Ciência e religião: uma relação impossível? 3/12, FCUP
Oral presentations
Gomes I, Prinz M, Pereira R, Bieschke E, Amorim A, Carracedo A, Gusmão L (2008) Hidden sequence
variation of the X-linked DXS6789 microsatellite. DNA in Forensics 2008. Ancona, Itália. 27-30/5.
OP15.
Gomes V, Pereira V, Amorim A, Sánchez-Diz P, Carracedo A, Prata MJ, Gusmão L (2008)
Mitochondrial DNA in people from Karamoja Uganda. DNA in Forensics 2008. Ancona, Itália. 2730/5. OP39.
Sánchez-Diz P, Alves C, Carvalho E, Carvalho M, Espinheira R, Garcia O, Pinheiro MF, Pontes L, Porto
MJ, Santapa O, Silva C, Sumita D, Valente S, Whittle M, Yurrebaso I, Carracedo A, Amorim A,
Gusmão L (2008) Population and segregation data on 17 Y-STRs: results of a GEP-ISFG
collaborative study. Ancona, Itália. 27-30/5. OP72.
Capelli C, Onofri V, Brisighelli F, Boschi I, Scarnicci F, Masullo M, Ferri G, Tofanelli S, Tagliabracci A,
Gusmão L, Amorim A, Gatto F, Brion Martinez M, Blanco Verea A, Romano V, Cali F, Pascali V
(2008) The Arabs in Europe: estimating mediaval North Africa male legacy into Southern Europe.
Ancona, Itália. 27-30/5. OP75.
Cíntia Alves - STRs cromossomas sexuais - XIII Jornadas GEP-ISFG, 23-24/6, Rio de Janeiro
Other
GABBA (Graduate Program in Areas of Basic and Applied Biology) Self-evaluation report (A Amorim)
Coordination (A Amorim, José J. Pestano Brito) of the Working Commission on Non-human Forensic
Genetics, GEP-ISFG
Coordination (A Amorim, L Gusmão) of the Working Commission on Sexual Chromosomes, GEP-ISFG
Vice-President GEP-ISFG (A Amorim)
Member of the Board (Treasurer) of the ISFG (L Gusmão).
47
2e. GENETICS, EVOLUTION AND PATHOLOGY
Group Composition
Group Leader: Jorge Rocha, BSc, PhD, University of Porto
Post-doc fellows: Susana Seixas (BSc, PhD, University of Porto) Sandra Beleza, (BSc, PhD, University
of Porto) and Nevyana Ivanova (MSc, PhD, University of Sofia; joined the group in October 2007).
PhD students: Margarida Coelho (BSc, University of Porto); João Pedro Oliveira (BSc, University of
Coimbra)
Project grant students: Zélia Ferreira (BQ; University of Porto joined the group in November 2007),
Joana Campos (BSc; University of Coimbra, joined the group in October 2007); Isabel Alves (Joined
the group in May 2008)
Undergraduate students: Joana Barbosa (Biological Sciences students, University of Porto; from
March to July 2008)
Research interests and goals
The major research goal of this group is to study the factors that shaped the present genetic
variability of human populations. Our research is focused both on population history and on the
evolution of specific genes involved in human disease and human adaptation. Presently, the
activities of the group include the following three major goals: (1) to study the genetic structure and
evolutionary history of populations from Cape Verde, Angola, Mozambique and São Tomé; 2) to
analyse the origin, evolution and spread of genetic variants involved in protease inhibition, malaria
resistance and lactose tolerance; 3) to use the admixed population of Cape Verde as a model to
understand the genetic basis of complex traits with anthropological relevance (like skin colour) or
biomedical interest (like obesity and hypertension).
General overview of 2008
1 Funding
We started to develop the research activities programmed in the following projects, that were
approved in 2007:
a) On the edge of the Bantu expansions: inference of recent population history with
independently evolving haplotypic systems. (Funded by FCT; PTDC / BIABDE / 68999/ 2006;
122 000 Euros)
b) Looking for evidences of human adaptation in the proteolysis universe: the case study of serine
protease inhibitors. (Funded by FCT; PTDC / SAU-GMG / 64043 / 2006; 178 700 Euros)
c) Understanding the genetic architecture and evolution of human pigmentary traits: admixture
mapping studies in Cape Verde. (Funded by FCT; PTDC / BIA-BDE / 64044 / 2006; 121 000
Euros)
d) Using Admixed Populations to Study the Genetic Basis of Obesity and Hypertension: the CaseStudy of Cape Verde and of the Portuguese Population from the Regions of Tejo, Sado and
Guadiana River Basins. (Funded by the pharmaceutical company Sanofi-Aventis; 111 000
Euros).
48
The projects are nested in our three major areas of research and are coordinated by different
Principal Investigators (see Annex 1): The first project, coordinated by Jorge Rocha, reflects our
interest in the genetic structure and history of African populations. The second project, coordinated
by Susana Seixas, is related with our interest in the evolutionary history of genes that may have a
medical interest or may be potential targets for selection. The third and the fourth projects,
coordinated by Sandra Beleza, are both centered on the use of the admixed population of Cape
Verde to study the genetic basis of complex traits. The third project, financed by FCT, is focused on
the analysis of pigmentation traits; the fourth project, financed by Sanofi-Aventis, is centred in the
study of obesity and hypertension. Details on the aims of these projects can be found in our
previous report (2007 report).
2 Participation in projects from other groups
In addition to the projects coordinated by our own researchers, we became involved in research
teams of projects led by colleagues from other groups in IPATIMUP. Jorge Rocha worked as a team
member of the project entitled Secretor and Lewis phenotypes/genotypes in Helicobacter pylori and
calicivirus infection led by Leonor David, which was approved by FCT during 2007.
3 Changes in group composition
During 2008, three researchers changed the nature of their link to the group. After her graduation,
Isabel Alves has won a grant contest to work in the project on the Bantu expansions. João Pedro
Oliveira has received a PhD grant and started to work in his PhD project entitled “The evolutionary
history and geographic spread of advantageous variants that confer resistance to malaria in SubSaharan African populations” (co-suervised by Jorge Rocha and Prof. Anna Di Rienzo) . Zélia Ferreira
successfully submitted an application for a PhD grant to FCT with the project entitled “The human
Whey-acidic-protein Four-Disulfide Core-domain (WFDC) cluster on 20q13 region: evolutionary history
and role in human health and disease”. This project will be co-supervised by Susana Seixas and Dr.
Belen Hurle from the National Human Genome Research Institute at the National Institutes of
Health in Bethesda, MD/USA (NHGRI/NIH).
4 Undergraduate training
As part of our support to the training of undergraduate students, we hosted Joana Barbosa Rebelo,
from the Faculty of Sciences of Porto University, who stayed in the lab from March to July 2007,
who made a graduation work on the genetic lineages of Cape-Verde origin in the present
populations of São Tomé.
This year we continued to collaborate with the University of Cape Verde in educational programs. In
March 2008, Jorge Rocha lectured a one week human genetics course at the Instituto Superior de
Educação (ISE), Santiago, which was attended by 40 Biology students and health workers from Cape
Verde. Sandra lectured a seminar on Forensic Genetics in 2nd of April 2008 in ISE, São Vicente, and
promoted our research proposal at local high schools and Superior Institutes of all islands. Sandra
also supervised one more Biology student from ISE, Crisolita Gomes, in her graduation thesis.
Crisolita learned how to measure all phenotypes related with the project and to perform sociodemographic questionnaires, and made part of the sampling team with Sandra and Joana. The
phenotype data she collected was used by her to conduct a study on the distribution of
hypertension and obesity-related phenotypes across the Cape Verde archipelago. In September,
49
Crisolita came to our lab to perform the necessary statistical analyses for her work. She also had the
opportunity to follow the lab routine of a scientific work.
We also helped the student Jailson Lopes to make an application to the Masters Course in
Biodiversity, Genetics and Evolution, from the Faculty of Sciences (Porto University). Jailson has
won a grant from the Gulbenkian Foundation and joined the course in October 2008. During the
second year of his Masters, Jailson will work on a thesis on the genetic structure of the Cape
Verdian population.
5 Graduate training
During 2008, Margarida Coelho preceded the activities related to the third year of her PhD work.
She concluded and submitted for publication a study on the genetic variation in southern Angola
populations, and continued to work on the development of a new type of polymorphisms,
UEPSTRS, that will be used to characterize populations at the edges of Bantu expansions, in
Mozambique and Angola (see below).
João Pedro Oliveira started his PhD by spending most of the year at the at Prof. Anna Di Rienzo’s lab
(Department of Human Genetics, University of Chicago), where he worked on the genotyping of
previously ascertained SNPs linked to three advantageous variants, i.e. HBB*S, HBA*-α3.7 and FY*O,
associated with resistance to malaria (see below). During his stay at Chicago João Pedro also
attneded the courses on “Human Genetic Variation and Disease”, led by Profs. Anna Di Rienzo and
Jonathan Pritchard, and “Population Genetics”, led by Prof. Richard Hudson.
6 Theses
6.1 Graduation theses
-
The southern diaspora: a study on the diffusion of Cape-Verdian mitochondrial DNA lineages
in the island of São Tomé (supervised by Jorge Rocha).
7 Participation in Scientific Meetings
Group members participated in the annual meeting of the Society for Molecular Biology and
Evolution held in June 2008 at Barcelona.
7.1 Poster presentations
-
-
Coelho M, Beleza S, Rocha J (2008) On the edge of the Bantu expansions: mtDNA, Ychromosome and lactase genetic variation in the Namibe desert of Angola. Annual meeting
of the Molecular Biology and Evolution (SMBE), Barcelona, Spain, June 2008.
Alves I, Beleza S, Martinho C, Parra E, Shriver M, Rocha J (2008) Patterns of microsatellite
variation within Kit Ligand (KITLG) and Tyrosinase Related Protein-1 (TYRP1) genes and the
evolutionary history of skin pigmentation in human populations. Annual meeting of the
Molecular Biology and Evolution (SMBE), Barcelona, Spain, June 2008.
50
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Ferreira Z, Ivanova N, Rocha J, Seixas S (2008) Searching for evidences of natural selection
on the human WFDC cluster located in the 20q13 region. Annual meeting of the Molecular
Biology and Evolution (SMBE), Barcelona, Spain, June 2008.
-
Ivanova N, Ferreira Z, Rocha J, Seixas S (2008) Loss and gain of function in Human
SERPINB11. Annual meeting of the Molecular Biology and Evolution (SMBE), Barcelona,
Spain, June 2008.
8 Publications
8.1 Published papers
- Coelho M, Alves C, Coia V, Luiselli D, Uselli A, Hagemeijer T, Amorim A, Destro- Bisol G, Rocha
J (2008) Human microevolution and the Atlantic slave trade: the case study of São Tomé
(Gulf of Guinea). Current Anthropology 49: 134-43.
- Saranga S, Prista A, Nhatumbo L, Beunen G, Rocha J, Blangero S, Maia J (2008) Heritabilities
of somatotype components in a population from rural Mozambique. American Journal of
Human Biology 20: 642-646.
- Canedo P, Durães C, Pereira F, Regalo G, Lunet N, Barros H, Carneiro F, Seruca R, Rocha J,
Machado JC (2008) Tumor necrosis factor alpha extended haplotypes and risk of gastric
carcinoma. Cancer Epidemiology, Biomarkers & Prevention 17: 2416-2420.
- Azevedo M, Eriksson S, Mendes N, Serpa J, Figueiredo C, Resende LP, Ruvoën-Clouet, Haas
R, Borén T, Le Pendu J, David L(2008) Infection by Helicobacter pylori expressing the BaBA
adhesin is influenced by the secretor phenotype. Journal of Pathology 215: 308-316.
8.2 Papers submitted for publication
- Coelho M, Sequeira F, Luiselli D, Beleza S, Rocha J. On the edge of Bantu expansions: mtDNA, Y
chromosome and lactase persistence genetic variation in southwestern Angola
Major research activities
1 Genetic structure and history of African populations
According to the aims of our project on the Bantu expansions (section 3.1) we begun to study
populations located on the southwest and southeast edges of the expansions, from southwestern
Angola and Mozambique. So far, Margarida Coelho has concluded and submitted for publication a
study on the mtDNA, Y chromosome and lactase persistence genetic variation of populations from
the Namibe desert in Southern Angola. This work fills an important gap in the analysis of the
western edge of the Bantu migrations, focusing in populations that have crossed the dry woodlands
to the south of the Cuanza river and become increasingly dependent on pastoralism. We assessed
the genetic differentiation between these populations and their levels of admixture with Khoe-San
groups, and examined their relationship with other sub-Saharan populations. We further combined
our dataset with previously published data on Y-chromosome and mtDNA variation to explore a
general isolation with migration model and infer the demographic parameters underlying current
genetic diversity in Bantu populations. Our analysis shows that the gene pool from southwestern
Angola is predominantly derived from West-Central Africa and that the pastoralist Herero-speaking
Kuvale people were additionally characterized by relatively high levels of assimilation of Y
chromosome (12%) and mtDNA (22%) Khoe-San lineages, as well as by the presence of the -14010C
51
lactase persistence mutation (6%), which likely originated in non-Bantu pastoralists from East Africa.
Inferred demographic parameters showed that both male and female populations underwent
significant size growth after the split between the western and eastern branches of Bantu
expansions occurring 4000 years ago. However, males had lower population sizes and migration
rates than females throughout the Bantu dispersals. We concluded that: 1) Genetic variation in
southwestern Angola essentially results from the encounter of an offshoot of West-Central Africa
with autochthonous Khoisan-speaking peoples from the south; 2) Interactions between the Bantus
and the Khoe-San likely involved cattle herders from the two groups sharing common aspects of
their social organization; 3) The presence of -14010C mutation in southwestern Angola provides a
link between the East and Southwest African pastoral scenes that might have been established
indirectly, through migrations of Khoe herders across southern Africa; 4) Differences in patterns of
mtDNA and Y chromosome intrapopulation diversity and interpopulation differentiation may be
explained by contrasting demographic histories underlying the current female and male genetic
variation.
Still related to the project on the Bantu expansions, Isabel Alves and Margarida Coelho developed a
suite of 15 non-recombining autosomal haplotype systems (UEPSTRs), each consisting of a unique
event polymorphism (UEP) linked to one short tandem repeat (STR), that are currently being used
to study of the relationship between population history, geographic distance and language
differentiation in Bantu-speaking populations from Mozambique. The Mozambican dataset will be
used together with contextual samples from southwestern Angola to infer key evolutionary
parameters of the Bantu expansions at the continental level.
Finally, we will use the Mozambican dataset together with contextual samples from southwestern
Angola to infer key evolutionary parameters of the Bantu expansions at the continental level. We
expect to provide novel insights into the use of a new generation of molecular markers and to shed
light on fundamental questions concerning recent human history in Africa.
According to the aims of the project on Cape Verde (section 3.1), Sandra Beleza and Joana Campos
started to assess the degree of substructuring of Cape Verdian male lineages through the analysis of
11 Y-chromosome microsatellite markers in the 449 males selected (125 from Santiago, 142 from
Fogo, 53 from São Vicente, 52 from Santo Antão, 48 from São Nicolau and 29 from Boa Vista).
Preliminary results from Fogo and Santiago islands indicate that the former presents a higher
number of haplotypes at intermediate frequency and fewer rare haplotypes than Santiago,
consistent with the presence of higher genetic drift possibly due to founder effects in this island. In
addition, different Y-chromosome backgrounds are observed between the two islands. Haplotype
match analysis with samples collected from the literature and with samples contained in the public
Y-chromosome Haplotype Reference database allowed us to conclude that Santiago’s male
component is mainly of African origin whereas Fogo’s male component is mainly European.
2. Study of the evolutionary history of genes involved in human adaptation and/or disease
2.1 Studies on the evolutionary history of Serine Protease Inhibitors (SERPIN)
According to the aims of our project on the evolution of SERPIN genes (section 3.1), we have
proceeded our work on the functional characterization of SERPINA2. In previous work, Susana
Seixas had found a strong signature of natural selection favoring a 2kb deletion lying in a genome
region that was considered to be a pseudogene: SERPINA2. Based on this result and on preliminary
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evidence that mRNA from a non-deletion variant of SERPINA2 was synthesized in different tissues,
we hypothesized that SERPINA2 had functional variants, but that natural selection was favoring the
active pseudogenization of this gene. During 2008, Susana has started to test the hypothesis that
SERPINA2 had functional variants, by attempting to isolate SERPINA2 protein isoforms. The work
involved clonning the DNA coding for three putatively functional isoforms (Leu308-Glu320, Pro308Glu320 e Pro308-Lys320), successful transfection of 293FT cells and the use of lentivirus particles
containing the SERPINA2 gene to transduce two mammalian cell lines (HeLa and CHO). We obtained
clear evidence that a SERPINA2 protein can be expressed after detecting recombinant SERPINA2
proteins (rSERPINA2) both in Western blot and intracellular immunoflurescence assays. The next
steps will involve imunoprecipitation of rSERPINA2 and the screening of SERPINA2 activity through
incubation of different amounts of rSERPINA2 with several proteases and colorimetric substrates.
Another aspect of the Susana’s work, carried out with Nevyana Ivanonova and Zélia Ferreira,
involved the survey of the public available HapMap databases for potential targets of selection
among serine protease inhibitor genes. Using this approach, we have identified SERPINB11 in chr18
for (Yoruba sample) and WFDC6-WFDC7-WFDC8 (CEPH sample) and SPINT4 (Yoruba sample) in chr20
as likely candidate genes. We further developed resequencing strategies for these 5 genes in
subsamples of 20 individuals from HapMap, in order to analyze their patterns of haplotype and
nucleotide diversity to search for variants with potential functional repercussions. We found an
unusually deep genealogy at the SERPINB11 locus, with two major functional divergent haplotypes.
While one haplotype was found to be associated to a premature stop codon at position 90, the
other haplotype has several amino acid replacements that are thought to alter the inhibitory activity
of the protein. For the WFDC6-WFDC7-WFDC8 region, we identified a candidate variant in the 5’
region of WFDC8 gene (rs7273669G-A) that was predicted to abolish the binding of two
transcription factors specific of the male reproductive tract, where this gene is known to be
preferably expressed. This variant was then typed in all HapMap samples and confirmed to be in
strong linkage disequilibrium with all SNPs for which we had previously found signals of natural
selection. Finally, for SPINT4 we identified a haplotype with potential repercussion both in protein
conformation and in gene regulation.
In order to access the major driving forces of SERPINB11, WFDC6, WFDC7, WFDC8 and SPINT4 gene
evolution during primate differentiation we used collected sequence data from at least six primates
to perform ω (dn/ds) calculations under distinct selective and neutral models. In general, these
genes were found be under strong selective constrains. This analysis has allowed us to test whether
some positions, which are selectively constrained or neutral in most primates, are under positive
selection in humans. Moreover the results suggest that the SERPINB11 might have acquired a new
function in the human lineage.
2.2 Studies on the evolutionary history of genes involved in malaria resistance
In agreement with is PhD working plan, João Pedro begun to undertake an empirical
characterization of the geographic structure of high resolution haplotypes linked to the -α3.7 αthalassemia deletion at the α-globin locus (HBA) and the null allele at the Duffy blood group locus
(FY), in order to infer their history of selection and dispersal in Sub-Saharan Africa. Working in the
lab of Prof. Anna di Rienzo, at the University of Chigago, João Pedro used the iPLEX™ assay on a
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Sequenom MassArray System to genotype sets of 40 SNPs, each linked to the HBA and FY loci, to
define long-range high-density haplotypes in samples from 7 different regions of Africa,
encompassing all four major linguistic families that are found in the continent.
This work expands our previous collection of data on the intra-allelic variation linked to the S
mutation of the β-globin gene (HBB*S) in African populations, which is presently being analyzed
using computer simulations. This approach relies on a computer program specifically developed by
Jorge Rocha and Prof. António Múrias, from the Center for Biodiversity Research (CIBIO) in the
University of Porto, which is designed to simulate temporal-spatial patterns of haplotypes linked to
a favored mutation diffusing across different populations, under various demographic scenarios.
The computer application, completed during 2008, as the added advantage of performing Monte
Carlo simulations that allow the simultaneous estimation of the age and selection coefficient of
selected alleles (see below).
2.3. Studies on the evolutionary history of skin pigmentation genes
By building upon preliminary data from Isabel Alves and Claudia Martinho, we have concluded a
study of the evolutionary history of human skin pigmentation focused on the estimation of the ages
and selection coefficients of derived alleles (linked to lighter pigmentation) at the pigmentation
genes TYRP1, KITLG, SLC24A5 and SLC45A2. Using a Monte Carlo approach implemented on a
computer program developed by Jorge Rocha and António Múrias (see above), we found that while
the derived allele shared by Europeans and Asians at KITLG started to rise in frequency around
40,000 years, lineages associated with lighter skin only in Europeans have remarkably concordant
ages in all three TYRP1, KITLG, SLC24A5 genes, ranging from 12,000 to 19,000 years. These data
suggest that two major selective episodes might have shaped pigmentary traits in Europeans. One
occurring right after the Out-of-Africa migration (as documented by KITLG) and the other occurring
around the Last Glacial Maximum (as documented by SLC45A2, SLC24A5 and TYRP1).
This work is part of the on skin pigmentation and has been developed with the collaboration of
Prof. Dr. Esteban Parra and Prof. Dr. Mark Shriver.
2.4 Characterization of admixed populations to study the genetic basis of complex phenotypes
In 2008, Sandra led the second phase of sampling in Cape Verde related with two of the group
grants in which Sandra is PI (section 3.1). The field work took place between 31st of March and 5th of
June 2008. During this time Sandra and Joana Campos visited the six islands planned to be sampled:
São Vicente, Santo Antão, São Nicolau, Fogo, Boa Vista e Santiago. Within each island, except São
Vicente and Boa Vista, Sandra and Joana visited the urban and the rural areas.
Taking also into account the first phase of sampling undertook at the end of 2007, 1502 samples of
Cape Verdians and respective pigmentation phenotypes (skin, eye and hair colour) were collected.
From these, 61 samples belong to related individuals of others also collected, amounting to a total
of 1431 samples suitable for analysis of the genetic structure of the archipelago and its relationship
with pigmentation. For the study of the genetic architecture of hypertension and obesity, blood
pressure, body mass index and waist perimeter values were obtained for 1394, 1207 and 1261
unrelated individuals of the sample, respectively. Moreover, and under our collaboration with
Professor Mark Shriver from Penn State University, 479 3D photos of the face were also collected.
54
After Sandra and Joana’s arrival, data from the socio-demographic questionnaires that each
volunteer filled in were inserted into a database. We have now the complete register of each
individual personal data, socio-economical status, diet, physical activity, smoking and drinking habits
and if and when was the last time that the volunteer took pills for hypertension.
From this database, a preliminary sample of 823 individuals (374 women and 449 men) was selected
for the study of the genetic structure of the archipelago of Cape Verde. From these 670 samples
(∼110 per island) were sent for the U.S Company Prevention Genetics, to be genotyped for 52
ancestral informative markers. These typings will give us information on individual’s admixture
proportions and average admixture proportions of each island, which in turn will allow the study of
the dynamics of the admixture process between Europeans and Africans in the archipelago and to
investigate the role of biogeographical ancestry in explaining phenotypic variation in skin
pigmentation, obesity and hypertension related traits.
We have also selected a sub-sample of 700 unrelated individuals that are going to be analysed for
550,000 genome-spanning SNP markers. The sub-sample was selected in a way that reflects the age,
sex, place of origin and phenotype distributions of the original sample. This study is going to be
performed in collaboration with Greg Barsh’s lab at Stanford University and aims at extending the
scope of the admixture mapping study in Cape Verde from a candidate gene approach to a whole
genome approach.
Work plan for 2009
Our major priorities for future research are to proceed with our activities according to the 3 major
axes that have been defined in section 2.
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2f. TUMOR EVOLUTION AND DEVELOPMENT
Goup leader:
Luís Filipe Marques Ribeiro Teixeira da Costa
Keywords:
Cancer, Evolution, Development, Genetics, Biotechnology
Funding, source, dates (2003-2007)
POCTI/MGI/41854/2001, Fundação para a Ciência e a Tecnologia, 2002-2005
POCTI/CBO/48218/2002, Fundação para a Ciência e a Tecnologia, 2004-2007
POCTI/MGI/48201/2002, Fundação para a Ciência e a Tecnologia, 2004-2007
UCAGT, Fundação Calouste Gulbenkian, 2006-2009
Team Members- non-PhD
Ana Cristina Lima Moreira Correia Branco
Ângela Maria Sousa Costa
Diana Nora Vaz Saleiro
Isabel Pereira de Castro
Nuno Miguel Guimarães de Sá Camboa
Objectives
The group’s research interests are at the interface of Cancer, Developmental and Evolutionary
Biology. Simply put, one could say that what drives our research is the question of how a few
genetic alterations can, by altering developmental programs, make (part of) an organism evolve into
another so radically different: the cancer parasite.
A consequence of having this objective is that we do not focus on an organ or tissue-specific type of
tumor, but instead use different models to try to answer specific fundamental questions within that
broad goal. Furthermore, the choice of questions to be addressed is conditioned by restrictions
associated with starting up an independent group under our specific conditions. Three examples of
the type of question we have been addressing are:
- How is TCF4 activity regulated in the colon?
- How does p53 inactivation contribute to genetic instability in tumors?
- What is the mechanism of beta-catenin regulation by Wnt signaling?
Development:
There are two kinds of activities we have been pursuing that I usually describe as “Development”
rather than “Research”. One relates to providing services to the community, in particular to
patients. For example, we have now been involved, for a number of years, in trying to set up
conditions for the routine clinical use of mutation screening in the management of lung cancer
patients. Another one is the refining or development of techniques. This has been done for three
main reasons: the available techniques are too expensive or present limitations that make them
unpractical for our purposes; the pursuit of technical excellence and the constant search for better
or cheaper methods is central to the type of training I want my team members to have; the
development of new methods has the potential to give the group a degree of financial stability that
would be extremely important, particularly under the conditions we face in Portugal.
56
Main achievements
We have identified two new TCF4 partners by yeast two-hybrid: Grg5 and a novel protein (“P149”).
We mapped the “core” Grg5-binding region of TCF4 to a 69aa fragment and identified 4 residues
critical for the interaction. We confirmed the Grg5-TCF4 interaction and demonstrated that Grg5 can
repress TCF4-mediated transcription in mammalian cells.
The P149-TCF4 interaction was confirmed in mammalian cells by two- and one-hybrid, and
demonstrated to be phylogenetically conserved. Deletion analysis showed that TCF4’s Grg5 and
P149 binding domains are similar, but not identical. We have found that P149 can also bind members
of the Groucho family, both in yeast and mammalian cells. P149 lacks an NLS, but
immunolocalization in human cell lines showed it to be nuclear, and it can repress TCF4-mediated
transcription in co-transfection assays. Expression analysis in a panel of human cell lines and mouse
tissues has shown that P149 is ubiquitously expressed. Phylogenetical analysis of has allowed us to
identify two new conserved domains in P149, one of which our results suggest is required for the
protein’s nuclear localization.
We have identified several new splice forms of human Grg4, some of which interact with other Grgs,
but not with TCF4, suggesting they might inhibit TCF4/Grg-mediated repression.
We have performed a mutational analysis of the SIX4 putative CAN gene in a large panel of ductal
carcinomas of the breast. No mutations were found, suggesting that SIX4 is actually not a CAN
gene.
We have generated a variety of expression vectors and cell lines’ subclones expressing multiple
forms of beta-catenin that will be used in a detailed analysis of the mechanism of beta-catenin
regulation by Wnt signaling in the intestinal epithelium.
We have generated more than 100 transgenic (F0) zebrafish to be used in a variety of studies on the
mechanisms of genetic instability, carcinogenesis and their relationship in this model organism.
Development:
We have developed: a large family of high-efficiency T/A cloning vectors based on a toxic cassette; a
method to simultaneously sequence both DNA strands of a PCR product with a single primer;
improved transposon-based vectors for stable expression of transgenes in mammalian cells and
model organisms; a simple method for producing a Western-blot molecular weight marker “in
house”.
10 publications in peer-review journals
Luís Teixeira da Costa Modeling of Genetic Instability – Looking for “Newton’s Binomial” of Colon
Cancer Cancer Biol. Therapy, 1(6):693-695, 2002
Joana Espiga Macedo, Ângela M. S. Costa, Inês A.M. Barbosa, Sandra Rebelo, Conceição Souto de
Moura, Luís Teixeira da Costa e Vensceslau Hespanhol Alterações genéticas no cancro do pulmão:
avaliação das limitações ao seu uso na rotina clínica. Rev. Port. Pneumol., 13(1):9-34, 2007
Paulo Matos, Carla Oliveira, Sérgia Velho, Vânia Gonçalves, Luís Teixeira da Costa, Mary P Moyer,
Raquel Seruca, Peter Jordan B-RafV600E cooperates with alternative spliced Rac1b to sustain
colorectal cancer cell survival Gastroenterology, in press
International Research Projects:
Forrest Spencer, The Johns Hopkins University/Shannon Fisher, University of Pennsylvania: studies
on the mechanisms of genetic instability, carcinogenesis and their relationship, using zebrafish as a
model.
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Future Research Objectives
As stated above, our research is driven by the question of how a few genetic alterations can, by
altering developmental programs, make (part of) an organism evolve into another so radically
different: the cancer parasite. This is clearly a long-term goal, and therefore we will continue to
pursue it in the next few years.
Compared to the first years of the lab, there will be, in the near future, two main alterations (that
are already taking place). The first is methodological: thanks to several colaborations we will be able
to resort more and more to the use of animal models such as mice and zebrafish, as these represent
the most promising approach to replicating tumor development. The second relates to the
questions being addressed, with the understanding of the roles played by P149 and the Grgs in
intestinal development, homeostasis and tumorigenesis becoming major priorities.
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2g. GENETIC DIVERSITY
Group Leader: Luísa Pereira
Staff members:
Haidé Margarida da Costa Martins – initiating PhD, Faculty of Arts, University of Bristol/IPATIMUP
Joana Isabel Barbosa Pereira – initiating PhD, Faculty of Biological Sciences, University of
Leeds/IPATIMUP
Marta Daniela Araújo da Costa – Grant BI; initiating PhD, Faculty of Biological Sciences, University of
Leeds/IPATIMUP
Verónica Cristina Neves da Nova Fernandes – Grant BI (initiation to research); Master Degree
student in Biochemistry
Fernando Miguel Laranjeira Freitas – Master Degree student in Computer Sciences
Rui Oliveira – Trainee of Bioinformatics
Objectives/Goals of the research activity
The basic aim of the group is to establish a bridge between population genetics and clinical
genetics. This symbiosis is of major importance when analysing non recombining genetic markers,
such as mitochondrial DNA (mtDNA) and Y-chromosome. For these markers it is extremely difficult
to disentangle between neutral and pathologic diversities because of its transmission in block and
its haplotypic distribution in human populations (many rare haplotypes). We will pursuit in a
detailed characterisation of worldwide genetic diversity, for the uniparental markers, and in the
design of studies of complex phenotypes, namely fertility and longevity. New developments in
biostatistics and bioinformatics will be essential for an efficient evaluation of genetic diversity and
mutation models in neutral and pathological conditions, and we intend in the near future to
experimentally test the theoretical inferences being contributed by integrative computational
analyses.
Background and major achievements during 2008:
(a) formation of new staff; successful application to three PhD grants from the Portuguese
Foundation of Science (FCT) in the areas of biological sciences (two in collaboration with Martin
Richards from Faculty of Biological Sciences, University of Leeds) and archaeology (one in
collaboration with João Zilhão from Faculty of Arts, University of Bristol);
(b) funding till May 2010, from two projects granted by FCT;
(c) renovation and establishment of international and national collaborations (listed bellow),
achieving to create a multidisciplinary network;
(d) collection of population samples from North Africa (Morocco, Tunisia, Egypt and Libya), East
Africa (Sudan, Ethiopia and Somalia), Arabian Peninsula (Yemen, Oman, Saudi Arabia and United
Arab Emirates), sub-Saharan Africa (Mozambique and Sahel region) and Europe (across all Europe).
(e) lines of research initiated with the group in June 2006 are beginning to be published.
Work plan for 2009:
We continue to work and to improve on our main lines of research:
. Applications to population genetics:
MtDNA and Y-chromosome are very useful tools to address many questions of human evolution,
demography and history. It is essential to have questions and hypotheses,
archaeological/anthropological evidences, good population samples and adequate statistical
analyses. Our group has established a multidisciplinary network (geneticists, archaeologists,
59
anthropologists and statisticians), possesses good population samples and is addressing questions
that were not being addressed by other groups working in the same field, from IPATIMUP or other
Portuguese Institutions, being successful in achieving funding for its research. Some results are now
published (see list of publication). The questions that we are addressing are:
a) Improvement of the Out-of-Africa model, evaluating alternative migration routes, via Levant
or via the Horn of Africa.
b) Evaluation of the Neolithic genetic influence in the Great Mediterranean, with new data
from North Africa
c) Evaluation of the trans-Saharan caravan slave trade from East Africa (mainly Sudan) to West
Africa (namely to Morocco).
. Applications to clinical genetics:
a) Evaluation of longevity in humans of African origin
. We published data for mtDNA diversity in Tunisian centenarians
. After almost one year of evaluation by the Mozambican Ethics Committee, we
prepared a collection of biological, anthropological and sociological data in old
people from Mozambique and in other age classes for comparison purposes; this
collection occurred already in February 2009.
b) Evaluation of longevity in North Portuguese. We are collaborating in a multidisciplinary
project leaded by Professor Henrique Almeida from IBMC. They are collecting a big number
(around 200) of blood samples from nonagenarians and centenarians from North Portugal
and will evaluate indices of ROS production and OXPHOS activity. We are going to classify
these samples in mtDNA haplogroups and choose some for complete mtDNA sequencing.
As far as we know, this will be the first study evaluating the relationship between mtDNA
haplogroups and ROS/OXPHOS indices in centenarians.
. Bioinformatics
a) Evaluation of the relationship between mtDNA binding energy and mutability. The Group
leader visited David C. Samuels at Virginia Bioinformatics Institute in December 2008 and
drafted the manuscript related with this issue in human mtDNA. We enlarged this study for
all 250 known mammal mtDNAs, as there seemed to be a correlation between binding
energy and life span; this work demanded extensive computer power, and we are now (by
the end of March 2009) finishing the in silico estimations of mtDNA binding energies in
mammals.
b) We developed a computer tool for the identification and qualification of mtDNA mutations
in huge datasets, and tested its application to the complete human mtDNA sequences
available in GenBank by the end of August 2008 (5,140). This paper is now submitted for
publication. It was done in collaboration with David C. Samuels, Valdemar Máximo, Vincent
Macaulay and Ricardo Rocha.
c) With Ana Teresa Freitas we developed an algorithm for alignment of circular sequences; this
paper is under revision.
d) With Nuno A. Fonseca and Rui Camacho, we are applying machine learning and data mining
strategies to a huge database of autosomal STR profiles (~70,000) in order to evaluate if a
few STRs used commonly in forensic routine can give information about ethnic affiliation of
samples. This has only been tested in big SNPs datasets or in 350 STRs screened in few
individuals; we are testing it in few STRs (at most 17) in many individuals screened, which is a
more realistic situation in forensic routine.
Financing/projects:
4- 06/2007-05/2010: “Longevity in humans of African origins - a genetic approach”. FCT
(PTDC/AFR/71422/2006) PI: Luísa Pereira; Financing: 80,000 €
60
5- 06/2007-05/2010: “Refining the geographical origin and dispersal routes of early modern humans
and early farmers of the Greater Mediterranean with high-resolution genetic techniques”. FCT
(PTDC/ANT/66275/2006); PI: Luísa Pereira; Financing: 87,000 €
Theses:
- Master thesis in Biochemistry – Verónica Cristina Neves da Nova Fernandes: “Caracterização da
diversidade genética mitocondrial no Norte e Leste de África; achegas genéticas para as migrações
"Back-to-Africa"” (“Characterisation of the mitochondrial DNA diversity in North and East Africa:
genetic insights into “Back-to-Africa” migrations”). Universidade da Beira Interior. Viva: 14-07-2008.
Supervisor: Luísa Pereira.
- Master Degree in Computer Sciences - Fernando Miguel Laranjeira de Freitas: “Aplicações
bioinformáticas ao estudo de DNA mitocondrial” (“Bioinformatic applications to the study of
mitochondrial DNA”). Faculdade de Ciências da Universidade do Porto. Viva: 15-07-2008. Supervisor:
Luísa Pereira.
- co-supervision of PhD - Ana Goios: “Dynamics of the mitochondrial genome – the moving boundary
between normal and pathogenic diversity”; Faculty of Sciences, University of Porto, IPATIMUP and
Department of Statistics, University of Glasgow. Fundação para a Ciência e a Tecnologia
(SFRH/BD/16518/2004). Viva on February 2009.
Main international collaborations
Vincent Macaulay, Department of Statistics, University of Glasgow, UK
Martin Richards, Institute of Integrative & Comparative Biology, Faculty of Biological Sciences,
University of Leeds, UK
Doron Behar, Molecular Medicine Laboratory, Rambam Health Care Campus, Haifa, Israel
Farida Alshamali, Dubai Police General Headquarters
David C. Samuels, Previously at Virginia Bioinformatics Institute, Virginia and now at Vanderbilt
University, Nashville, Tennessee, USA
Mathias Currat and Estella Poloni, Départment d’anthropology et d’ecologie, Université de Geneve,
Switzerland
Viktor Cerny, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague
João Zilhão, Department of Archaeology and Anthropology, Faculty of Arts, University of Bristol, UK
Nourdin Harich and Mostafa Kandil, University of El Jadida, Morocco
Main national collaborations
João Gonçalves, Leader of the group “Pathology of the sexual development”, Centre of Human
Genetics, National Institute of Health, Lisbon
Henrique Almeida, Leader of the group “Stress in Animals”, IBMC
Ricardo Rocha, Departamento Ciências Computadores, Faculdade de Ciências da Universidade do
Porto
Ana Teresa Freitas, INESC-ID/KDBIO and Instituto Superior Técnico da Universidade de Lisboa
Nuno A. Fonseca, IBMC and Rui Camacho, Faculdade de Engenharia da Universidade do Porto
Main IPATIMUP collaborations
Valdemar Máximo, Group of “Cancer Biology”
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Publications in 2008
1. Pereira L, Gonçalves J, Bandelt H-J (2008) Mutation ‘C11994T’ in the mitochondrial ND4 gene is not
a cause of low sperm motility in Portugal. Fertil Steril. 89: 738-741. (IF=3.168; nº C=0)
2. Behar DM, Metspalu E, Kivisild T, Rosset S, Tzur S, Hadid Y, Yudkovsky G, Rosengarten D, Pereira
L, Amorim A, Kutuev I, Gurwitz D, Bonne-Tamir B, Villems R, Skorecki K (2008) Counting the
founders: the matrilineal genetic ancestry of the Jewish Diaspora. PLoS ONE. 3:e2062. (IF=-; nº
C=0)
3. Behar DM, Villems R, Soodyall H, Blue-Smith J, Pereira L, Metspalu E, Scozzari R, Makkan H, Tzur S,
Comas D, Bertranpetit J, Quintana-Murci L, Tyler-Smith C, Wells RS, Rosset S, & The Genographic
Consortium (2008) The dawn of human matrilineal diversity. Am. J. Hum. Genet. 82: 1130-1140.
(IF=11.092; nº C=9)
4. Cerny V, Mulligan CJ, Ridl J, Zaloudkova M, Edens CM, Hajek M, Pereira L (2008) Regional
differences in the distribution of the sub-Saharan, West Eurasian and South Asian mtDNA lineages
in Yemen. Am. J. Phys. Anthropol. 136: 128-137. (IF=2.273; nº C=0)
5. Goios A, Prieto L, Amorim A, Pereira L (2008) Specificity of mtDNA-directed PCR – influence of
NUMT contamination in routine samples and techniques. Int. J. Legal Med. 122: 341-345. (IF=3.030; nº
C=0)
6. Goios A, Gusmão L, Rocha AM, Fonseca A, Pereira L, Bogue M, Amorim A (2008) Identification of
mouse inbred strains through mitochondrial DNA single-nucleotide extension. Electrophoresis 29:
4795-4802. (IF=3.609; nº C=0)
7. Pereira F, Soares P, Carneiro J, Pereira L, Richards MB, Samuels DC, Amorim A (2008) Evidence for
variable selective pressures at a large secondary structure of the human mitochondrial DNA
control region. Mol Biol Evol. 25: 2759-2770. (IF=6.438; nº C=0)
2009 and in press
8. Freitas F, Oliveira S, Rocha R, Pereira L (2009) mtDNA GeneExtractor: a computer tool for mtDNA
gene/region information extraction. Mitochondrion 9: 36-40. (IF=3.209; nº C=0)
9. Costa MD, Fernandes V, Freitas F, Cherni L, El Gaaied ABA, Pereira L (2009) Data from complete
mtDNA sequencing of Tunisian centenarians: testing haplogroup association and the "golden
mean" to longevity. Mech Ageing Dev. 130: 222-226. (IF=4.308; nº C=0)
10. Cerny V, Pereira L, Kujanová M, Hájek M, Vasikova A, Morris M, Mulligan C (2009) Out of Arabia –
the settlement of island Soqotra as revealed by mitochondrial and Y chromosome genetic
diversity. Am. J. Phys. Anthropol. 138: 439-447. (IF=2.273; nº C= 0)
11. Cherni L, Fernandes V, Pereira JB, Costa MD, Goios A, Frigi S, Yacoubi-Loueslati B, Amor MB,
Slama A, Amorim A, El Gaaied ABA, Pereira L (2009) Post-Last Glacial Maximum expansion from
Iberia to North Africa revealed by fine characterisation of mtDNA H haplogroup in Tunisia. Am. J.
Phys. Anthropol. (in press) (IF=2.273; nº C=0)
12. Alshamali F, Pereira L, Budowle B, Poloni ES, Currat M (2009) Local Population structure in
Arabian Peninsula revealed by Y-STR diversity. Hum Hered. (in press) (IF=2.155; nº C=0)
13. Kujanová M, Pereira L, Fernandes V, Pereira JB, Cerny V (2009) Predominant Neolithic
contribution to the population history of the Egyptian Western Desert; mtDNA and Y-chromosome
analyses from the oasis of el-Hayez. Ann. Hum. Genet. (in press) (IF=2.307; nº C=0)
14. Cerny V, Fernandes V, Costa MD, Hájek M, Mulligan CJ, Pereira L (2009) Migration of Chadic
speaking pastoralists within Africa based on population structure of Chad Basin and
phylogeography of L3f haplogroup. BMC Evol. Biol. (in press) (IF=4.091; nº C=0)
Publications in Congress Series 2008:
1. Afonso C, Alshamali F, Pereira JB, Fernandes V, Costa M, Pereira L (2008) mtDNA diversity in
Sudan (East Africa). Forensic Sci. Int.: Genetics Supplement Series 1:257-258. 22nd Congress of the
International Society for Forensic Genetics. Copenhagen, Denmark. 22-25/07.
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2. Freitas F, Pereira L (2008) Heterogeneity in coding mtDNA mutation rates: implications in forensic
genetics. Forensic Sci. Int.: Genetics Supplement Series 1:274-276. 22 nd Congress of the
International Society for Forensic Genetics. Copenhagen, Denmark. 22-25/07.
3. Pamplona JP, Freitas F, Pereira L (2008) A worldwide database of autosomal markers used by the
forensic community. Forensic Sci. Int.: Genetics Supplement Series 1:656-657. 22 nd Congress of the
International Society for Forensic Genetics. Copenhagen, Denmark. 22-25/07.
4. Goios A, Gusmão L, Rocha M, Pereira L, Bogue M, Amorim A (2008) A SNaPshot multiplex kit for
mtDNA identification of mouse inbred strains. Forensic Sci. Int.: Genetics Supplement Series 1:596597. 22 nd Congress of the International Society for Forensic Genetics. Copenhagen, Denmark. 2225/07.
63
2h. PUBLIC HEALTH AND CANCER
(Department of Hygiene and Epidemiology, Porto University Medical School – IPATIMUP)
Início da colaboração: 2006
Constituição actual do grupo:
Nuno Lunet, PhD
Bárbara Peleteiro (bolseira de Doutoramento FCT)
Joana Bastos (bolseira de Doutoramento FCT)
Marta Pereira (bolseira de Doutoramento FCT)
Marlene Pinto
Publicações por extenso em revistas internacionais, desde 2003 (as publicações
sublinhadas incluem o IPATIMUP na lista de afiliações):
1. Lunet N, Rodrigues T, Barros H. Pregnancy planning and vitamin/mineral use during pregnancy:
results from a study in Portugal [letter]. Prev Med 2003;37:71.
2. Lunet N, Barros H. Use of water by breastfed children in Maputo, Mozambique [letter]. J Trop
Pediatrics 2003;49:193.
3. Barros H, Lunet N. Association between child-care and acute diarrhea: a study in Portuguese
children. Rev Saude Publica 2003;37:603-8.
4. Falcão H; Lunet N, Gomes E, Cunha L, Barros H. Drug allergy in university students from
Porto, Portugal. Allergy 2003;58:1210.
5. Lunet N, Barros H. Helicobacter pylori infection and gastric cancer: facing the enigmas. Int J
Cancer 2003;106:953-60.
6. Lunet N, Barros H. Helicobacter pylori infection and gastric cancer: facing the enigmas (part II).
[letter]. Int J Cancer 2004;112:168-9.
9. Serpa J, Lunet N, Mendes N, Barros H, David L. Lewis and Secretor status and Helicobacter pylori
eradication [letter]. Epidemiol Infect 2004;132:997-8.
10. Lunet N, Barros H. Does vitamin C dietary intake modify the association between Helicobacter.
pylori infection and gastric cancer [letter]? Eur J Epidemiol 2004;19:1061-2.
11. Lunet N, Pina F, Barros H. Regional trends in Portuguese gastric cancer mortality (19841999). Eur J Cancer Prev 2004;13:271-6.
12. Lunet N, Carvalho R, Barros H. An appraisal of gastric cancer research in cancer journals. Gastric
Cancer 2004;7:172-5.
13. Falcão H, Lunet N, Lopes C, Barros H. Food hypersensitivity in Portuguese adults. Eur J Clin Nutr
2004;58:1621-5.
14. Xavier P, Beires J, Belo L, Rebelo I, Martinez-de-Oliveira J, Lunet N, Barros H. Are we employing
the most effective CA 125 and CA 19-9 cut-off values to detect endometriosis [letter]? Eur J Obstet
Gynecol Reprod Biol 2005;123(2);254-5.
15. Lunet N, Falcão H, Sousa M, Bay N, Barros H. Self-reported food and drug allergy in Maputo,
Mozambique. Public Health 2005;119:587-9.
16. Lunet N, Lacerda-Vieira A, Barros H. Fruit and vegetables consumption and gastric cancer: a
systematic review and meta-analysis of cohort studies. Nutr Cancer 2005;53(1):1-10.
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17. Lunet N, Williams L, Govind M, Silinto A, Zucua I, Damasceno A, Barros H. Tobacco advertising in
Maputo, Mozambique: how will they keep pressing [letter]? Gac Sanit 2006;20(3):251-2.
18. Xavier P, Beires J, Belo L, Rebelo I, Martinez-de-Oliveira J, Lunet N, Barros H Serum levels of VEGF
and TNF-α and their association with C-reactive protein in patients with endometriosis. Arch Gynecol
Obstet 2006;273(4):227-31.
19. Botelho F, Lunet N, Barros H. Coffee and gastric cancer: systematic review and metaanalysis. Cad
Saude Publica 2006;22(5):889-900.
20. Mesquita P, Almeida R, Lunet N, Reis CA, Santos Silva LF, Serpa J, van Seuningen I, Barros H,
David L. Metaplasia - a transdifferentiation process that facilitates câncer development. The model
of gastric intestinal metaplasia. Crit Rev Oncog 2006;12(1-2):3- 26.
21. Lunet N, Valbuena C, Carneiro F, Lopes C, Barros H. Antioxidant vitamins and risk of gastric
cancer: a case-control study in Portugal. Nutr Cancer 2006;55(1):71-7.
22. Rocha O, Lunet N, Costa L, Barros H. [Osteoporosis treatment in Portugal: trends and
geographical variation]. Acta Med Port 2006;19(5):373-80.
23. Peleteiro B, Lunet N, Figueiredo C, Carneiro F, David L, Barros H. Smoking, Helicobacter
pylori virulence, and type of intestinal metaplasia in Portuguese males. Cancer Epidemiol Biomarkers
Prev 2007;16:322-6.
24. Peleteiro B. Lunet N, Santos Silva F, David L, Figueiredo C, Barros H. Short mucin 1 alleles are
associated with infection with (low virulent) Helicobacter pylori strains [letter]. World J
Gastroenterol 2007;13(12):1884-5.
25. Lunet N, Valbuena C, Lacerda-Vieira A, Lopes C, Lopes C, David L, Carneiro F, Barros H. Fruit and
vegetables consumption and gastric cancer by location and histological type: case-control and metaanalysis. Eur J Cancer Prev 2007;16(4):312-327.
26. Bastos J, Barros H, Lunet N. [Breast cancer mortality trend in Portugal (1955-2002)]. Acta Med
Port 2007;20:139-44.
27. Padrão P, Lunet N, Santos AC, Barros H. Smoking, alcohol and dietary choices: evidences from
the Portuguese national health survey. BMC Public Health 2007;7:138.
28. Pinto M, Lunet N, Williams L, Barros H. Food and beverages billboard advertising is frequent in
Maputo, Mozambique [letter]. Food Nutr Bull 2007;28(3):365-6.
29. Lucas R, Lunet N, Carvalho R, Langa J, Muanantatha M, Nkunda LP, Barros H. Pattern of
medication use by students in a University from Maputo, Mozambique. Cad Saude Publica
2007;23(12):2845-52.
30. Lunet N, Bastos J, Cumaio F, Silva P, Dias E, Barros H. Recall of drug utilization depends on subtle
structural questionnaire characteristics. Pharm World Sci 2008:30(2):175-81.
31. Canedo P, Castanheira-Vale AJ, Lunet N, Pereira F, Figueiredo C, Gioia-Patricola L, Canzian F,
Moreira H, Suriano G, Barros H, Carneiro F, Seruca R, Machado JC. The interleukin-8-251*T/*A
polymorphism is not associated with risk for gastric carcinoma development in a Portuguese
population. Eur J Cancer Prev 2008;17(1):28-32.
32. Gomes A, Lunet N, Santos AC, Barros H. Social, demographic, clinic and lifestyle determinants of
dental care visits in an urban sample of Portuguese adults. Oral Health Prev Dent 2008;6:3-11.
30. Lunet N, Rodrigues T, Correia S, Barros H. Folic acid, iron and vitamins during pregnancy: a study
in Portuguese women. Cad Saude Publica 2008;24(5):1151-7.
33. Falcão H, Lunet N, Neves E, Iglésias I, Barros H. Anisakis simplex as a risk factor for relapsing
acute urticaria: a case-control study. J Epidemiol Community Health 2008;62(7):634-7.
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34. Peleteiro B, Bastos J, Barros H, Lunet N. Systematic review of gastric intestinal metaplasia
prevalence and its area level association with smoking. Gac Sanit 2008;22(3):236-47.
35. Ladeiras-Lopes R, Pereira AK, Nogueira A, Pinheiro-Torres T, Pinto I, Santos-Pereira R,
Lunet N. Smoking and gastric cancer: a systematic review and meta-analysis of cohort studies.
Cancer Causes Control 2008;19(7):689-701
36. Canedo P, Corso G, Pereira F, Lunet N, Suriano G, Figueiredo C, Pedrazzani C, Moreira H, Barros
H, Carneiro F, Seruca R, Roviello F, Machado JC. The interferon gamma receptor 1 (IFNGR1) -56C/T
gene polymorphism is associated with increased risk of early gastric
carcinoma. Gut 2008;57(11):1504-8.
37. Canedo P, Durães C, Pereira F, Regalo G, Lunet N, Barros H, Carneiro F, Seruca R,
Rocha J, Machado JC. Tumour necrosis factor extended haplotypes and risk of gastric
carcinoma. Cancer Epidemiol Biomarkers Prev 2008;454(2):153-60.
38. Lucas R, Rocha O, Bastos J, Costa L, Barros H, Lunet N. Pharmacological management of
osteoporosis in a Portuguese urban population: the EpiPorto study (2005-2007). Clin Exp Rheumatol
2008 [in press]
39. Gama H, Ismael A, Sitoi F, Matola A, Barros H, Lunet N. Factors associated with chloroquine
induced pruritus during malaria treatment in Mozambican University students. Gac Sanit 2008 [in
press]
40. Gama H, Correia S, Lunet N. Questionnaire design and the recall of pharmacological treatments:
a systematic review. Pharmacoepidemiol Drug Saf 2008 [in press]
41. Carrilho C, Modcoicar P, Cunha L, Ismail M, Guisseve A, Lorenzoni C, Fernandes F, Peleteiro B,
Almeida R, Figueiredo C, David L, Lunet N. Prevalence of Helicobacter pylori infection, chronic
gastritis, and intestinal metaplasia in Mozambican dyspeptic patients. Virchows Arch 2008 [in press]
Livros/capítulos de livros
1. Lunet N, Peleteiro B, Bastos J, Barros H. Life course approaches to gastric cancer etiology:
current knowledge, potentials and promise. In: Tompkins MB, editor. Gastric Cancer Research Trends.
New York: Nova Publishers; 2007. p. 129-146.
2. Peleteiro B, Lunet N. Gastric cancer etiology: contribution from molecular epidemiology. In:
Degiuli M, editor. Management of gastric cancer: recent advances. Turin: Edizioni Minerva Medica,
2008. pp. 23-33.
3. Miranda A, Mayer Pereira A, Mesquita C, Bastos J, Ribeiro M, Lunet N. Os 10 tumores mais
frequentes na população portuguesa adulta na região sul de Portugal, no período 2000|2001.
Registo Oncológico Regional Sul (ROR-Sul), 2007. [in press]
4. Peleteiro B, Lunet N. Gastric Cancer Etiology: Contribution from Molecular Epidemiology. In: Degiuli
M, editor. Management of Gastric Cancer: Recent Advances. Turin: Edizioni Minerva Medica; 2008.
pp. 23-33.
Teses de mestrado
1. Peleteiro B. Risk factors for gastric intestinal metaplasia. MSc Thesis. University of Porto,
2007.
2. Bastos J. [Survival analysis. Application to patients with skin malignant melanoma.]. MSc
Thesis. University of Lisbon, 2007.
Projectos de investigação em colaboração com outros grupos do IPATIMUP:
66
1. Exposições ambientais e expressão do gene CDX2 em casos de cancro gástrico Helicobacter pyloripositivo (POCTI/SAU-ESP/61685/2004).
2. Genetic and non-genetic factors contributing for phenylketonuria phenotype diversity: a study
based on the Portuguese Neonatal Screening Program (PTDC/SAU-ESA/72663/2006).
3. Estudo de factores biológicos e de estilos de vida que contribuam para compreender as
diferenças na incidência de carcinoma gástrico em dois países com elevadas prevalência de infecção
por Helicobacter pylori: Moçambique e Portugal. Lesões da mucosa gástrica em Moçambique e
Portugal: o enigma Africano (projecto n.º FC-68697 de 2004).
4. Avaliação do risco do consumo de sal e da infecção por Helicobacter pylori no desenvolvimento de
carcinoma gástrico e das suas lesões precursoras em Portugal (Agência
Portuguesa de Segurança Alimentar).
Outras actividades:
1. Organização do Porto Cancer Meeting em 2007
2. Consultorias diversas
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2i. TUMOUR MOLECULAR MODELS
Group Leader: Filipe Santos Silva
Staff members during 2008:
Natália Costa – PhD Student (grant SFRH/BD/36961/2007) “Identification of signaling pathways
mediated by MUC1 mucin and its relevance in gastric carcinogenesis”, Faculty of Medicine,
University of Porto.
Margarida Reis – Grant BI (initiation to research) in the project “Identification of signaling pathways
mediated by MUC1 oncogene in gastric carcinoma cell lines and immortalized gastric normal cells” PTDC/SAU-OBD/65616/2006.
Andreia Sousa - Master degree student in Biology, Faculty of Sciences, University of Porto.
Rita Freitas – BSc Biology, Faculty of Sciences, University of Porto.
Pedro Salgueiro - Master degree student in Biochemistry, ICBAS – Instituto de Ciências Biomédicas
Abel Salazar, University of Porto.
Objectives/Goals of the research activity
The major research interest of the group is to decode the molecular models beneath the initiation
and progression of epithelial tumors with a specific emphasis on the study of cancer stem cells.
Cancer stem cells may generate different tumor cell lineages being responsible for critical functions
in tumor progression and disease relapse. To understand the molecular biology of these cancer
stem cells and their potential to be used as elective targets for therapeutic strategies constitutes
our major objectives.
The MUC1 glycoprotein is our primary target due to the frequent alterations of the molecule
(expression levels and/or glycosylation) observed in several tumour types, and to the large
multitude of functions and partners recently described. Considering the over-expression of MUC1 in
pancreatic cancer cells and the involvement of MUC1 in signaling cascades and differentiation
processes, our central hypothesis is that MUC1 oncoprotein is a key player in pancreatic cancer stem
cells biology. We think that MUC1 expression levels, alternative splicing variation and posttranslational modifications (glycosylation, sialylation and phosphorylation) in pancreatic cancer
stem cells conditions either intracellular signaling as well as the cross talk between cells (stem cells
niche effect) and consequently the differentiation and cell survival processes. Using MUC1 as a
paradigm, the research plan strategically encompasses biochemistry, molecular and cell biology
approaches, aiming to advance comprehensive models of MUC1 biology in pancreatic cancer stem
cells. The research might contribute to the development of MUC1 based therapies that effectively
overcome pancreatic cancer resilience to current available treatments and will further advance the
knowledge of pancreatic cancer stem cells model.
Background and major achievements during 2008:
The main achievements obtained were:
(a) formation of new staff: in this initial phase of consolidation of the group we invested mainly in
the formation of master degree students integrated in one year projects, their performance will
determine a potential evolution to PhD programs.
68
(b) funding: we were successful in getting funding for one project - “ Identification of signaling
pathways mediated by MUC1 oncogene in gastric carcinoma and immortalized gastric cells”. Ref#
PTDC/SAU-OBD/65616/2006. Sponsored by FCT. October 2008- October 2011. 139.760 euros. (100%
successful rate);
(c) recruiting new staff: Margarida Rei was selected to a project grant, and Andreia Sousa (master
degree student) and Rita Freitas also join the group. Furthermore, under the governmental initiative
Ciência 2008 supported by the Foundation for Science and Technology (FCT), we open a position for
a doctorate researcher. The selected candidate is Luisa Helguero from Karolinska Institute;
(d) renovation and establishment of international and national collaborations (listed bellow),
achieving to create a multidisciplinary network;
Publications in 2008 reflect mainly previous research, namely in the field of mucins and gastric
cancer, but a better image of the group’s lines of research can be retrieved from the work plan for
2009, already initiated with new collaborators and new staff, and included in the new research
projects submitted for funding.
Work plan for 2009:
During 2009 the group will be conducting the following lines of research:
1-
We will continue to identify the signaling pathways mediated by MUC1 mucin and its
relevance in carcinogenesis. Namely the characterization of MUC1 mucin mediated signaling
pathways in “normal” gastric and pancreatic cells and in gastric and pancreatic carcinoma
cell lines. We aim to characterize MUC1 phosphorylation status and identify interaction
partners in immortalized gastric and pancreatic cells, in order to reveal the involvement of
MUC1 in the signaling network of “normal” gastric and pancreatic epithelial cells. We will
also characterize MUC1 phosphorylation status and identify interaction partners in order to
reveal the involvement of MUC1 in the signaling network of gastric and pancreatic
carcinoma cells. Evaluations of the results obtained in immortalized cells and in carcinoma
cells, will show the relevance of MUC1 mediated signaling to gastric and pancreatic
carcinogenesis.
2- We will initiate the study of MUC1 protein relevance for tumorigenic potential of cancer
stem cells. Namely we will isolate and purify cancer stem cells (CSCs) populations. In
collaboration with Prof. Angie Rizzino group at UNMC we will develop strategies to grow
the isolated CSCc populations, namely using bioreactors and inhibitory media that will
condition the differentiation of CSCs.This model will be used to characterize the MUC1
expression and MUC1-mediated oncogenic signalling in pancreatic cancer stem cells
population. The isolated population of pancreatic cancer stem cells will permit the
evaluation of the impact of MUC1 expression modulation (transfections and siRNA assays) in
the tumorigenic potential of CSCs.
3- We will improve the on going collaboration with IPATIMUP’s group “Cancer Biology”,
namely with Helena Vasconcelos e Gabriela Almeida, addressing the problem of pancreatic
cancer stem cells chemoresistance and developing new approaches (nanoparticles loaded
69
with siRNAs) that can specifically target in these cells the relevant mechanisms involved in
drug resistance.
Financing/projects:
Project - “ Identification of signaling pathways mediated by MUC1 oncogene in gastric carcinoma
and immortalized gastric cells”. Ref# PTDC/SAU-OBD/65616/2006. Sponsored by FCT. October
2008- October 2011. 139.760 euros.
Project - “Clarification of the relevance of MUC1 mucin polymorphism in Helicobacter pylori
infection”. Ref# POCI/SAU-IMI/56895/2004. Sponsored by FCT. October 2005 - October 2008.
100.000 euros.
Project – “MUC1 mucin polymorphism – a new susceptibility and prognostic marker in lung
carcinogenesis “. Ref# PIC/IC/83153/2007. Sponsored by FCT. 86.120 euros. Pending re-evaluation.
Project – “MUC1 protein – a new approach to target oncogenic signaling in pancreatic cancer stem
cells”. Ref# PTDC/SAU-OBD/101331/2008. Sponsored by FCT. 196.824 euros. Pending evaluation.
Theses – ongoing:
Supervision of PhD – Natália Costa: “Identification of signaling pathways mediated by MUC1 mucin
and its relevance in gastric carcinogenesis”, Faculty of Medicine, University of Porto.. Since October
2007.
Supervision of Masters - Andreia Sousa: “Characterization of pancreatic cancer stem cells
mechanisms involved in drug resistance”. Faculty of Sciences, University of Porto. Since December
2008.
Main international collaborations
The group has the following international collaborations:
Michael Anthony Hollingsworth - Eppley Cancer Institute. University of Nebraska Medical Centre.
Omaha. Nebraska. USA.
Michele Ouellette - Department of Biochemistry and Molecular Biology. University of Nebraska
Medical Centre. Omaha. Nebraska. USA.
Angie Rizzino - Department of Biology and Microbiology. University of Nebraska Medical Centre.
Omaha. Nebraska. USA.
Hideaki Tsutsumida - Department of Human Pathology, Field of Oncology, Kagoshima University
Graduate School of Medical and Dental Sciences. Sakuragaoka. Kagoshima. Japan.
Sara Linden - Mucosal Immunology and Vaccine Center. Sahlgrenska Academy
Gothenburg University. Gothenburg. Sweden.
Main national collaborations
The group has the following national collaborations:
Alexandre do Carmo, leader of the group “Cell activation and Gene expression”, IBMC.
Anabela Cordeiro, leader of the group “Parasite Disease”, IBMC.
Paula Alves, leader of the group “Animal Cell Technology, ITQB.
70
Main IPATIMUP collaborations
Helena Vasconcelos e Gabriela Almeida, Group of “Cancer Biology”.
Publications in 2008
- Barros R, Pereira B, Duluc I, Azevedo M, Mendes N, Camilo V, Jacobs R, Paulo P, Santos-Silva F, van
Seuningen I, van den Brink G, David L, Freund JN, Almeida R (2008). Key elements of the BMP/SMAD
pathway co-localized with CDX2 in intestinal metaplasia and regulated CDX2 expression in human
gastric cell lines. J Pathol. 215(4):411-20.
- Marcos NT, Magalhães A, Ferreira B, Oliveira MJ, Carvalho AS, Mendes N, Gilmartin T, Head SR,
Figueiredo C, David L, Santos-Silva F, Reis CA (2008). Helicobacter pylori induces beta3GnT5 in
human gastric cell lines, modulating the expression of the SabA ligand sialyl-Lewis x. J Clin Invest.
118 (6): 2325-36.
- Costa N, Mendes N, Marcos NT, Reis CA, Caffrey T, Hollingsworth MA, Santos-Silva F (2008).
Relevance of MUC1 mucin variable number of tandem repeats polymorphism in Helicobacter pylori
adhesion to gastric epithelial cells. World J Gastroenterol. 14 (9): 1411-4.
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3. RELATÓRIO DE ACTIVIDADES DA UNIDADE DE EDUCAÇÃO CONTÍNUA E
DIFUSÃO CIENTÍFICA
A UNIDADE DE EDUCAÇÃO CONTÍNUA E DIFUSÃO CIENTÍFICA do IPATIMUP (UECDC-IPATIMUP)
desenvolveu durante o ano de 2008 um conjunto de iniciativas em diversos domínios da promoção
do pensamento e cultura científica:
A- Projectos
1. Laboratório Aberto
O projecto “Laboratório Aberto”, financiado pela Agência Ciência Viva, encerrou no ano de 2008. Ao
longo do ano contou com 3530 alunos que desenvolveram as activadas previamente seleccionadas.
No sentido de dar continuidade ao projecto, iniciou-se as conversações com a Câmara Municipal do
Porto de modo a assegurarem o financiamento do laboratório Aberto, estando neste momento o
protocolo para assinar na Câmara Municipal do Porto. Desta forma, os primeiros meses de 2009 já
contam com mais de 1600 visitas.
2. “Autolaboratório”
A UECDC do IPATIMUP encerrou a execução do projecto “AUTOLABORÁTORIO” (ref# CV / 138 /
2005) financiado pela Ciência Viva. Foram efectuadas 137 sessões em 29 escolas, que abrangeram
uma população de 2786 alunos. Foi concluída a instalação do website do projecto
(www.autolaboratório.com).
3. “A Magia da Ciência”
A UECDC-IPATIMUP encerrou a execução do projecto “A magia da Ciência – POCTI/DIV/2005/00061”
financiado pela FCT – Programa POCTI do III Quadro comunitário de apoio - Medida 3.1. - “Atribuição
de Financiamento para projectos de divulgação da cultura científica e tecnológica”. Foi finalizado o
desenvolvimento de : a) Software Educativo sobre Biologia Celular em que se proporciona a
abordagem ao estudo das células através do recurso a um microscópio virtual (MICE), b) Software
educativo sobre Biotecnologia em que se possibilita num laboratório virtual, a manipulação e a
investigação virtual de técnicas da Biologia Molecular, nomeadamente: electroforese, PCR,
southern blotting, análise de mapas de restrição, chips de DNA, c) um conjunto de DVDs sobre
seminários focados na temática da investigação do cancro na sua vertente de biologia celular e
molecular.
4. “Despertar para a Ciência”
A UECDC-IPATIMUP encerrou a execução do projecto “Despertar para a Ciência – CV/PVI/272”.
Foram desenvolvidos vários materiais pedagógicos com destaque para um conjunto protocolos
experimentais com particular ênfase para os alunos do primeiro ciclo. Foram visitadas 10 escolas do
1º ciclo, e 3 escolas nos restantes níveis de ensino, com um total de 116 sessões em que participaram
1687 alunos.
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A UECDC-IPATIMUP iniciou o protocolo de colaboração com a C.M. Trofa possibilitando a
continuidade do projecto “Despertar para a Ciência”. Foi desenvolvida toda a imagem do projecto
com criação do logótipo “EUREKA” para as sessões experimentais. Na Semana da Educação
promovida pelo Pelouro da Educação da Câmara da Trofa foi efectuada uma divulgação alargada do
projecto às várias escolas do concelho com a demonstração in loco de algumas das actividades
integrantes das sessões experimentais (20 sessões envolvendo 430 alunos).
Foi realizado um Curso de Formação (acreditado pelo CCPFC) sobre Ensino Experimental da Ciência,
com a participação de 15 Professores do 1º ciclo do ensino básico do agrupamento vertical da Trofa.
5. Projecto “EEA – Grants”
No âmbito da actividade “CancerMOBILE”, a UECDC-IPATIMUP desenvolveu competências técnicas
e desenvolveu vários conteúdos multimédia e experimentais a serem integrados nas sessões
públicas que iniciarão em 2009. Foi desenvolvido um conjunto de materiais sobre prevenção de
cancro, que engloba vários modelos virtuais ilustrativos:
1- Modelo virtual animado, desenvolvido com o software ADOBE FLASH para ilustração dos
conceitos sobre cancro familiar e esporádico.
2- Modelo virtual animado, desenvolvido com o software ADOBE FLASH para ilustração de
aparecimento do melanoma, do aparecimento do carcinoma baso-celular e das alterações a
nível de sinais da pele (regra ABCD) que podem estar associadas a um risco potencial de
aparecimento de cancro de pele.
3- Modelo virtual 3D animado, desenvolvido com o software MAYA para ilustração do processo
de invasão das células tumorais num vaso sanguíneo.
B- Programas
1. Rede de Residências: Experimentação Arte | Ciência e Tecnologia
No dia 3 de Março, na FNAC do Porto, a UECDC-IPATIMUP participou na apresentação dos
resultados do projecto “What we are and Who we are”da artista Sónia Moreira, desenvolvidos no
âmbito do programa “Rede de Residências: Experimentação Arte | Ciência e Tecnologia” promovido
pela Direcção Geral das Artes / Ministério da Cultura e a Ciência Viva.
2. Programa “Porto de Crianças”
Assinatura e arranque do protocolo com o Pelouro da Educação da Câmara Municipal do Porto Programa “Porto de Crianças” – proporcionou o ensino experimental das ciências experimentais na
sala de aula de cinco escolas do primeiro ciclo, perfazendo cerca de 90 alunos do grande Porto.
3. Programa “Ciência Viva em Férias”
O Programa “Ciência Viva em Férias” facultou a 30 alunos (26 portugueses e4 espanhóis) um
estágio de duas semanas, que decorreu entre os meses de Junho a Setembro, 2007, integrado no
“Ciência Viva”.
4. Segunda há Ciência.
O programa de visitas de escolas ao IPATIMUP, proporcionou a 40 alunos do Norte e centro do País
o contacto directo com os Investigadores do IPATIMUP.
73
C- Conferências, Colóquios e Seminários
1. Colóquios sobre – Medicina e cancro
2. XI Conferencia do Equinócio que decorreu a 20 de Outubro
3. Palestras
A UECDC-IPATIMUP promoveu durante o ano de 2008, a realização de palestras sobre temas como
a Biologia, a Genética, o Cancro, em várias escolas secundárias (Esc. Sec. Sra. Hora – Novembro
2008; Colégio Casa Mãe Baltar; E. S. Cinfães; E. S. Gondomar ).
D- Actividades de Divulgação Científica
1. Escola das Ciências da Vida e da Saúde – Universidade Júnior
Nas férias do Verão, o IPATIMUP proporcionou a 6 alunos uma semana de estágio.
2. Dia do IPATIMUP
No dia da comemoração do aniversário do IPATIMUP, tivemos a visita de três escolas resultando em
64 alunos que puderam visitar o IPATIMUP.
3. Traz um amigo também
Nesta semana, o IPATIMUP está de portas abertas, recebendo os alunos que fizeram o Ciência Vive
em Férias
4. Participação no dia da Universidade
No dia da Universidade 10 a 13 de Abril, o IPATIMUP participou na Mostra da Universidade do Porto.
5 - Noite dos Investigadores
A 17 de Outubro o IPATIMUP participou com um conjunto de actividades na noite dos
investigadores.
74
4. SERVIÇO Á COMUNIDADE
4a. UNIDADE DE PRESTAÇÃO DE SERVIÇOS (UPS)
Introdução
O principal objectivo da Unidade de Prestação de Serviços (UPS) em 2008 foi o de obter a
certificação do Laboratório através da Norma ISO 9001 bem como manter o Sistema de Gestão de
Qualidade definido desde 2003, de acordo com as normas propostas pelo CAP e manter esta
Acreditação após a segunda inspecção efectuada pelos inspectores da CAP “in loco” em Março de
2007. No princípio de 2009 irá ocorrer a terceira inspecção. O número total de exames da Unidade
foi de 14099. Como vem sucedendo há vários anos, continuámos a actuar como um centro de
formação profissional pós-graduado, tendo recebido, em 2008, 4 patologistas e 9 técnicos. Sete
destes técnicos estagiaram por um período de 10 semanas cada um, no âmbito do protocolo
estabelecido com a CESPU e ESTES-P.
1.
Recrutamento de pessoal:
•
Foi contratado pelo período de 9 meses, para auxiliar a ADF no período de licença de
maternidade de Susana Silva, o administrativo Marco César.
2. Aquisição de Equipamento e Testes de Proficiência:
Com a finalidade de equipar o laboratório de rotina diagnostica, no âmbito do Programa de
Acreditação da Unidade via CAP, foram adquiridos os seguintes equipamentos e testes de
proficiência.
Fotocopiadora Canon iR1022
Disco externo
Balança analítica Sartorius
Arquivo de lâminas e blocos para autópsias
Testes de Proficiência do Colégio Americano de
Patologistas
Testes de Proficiência da Sociedade Brasileira de
Patologia-PICQ
Testes de Proficiência do UK-NEQAS
Serviços de consultadoria para implementação de
SGQ ISO 9001:2000
Certificação SGS
75
3. Estágios de internos e técnicos:
Estágios
Nome
Bela Maria Maia Guerra, Técnica de
Anatomia
Patológica,
Centro
Hospitalar do Alto Minho, Minho,
Portugal
Ana Conceição Saraiva e Sousa
Tavares, Citotécnica, Hicislab, Porto,
Portugal
Ana Carolina Rodrigues, Interna de
Patologia da Faculdade de Medicina de
Botucatu, São Paulo, Brasil
Fernanda Figueiroa, Interna de
Patologia da Faculdade de Medicina
Veterinária UNESP,
Danielle Chacon, Interna de Patologia,
Hospital Heliópolis, São Paulo, Brasil
Gisele Alborgheti, Especialista em
Anatomia Patológica da Faculdade de
Medicina da Unoeste, Presidente
Prudente, Brasil
Período
14/04/2008 a
24/04/2008
Tipo de Estágio
Situação Actual
Concluído
Imunocitoquímica
07/04/2008 a
28/04/2009
Citotécnica
Em curso
27/09/2008 a
24/11/2008
Citopatologia
Concluído
02/05/2008 a
31/05/2008
Patologia
Veterinária
Concluído
01/01/2008 a
31/05/2008
07/01/2008 a
01/02/2008
Citopatologia
Concluído
Técnica de
Hibridização in
situ
Concluído
4. Publicações com material da U.P.S.
Vieira DS, Dufloth RM, Schmitt FC, Zeferino LC. Carcinoma de mama: novos conceitos na
classificação. Rev Bras Ginecol Obstet 30: 42-47, 2008.
Silva F, Carvalho S, Milanezi F, Schmitt FC. Carcinoma da mama de tipo basal. Acta Med Port 21: 387392, 2008.
Costa S, Pinto D, Pereira D, Rodrigues H, Cameselle-Teijeiro J, Medeiros R, Schmitt F. Importance of
TP53 codon 72 and intron 3 duplication 16bp polymorphisms in prediction of susceptibility on breast
cancer. BMC Cancer 8: 32, 2008, doi:10.1186/1471-2407-8-32.
Schmitt FC, Longatto-Filho A, Valent A, Vielh P. Molecular techniques in cytopathology practice. J
Clin Pathol 61:258-267, 2008.
Simpson PT, Reis-Filho JS, Lambros MBK, Jones C, Steele D, Mackay A, Iravani M, Fenwick K, Dexter
T, Jones A, Reid L, Da Silva L, Shin SJ, Hardisson D, Ashworth A, Schmitt FC, Palacios J, Lakhani SR.
Molecular profiling pleomorphic lobular carcinomas of the breast: evidence for a common
molecular genetic pathway with classic lobular carcinomas. J Pathol 215: 231-244, 2008.
76
Marchio C, Iravani M, Natrajan R, Lambros MB, Savage K, Tamber N, Fenwick K, Mackay A, Senetta
R, Di Palma S, Schmitt FC, Bussolati G, Ellis IO, Ashworth A, Sapino A, Reis-Filho JS. Genomic and
immunophenotypical characterization of pure micropapillary carcinomas of the breast. J Pathol 215:
398-410, 2008.
Di Palma S, Collins N, Bilous M, Sapino A, Mottolese M, Kapranos N, Schmitt F, Isola J. A quality
assurance exercise to evaluate the accuracy and reproducibility of chromogenic in situ hybridization
for HER2 analysis in breast cancer. J Clin Pathol 61: 757-760, 2008.
Paredes J, Correia AL, Ribeiro AS, Milanezi F, Cameselle-Teijeiro J, Schmitt FC. Breast carcinomas
that co-express E- and P-cadherin are associated with p120-catenin cytoplasmic localisation and poor
patient survival. J Clin Pathol 61: 856-862, 2008.
Maia CJB, Socorro S, Schmitt F, Santos CRA. Characterization of oligoadenylate synthetase-1
expression in rat mammary gland and prostate: effects of 17-estradiol on the regulation of OAS1g in
both tissues. Mol Cell Biochem 314: 113-121, 2008.
Costa S, Pinto D, Pereira D, Rodrigues H, Cameselle-Teijeiro J, Medeiros R, Schmitt F. XRCC1
Arg399Gln and RAD51 5’UTR G135C polymorphisms and their outcome in tumor aggressiveness and
survival of Portuguese breast cancer patients. Breast Cancer Res Treat 109: 183-185, 2008.
Velho S, Moutinho C, Cirnes L, Albuquerque C, Hamelin R, Schmitt F, Carneiro F, Oliveira C, Seruca R.
BRAF, KRAS and PI3KCA mutations in colorectal serrated polyps and cancer: primary or secondary
genetic events in colorectal carcinogenesis ? BMC Cancer 8: 255, 2008.
Pinheiro C, Longatto-Filho A, Ferreira L, Pereira SM, Etlinger D, Moreira M, Jubé LF, Queiroz GS,
Schmitt F, Baltazar F. Increasing expression of monocarboxylate transporters 1 and 4 along
progression to invasive cervical carcinoma. Int J Gynecol Pathol 27: 568-574, 2008.
Maia CJ, Socorro S, Schmitt F, Santos CR. STEAP1 is over-expressed in breast cancer and downregulated by 17B-estradiol in MCF-7 cells and in the rat mammary gland. Endocrine DOI
10.1007/s12020-008-9113-7, 2008.
5. Exames realizados na U.P.S.
Nº total de exames: 14.099
Captura híbrida: 267
Citologias ginecológicas: 7.370
Citologias não ginecológicas: 440
Citologias aspirativas: 3049
Histológicos: 2.141 (1.070 Autópsias)
Histoquímicos: 86
Imuno-histoquímicos: 130 (inclui hepáticas com imuno)
Hibridização in situ: (Projecto ROCHE): 348
Imunofluorescência directa: 12
Relatório complementar: 17
77
Casos em consulta*: 237
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Os casos em consulta foram oriundos das seguintes instituições:
Achim Weber - UniversitätsSpital Zürich – Zurique - Alemanha
Adriana Crespo – São Paulo - Brasil
Agostinho Sanches – Centro Hospitalar do Alto Ave - Guimarães - Portugal
Alain Sutter - Laboratoire Argot Lab – Lausanne - Suiça
Ana Catarino – Hospital da Luz – Lisboa - Portugal
Ana Félix – Instituto Português de Oncologia – Lisboa – Portugal
Ana Paula Farina - Hospital Universitário - Florianópolis – Santa Catarina - Brasil
Angela Flávia Logullo – Universidade Federal de São Paulo – Brasil
Anne Marie O’Shea - Beaumont Hospital – Dublin – Alemanha
B. Iglesias - Centro Médico POVIS - Vigo (Pontevedra) - Espanha
Benno Küsters - Radbound University Nijmegen – Nijmegen - Holanda
Carla Barbedo – CPD-Porto - Portugal
Carla Carrilho – Hospital Central de Maputo - Moçambique
Carlos Quintana – Lapcir – Setúbal – Portugal
Carlos Seabra – Hospital Infante D. Pedro – Aveiro - Porto
Cesaltina Lorenzoni – Hospital Central de Maputo – Maputo – Moçambique
Christophe Girardet - Institut Central des Hôpitaux Valaisans – Sion - Suiça
César Augusto Alvarenga - Instituto de Patologia de Campinas - Vila Itapura - Brasil
Daniella Serafin Couto Vieira - Hospital da Caridade – Florianopolis - Brasil
Dolores López – Centro Hospitalar de Lisboa Norte – Lisboa - Portugal
Eduardo De Miguel Herran - Hospital de Galdakao - Vizcaya - Espanha
Eduardo Studart - Laboratório Silvany Studart - Hospital Português – Salvador – Bahia - Brasil
Élbio C. de Paula - Goiânia - Goias - Brasil
Florence Mishellany – Centre Jean Perrin - Clermont Ferrand - França
Francisco Cadarso – Centro Hospitalar do Tâmega e Sousa – Vale do Sousa - Portugal
Fred Ellinger - Marilia – São Paulo - Brasil
Fátima Magalhães – Unidade Local de Saúde de Matosinhos – Porto - Portugal
Geneviève Fouilhoux - Departemente D' Anatomie et de Cytologie - Clermont- Ferrand França
Gianni Bussolati - Universitá di Torino - Itália
H. Van Dick - Laboratorium Voor Pathologische Ontleedkunde – Duffel - Bélgica
Halil Diçer Azizlerli - Mediteks Saglik Hizm. Tibbi Malz.San. Ve Disticas – Istambul - Turquia
Hanifa Bouzourene - Centre Hospitalier Universitaire Vaudois – Lausanne - Suiça
Helena Garcia – CEDAP – Coimbra - Portugal
Hugo Leite Farias Brito – Universidade Federal de Sergipe – Sergipe – Brasil
Hulya Akgun – Erciyes University Medical Faculty – Kayseri - Turquia
Igone Imaz Murga - Hospital de Galdakao - Vizcaya - Spain
Igor Letovanec - Viollier Weintraub Sa – Genéve - Suiça
Isabel Amendoeira – Hospital S. João – Porto - Portugal
Jera Jeruc - Institut Za Patologijo – Ljubljana - Eslovénia
José António Ortiz - Povisa Centro Médico – Vigo - Espanha
José António Alvarez Martinez - Hospital de Galdakao - Vizcaya - Espanha
José Cameselle Teijeiro - Hospital Clínico Universitario - Santiago de Compostela - Espanha
José Lima – Hospital Distrital de Santarém – Santarém – Portugal
José Melo Cabral - Hospital Divino Espirito Santo – Ponta Delgada – Açores – Portugal
José Parra – Centro Hospitalar do Barlavento Algarvio – Portimão – Portugal
José Vílchez - Centro Hospitalar do Barlavento Algarvio, EPE – Algarve – Portugal
Juana Maria Rodríguez - Hospital de Mendaro – Gipuzkoa - Espanha
Kamil R. Peker - Istanbul Patoloji Grubu - Vali Konagi – Istambul - Turquia
Krystyna Kotanska-Groholt - The Norwegian Radium Hospital – Oslo - Noruega
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Lia Menasce - Christie Hospital – Manchester – U.K.
Luciano Espinheira Jr. - Universidade Federal da Bahia – Bahia - Brasil
Lucília Monteiro – Centro Hospitalar de Lisboa Ocidental – Lisboa - Portugal
Luís Grangeia – Hospital Militar Regional Nº 1 – Porto - Portugal
Luis Wayllace - Institut de Pathologie de Génétique – Gerpinnes - Bélgica
Manuela Sousa Lima - Centro Hospitalar de Lisboa Ocidental – Lisboa - Portugal
Marcello Franco - UNIFESP/EPM - São Paulo - Brasil
Marco Ferreira – Hospital Doutor Fernando Fonseca – Amadora Sinta - Portugal
Maria Elena Pérez Martín - Hospital Universitário Rio Hortega – Valladolid - Espanha
Maria Isabel Lourenço – Hospital Pulido Valente – Lisboa - Portugal
Maria José Brito - Hospital Garcia da Orta, S.A. Almada - Portugal
Maria João Martins – Hospitais da Universidade de Coimbra – Coimbra - Portugal
Marta Couce - Hospital Universitário Son Dureta - Palma Maiorca - Espanha
Martinha Chorão - Centro Hospitalar de Lisboa Ocidental – Lisboa - Portugal
Mary Toner - University Teaching Hospit. Trinity College Dublin - Irlanda
Massimo Bongiovanni - HUG - Hôpitaux Universitaries de Genéve – Genève - Suiça
Mete Düren - Istanbul - Turquia
Müller-Hermelink - Inst. Universität Würzburg – Würzbur - Alemanha
Noureddine Bouzourene - Laboratoire Argot Lab - Lausanne - Suiça
Paola Souza - Souza Anatomia Patológica - Brasil
Patrícia Sabino de Matos - FCM/ Unicamp – Campinas - Brasil
Patrick Agostini - Lab. de Anatomia Patológica Dr. Patrick Agostini – Portimão - Portugal
Peter Vermeulen - Laboratorium voor Pathologishe Anatomie en Cytolog – Wilrijk – Bélgica
Philippe Rochaix - Institut Claudius Regaud – Toulouse – França
Pilar San Miguel - Hospital Povisa – Vigo – Espanha
R. Heimann – Bruxelas - Bélgica
Richard Wasicky - Intitute of Pathology and Bacteriology - Vienna - Austria
Ronald de Krijger - Erasmus MC - Holanda
Rosa Gouveia - Centro Hospitalar de Lisboa Ocidental – Lisboa - Portugal
Rosa Madureira – Hospital Nossa Senhora do Rosário – Barreiro - Portugal
Ruegsegger - Hôpital du Chablais Monthey – Monthey - Suiça
Salomite Domingues – Centro de Saúde de Aldoar – Porto – Portugal
Sancia Ramos - Centro Hospitalar de Lisboa Ocidental – Lisboa - Portugal
Sofia Loureiro Santos – Hospital Garcia da Orta – Lisboa - Portugal
Suna Erkilic - Gaziantep University - Tuquia
Susanne Van Eeden - Universiteit Van Amsterdam – Amsterdam - Holanda
Teresa Aramendi Sanchez - Hospital Infanta Leonor – Madrid - Espanha
Teresa Braudier – Hospital S. João – Porto - Portugal
Teresa Fonseca – Centro Hospitalar do Tâmega e Sousa – Vale do Sousa - Portugal
Th. Rüdiger - Pathologisches Institut der Universität Würzburg – Würzburg - Suiça
Tulio Geraldo de Sousa e Souza - Hospital Aliança – Bahia - Brasil
Umit Ince - Oruc Patoloji ve Sitoloji Lab. - Turquia
Vicki Save - Cambridge University Hospitals – Cambridge –Reino Unido
Vinicius Duval da Silva - Hospital São Lucas - Porto Alegre - RS - Brasil
Vitor Carneiro – Hospital do Divino Espírito Santo – Ponta Delgada - Açores
Yesim Ertan - University of Ege - Faculty of Medicine – Izmir – Turquia
79
6. Controle de Qualidade
•
•
Data de Instituição 19-01-1998
Membros
• Prof. Fernando Schmitt
• Drª Fernanda Milanezi
• D. Susana Silva
O Sistema de Controle de Qualidade foi realizado através do sistema informático Sislab, cujos
resultados estão publicados no Manual da Qualidade da UPS-2008. Os principais achados
comparativamente aos últimos 3 anos foram:
Total nº de casos
Casos revistos
2005
13.573
311
2006
13.413
573
2007
13.214
670
2008
14.099
465
Tipo de Exames
Citologia aspirativa por agulha fina
Citologia não ginecológica
Histológico de biópsias
Histológico de peças cirúrgicas
Biópsia hepatica sem imuno-histoquímica
Biópsia hepatica com imuno-histoquímica
Biópsia gástrica com pesquisa de H. Pylori
Consultas
Citologia ginecológica a)
Imunofluorescência
Relatório complementar
Imunocítoquímico
2005
164
6
24
91
2
11
9
3
N/A
1
N/A
0
2006
375
18
37
97
7
25
11
2
N/A
1
N/A
0
2007
399
62
81
101
3
14
5
3
N/A
2
N/A
0
2008
259
30
56
86
0
14
3
11
N/A
1
2
3
a)
Desde Abril de 2004 os casos de citologia ginecológica foram avaliados separadamente de acordo
com o procedimento PR.MED.01
Valores de discordância:
Critério
Identificação do espécime, arquivo e
macroscopia
Diagnóstico
Codificação
2005
2.6%
2006
1.7%
2007
0,45%
2008
0,01%
0.6%c)
0.6%
0.0%
0.2%
0.0%
0.0%
0,01%
0.0%
“Turn-around-time”
2005
2006
2007
2008
Citologia aspirativa por agulha fina
1.8 dias
0.31 dias
Citologia não ginecológica
4.7 dias
0.8
dias
1.7
dias
0.24
dias
1 dia
1 dia
80
Histológico de biópsias
2.4 dias
Histológico de Peças cirúrgicas
3.2 dias
Biópsia hepatica sem imuno-histoquímica
5.0 dias
Biópsia hepatica com imuno-histoquímica
5.2 dias
Biópsia gástrica com pesquisa de H. Pylori
1.9 dias
Consultas
Citologia ginecológica
N/A
2.4 dias
1.3
dias
1.7
dias
3.8
dias
4.6
dias
1.5
dias
N/A
3 dias
1.82 dias
2.2 dias
2 dias
4.25
dias
2 dias
N/A
1.7 dias
1.85
dias
1.84
dias
4.75
dias
5.36
dias
1.89
dias
N/A
N/A
Na análise do controle de qualidade de citologia ginecológica, os principais resultados foram os
seguintes:
2005
2006
2007
2008
Total de casos
8.952
8.780
7.299
7370
Casos revistos
2123
1970
1438
1368
Concordância entre
patologistas e
citotécnico
Discordância entre
patologista e citotécnico
2005
2006
2007
2008
1962
1758
1313
1223
(92,4%)
(89,2%)
(91,3%)
(89,4%)
125
145
(8,6%)
(10,6%)
161
(7,5%)
214 (10,8%)
O número total de citologias consideradas não satisfatórias para a análise foi de 0.8% (1,1% em 2007)
o que representa uma diminuição conforme um dos objectivos propostos no último ano.
Ascus/Agus foi diagnosticado em 140 dos casos com uma relação ASCUS/Lesão de 1.9 (3,2em 2007)
Para além da participação, com aprovação, em todos os testes de proficiência da CAP, continuámos
a participar de forma positiva nos programas de controlo de qualidade externo das técnicas de
imuno-histoquímica do UK-NEQAS e do Programa de Qualidade da Sociedade Brasileira de Patologia
(PIQ). Todas estas actividades estão registadas de acordo com o Procedimento Regulamentador PR
MED-05 – Programas Externos de Educação e Avaliação Contínua.
81
4b. UNIDADE DE PRESTAÇÃO DE SERVIÇOS (UPSI)
1. Exams
1.1
Nº of requested exams
Cancelled requests
Ongoing (still to be concluded or lacking one or more samples)
1.2
110
1
5
Types of Exams:
Genetic Characterisations/Identifications
11
Paternities
With 1 alleged father, without analysis of mother 19
With 2 offspring 1
With 1 alleged father and analysis of mother 64
With 2 offspring 2
With 2 alleged fathers and analysis of mother 5
Other kinship analyses
Consultations
Sample collections
Parentage tests in dogs
* three processes involving 21 paternity tests.
1.3
1
3
1
3*
Request locations:
Location
Germany
Anadia
Arouca
Bragança
Celorico de Basto
Coimbra
Spain (Madrid)
Estoril
Fátima
Leiria
Lisboa
Matosinhos
Paredes
Penafiel
Ponte de Lima
Porto
Póvoa de Varzim
Santa Maria da Feira
São João da Madeira
Valongo
Vila do Conde
Courts
0
0
2
2
0
0
0
0
0
0
0
0
0
7
0
0
0
4
1
0
5
Private
1
1
0
2
1
1
1
1
1
1
25
2
1
0
1
10
1
1
0
1
0
Total
1
1
2
4
1
1
1
1
1
1
25
2
1
7
1
10
1
5
1
1
5
82
1.4
Vila Nova de Gaia
Vinhais
Total
Nº of exams per client
35
1
57 (51,8%)
Client
1
0
53 (48,2%)
36
1
110
Total
Courts:
Trib. Família e Menores de Vila Nova de Gaia
Trib. Judicial de Vila Nova de Gaia
Trib. Penafiel
Trib. Bragança
Trib. Vila do Conde
Trib. Arouca
Trib. São João da Madeira
Trib. Santa Maria da Feira
Trib. Vinhais
32
3
7
2
5
2
1
4
1
Private
Clínica Dr. Joaquim Chaves - Lisboa
Internal (IPATIMUP)
Other
24
4
25
Total
110
2. Publications
International Journals
2.1.
Sanchez-Diz P, Alves C, Carvalho E, Carvalho M, Espinheira R, García O, Pinheiro MF, Pontes
L, Porto MJ, Santapa O, Silva C, Sumita D, Valente S, Whittle M, Yurrebaso I, Carracedo A,
Amorim A, Gusmão L; GEP-ISFG (The Spanish and Portuguese Working Group of the
International Society for Forensic Genetics) (2008): Population and segregation data on 17 YSTRs: Results of a GEP-ISFG collaborative study. Int J Legal Med. 122(6):529-533.
2.2
Prieto L, Alonso A, Alves C, Crespillo M, Montesino M, Picornell A, Brehm A, Ramírez JL,
Whittle MR, Anjos MJ, Boschi I, Buj J, Cerezo M, Cardoso S, Cicarelli R, Comas D, Corach D,
Doutremepuich C, Espinheira RM, Fernández-Fernández I, Filippini S, Garcia-Hirschfeld J,
González A, Heinrichs B, Hernández A, Leite FP, Lizarazo RP, López-Parra AM, López-Soto M,
Lorente JA, Mechoso B, Navarro I, Pagano S, Pestano JJ, Puente J, Raimondi E, RodríguezQuesada A, Terra-Pinheiro MF, Vidal-Rioja L, Vullo C, Salas A (2008) 2006 GEP-ISFG
collaborative exercise on mtDNA: reflections about interpretation, artefacts, and DNA
mixtures. Forensic Sci Int Genet 2(2):126-33.
83
2.3
Amorim A (2008) A cautionary note on the evaluation of genetic evidence from
uniparentally transmitted markers. Forensic Sci Int Genet 2(4): 249-384.
2.4
Gusmão A, Gusmão L, Gomes V, Alves C, Calafell F, Amorim A, Prata MJ (2008) A perspective
on the history of the Iberian gypsies provided by phylogeographic analysis of Y-chromosome
lineages. Ann Hum Genet 72:215-27.
2.5
Gusmão L, Sánchez-Diz P, Alves C, Gomes I, Zarrabeitia MT, Abovich M, Atmetlla I, Bobillo C,
Bravo L, Builes J, Cainé L, Calvo R, Carvalho E, Carvalho M, Cicarelli R, Catelli L, Corach D,
Espinoza M, García O, Malaghini M, Martins J, Pinheiro F, João Porto M, Raimondi E, Riancho
JA, Rodríguez A, Rodríguez A, Rodríguez Cardozo B, Schneider V, Silva S, Tavares C,
Toscanini U, Vullo C, Whittle M, Yurrebaso I, Carracedo A, Amorim A. A GEP-ISFG
collaborative study on the optimization of an X-STR decaplex: data on 15 Iberian and Latin
American populations. Int J Legal Med. 2008 Dec 12. [Epub ahead of print].
2.6
Gomes V, Sánchez-Diz P, Alves C, Gomes I, Amorim A, Carracedo A, Leonor Gusmão.
Population data defined by 15 autosomal STR loci in Karamoja population (Uganda) using
AmpF/STR
Identifiler
kit.
Forensic
Science
International:
Genetics
DOI:
10.1016/j.fsigen.2008.06.005.
3. Participation in Congresses/Poster Communications/Oral Communications by invitation
3.1
Cíntia Alves: 2008 Collaborative Exercise Results – Sex Chromosomes (Resultados do
Exercício Colaborativo 2008 - Cromossomas Sexuais). XIII Jornadas GEP-ISFG. Rio de Janeiro,
Brazil, 23-24 June 2008.
3.2
Leonor Gusmão: Structure and goals of the GEP-ISFG (Estrutura e objectivos do GEP-ISFG). III
Simpósio Internacional de Identificação Humana por DNA. Rio de Janeiro, Brazil, 24-26 June
2008.
3.3
Leonor Gusmão: X and Y chromosome markers in kinship and criminal investigations
(Utilização de marcadores dos cromossomas X e Y em investigação de vínculos genéticos e
criminais). III Simpósio Internacional de Identificação Humana por DNA. Rio de Janeiro, Brazil,
24-26 June 2008.
3.4
Leonor Gusmão: Utility of different DNA markers in population genetics (Utilidad de los
distintos marcadores de ADN en genética de poblaciones). I Congreso Latinoamericano de
84
Genética Humana y IX Congreso Colombiano de Genética. Cartagena de Indias, Colombia, 8-10
October 2008.
3.5
Leonor Gusmão: lectured “Special Topics in Biology: Statistics Applied to Forensic Genetics”
(Tópicos Especiais em Biologia: Estatística Aplicada à Genética Forense) and “Special Topics in
Biology: Forensic Molecular Genetics” (Tópicos Especiais em Biologia: Genética Molecular
Forense). Post Graduate program in Biology, Área de concentração em Biociências Nucleares
da da UERJ (University of the state of Rio de Janeiro), Brazil, 25 June to 11 July 2008.
3.6
Leonor Gusmão: lectured “Typing of SNP polymorphisms of importance in forensic
genetics” (Tipificación de polimorfismos de nucleotido simple (SNPs) de importancia en
genética forense). I Congreso Latinoamericano de Genética Humana y IX Congreso Colombiano
de Genética. Cartagena de Indias, Colombia, 5-7 October 2008.
3.7
Leonor Gusmão: lectured the Population Genetics discipline (40 hours) of the Masters
course on Basic Biomedical Sciences of the Escuela de Medicina de la Facultad de Salud de la
UIS (Industrial University of Santander), Colombia, 15-22 October 2008.
3.8
António Amorim: Human Identification by DNA: Historical perspective, Applications and
Development (A Identificação Humana por DNA: Perspectiva Histórica, Aplicações e
Desenvolvimento). Opening Conference, III Simpósio Internacional de Identificação Humana
por DNA, Rio de Janeiro, Brazil, 24-26 June 2008.
3.9
António Amorim: Quantification of genetic evidence (Quantificação da prova genética). II
Congresso Nacional de Genética Forense, Brasília, Brazil, 5-7 November 2008.
3.10
Gomes I, Prinz M, Pereira R, Bieschke E, Amorim A, Carracedo A, Gusmão L (2008) Hidden
sequence variation of the X-linked DXS6789 microsatellite. DNA in Forensics 2008. Ancona,
Italy. 27-30/5. OP15.
3.11
Sánchez-Diz P, Alves C, Carvalho E, Carvalho M, Espinheira R, Garcia O, Pinheiro MF, Pontes
L, Porto MJ, Santapa O, Silva C, Sumita D, Valente S, Whittle M, Yurrebaso I, Carracedo A,
Amorim A, Gusmão L (2008) Population and segregation data on 17 Y-STRs: results of a GEPISFG collaborative study. Ancona, Italy. 27-30/5. OP72.
4. Activities/Other
4.1
Participation in the 2008 Quality Control Exercise (Paternity and Forensics) of the GEP-ISFG
(Spanish and Portuguese Group of the International Society for Forensic Genetics).
Certificates are in attach.
85
4.2
Participation in Committees and International Representations:
- Leonor Gusmão
- Member of the Forensic Science International: Genetics Editorial Board (Elsevier
Science, London. ISSN: 1872-4973);
- Secretary and member of the Executive Committee of the GEP-ISFG since June
2004 until June 2008;
- Treasurer and member of the Executive Committee of the ISFG since January 2008.
- António Amorim
- Member of the Editorial Board of the Open Forensic Science Journal (Bentham
Open. ISSN: 1874-4028);
- President of the GEP-ISFG since June 2004 until June 2008;
- Vice-President of the GEP-ISFG since June 2008.
4.3
Organisation of Quality Control Exercises in GEP-ISFG:
- Sex Chromosomes Working Group - Collaborative study on X chromosome STRs aiming to
evaluate a multiplex PCR reaction (X-STR Decaplex, developed in IPATIMUP) – concluded in
2008 (scientific article in publication);
- Non-Human Forensic Genetics Working Group – extension of the first collaborative exercise
on mitochondrial DNA in Canis familiaris hair (scientific article submitted).
4.4
Participation in an international collaborative study, coordenated by Reinhard Szibor
(Institut für Rechtsmedizin, Otto-von Guericke Universität Magdeburg, Alemanha), for the
estimation of X chromosome recombination rates using grandfather-daughter-grandson
trios analysed with the commercial kit Mentype Argus X-8 (Biotype AG) – to be concluded in
2009.
4.5
Initiated the development of a mitochondrial DNA complete control region database of the
Portuguese population, for forensic/identification applications and participation in EMPOP
(Mitochondrial DNA Control Region Database, www.empop.org).
86
4c. UNIDADE DE PRESTAÇÃO DE SERVIÇOS DE SUSCEPTIBILIDADE
GENÉTICA(UPSS)
Resumo
O objectivo primordial da UPSS para o ano 2008 continuou a ser a consolidação da sua actividade
como prestador de serviços. Este objectivo foi conseguido através:
1.
Do aumento do número de testes de diagnóstico genético (mais 65% relativamente a 2007)
realizados em áreas que consideramos chave para a unidade, como a oncologia e a cardiovascular;
2.
Do estabelecimento e implementação de novos testes nas áreas cardiovascular e oncologia.
Para 2009 a UPSS estabeleceu como principais objectivos:
1. Aumentar o número de testes de diagnóstico genético realizados em áreas que
consideramos chave para a unidade, como a oncologia e cardiovascular;
2. Dar continuidade ao programa de estabelecimento e implementação de novos testes.
2005
alfa1-Antitripsina
Braf
BRCA
caderina - E
CARD15/NOD2
C-KIT/PDGFRA
CYP21
DAVD
EGFR
Estenose Supravalvular
H. Pylori
Hipercolesterolemia familiar
hMLH1 e hMSH2
HPV
KRAS
Marfan
Miocardio não-compactado
Miocardiopatia Dilatada
Miocardiopatia hipertrófica
MSI
N-myc/1p
OTC
P53
polimorfismos pró-inflamatórios
Prader-Willi/Angelman
RET
Síndrome de Brugada
Síndrome QT-Longo
SMAD4
Tipagem de HLA
TPMT
Translocações
UBE3A
2006
95
0
15
5
3
0
0
0
0
0
2
0
1
6
0
0
0
0
0
19
3
5
1
1
64
4
0
0
0
0
0
8
10
2007
132
8
13
12
1
5
0
0
20
1
7
0
1
3
0
4
0
4
14
22
3
15
1
0
100
12
13
2
1
3
0
2
9
161
1
94
6
4
9
10
15
58
0
12
11
1
4
5
8
10
20
49
39
2
22
4
1
95
14
30
5
1
1
3
4
8
2008
193
1
119
11
0
8
4
7
36
0
1
7
0
13
441
18
10
27
82
33
3
11
3
28
49
15
10
4
0
0
2
3
6
87
X-Frágil
Trombofilia
SRHT
Outros
Total
3
4
2
0
245
0
412
4
713
1
5
11
16
1178
Exames realizados na UPSS
As figuras 1 e 2 representam a distribuição e o número total, respectivamente, de exames realizados
na UPSS por área médica. O facto de maior relevo é o claro aumento da actividade da UPSS,
independentemente da área considerada. Ainda assim, a área da oncologia foi aquela que mais
contribuiu para este crescimento.
Fig. 1: Distribuição dos exames realizados pela UPSS por área médica.
88
Fig. 2: Número de exames realizados pela UPSS por área médica.
Novos exames implementados na UPSS
Área Oncologia
• Pesquisa de polimorfismos genéticos associados a risco de trombofilia
Área Oncologia
•
Pesquisa de mutações no gene KRAS
•
Pesquisa de mutações no gene SRHT
89
5. RECÉM-DOUTORADOS
Vítor Manuel Trovisco Gradíssiomo
Orientador: Manuel Sobrinho Simões
Data de conclusão: 19 de Fevereiro de 2008
Títuklo da tese: Papel das alterações do Gene Braf na História Natural do Carcinoma Papilar da
Tireóide
João Pedro Leal Nogueira Simas Leite
Orientador: Manuel Sobruinho Simões
Data de conclusão: 20 de Junho de 2008
Títuklo da tese: Controlo molecular da apoptose e sua relação com a resistência farmacológica em
leucemias humanas
Catarina de Castro Tavares Alves
Orientador: Fátima Carneiro
Data de conclusão: 24 de Julho de 2008
Títuklo da tese: Papel do Slug no carcinoma gástrico. Da expressão tecidular a análise funcional,
usando um modelo in vitro.
Rachid Arangurem Karam
Orientador: Carla Isabel Gonçalves de Oliveira
Defesa: 2-12-2008
O papel do nonsense-mediated mRNA decay (NMD) na regulação da expressão do gene CDH1 e no
desenvolvimento tumoral
90
6. RESUMO DOS PROJECTOS
FUNDAÇÃO PARA A CIÊNCIA E TECNOLOGIA
“O papel de novos mecanismos regulatórios na perda de expressão da caderina-E” – 2007-2010 – 36
meses – IR: Carla Oliveira
“Análise Trans-Específica do Impacto Fisiológico de Genes Inactivados” – 2007-2010 – 36 meses – IR:
Luísa Azevedo
“Autoregulação do CDX2 na reversibilidade/irreversibilidade da metaplasia intestinal gástrica” –
2008-2011 – 36 meses – IR: Raquel Almeida
“Fenótipos/genótipos secretor e Lewis na infecção por Helicobacter pylori e calicivirus” – 2007-2010
– 36 meses – IR: Leonor David
“O papel da desregulação do tráfico da caderina-E na progressão do cancro epitelial” – 2008-2011 –
36 meses – IR: Gianpaolo Suriano
“Estudo da daptação humana no universo proteolítico: o exemplo dos inibidores de proteases de
serina” – 2007-2010 – 36 meses – IR: Susana Seixas
“Na Fronteira das expansões Bantu: inferência da história recente de populações africanas com
sistemas haplotípicos de evolução independente” – 2008-2011 – 36 meses – IR:Jorge Rocha
“Análise da arquitectura genética e história evolutiva de fenótipos pigmentares na espécie humana:
estudos de mapeamento por miscigenação na população de Cabo Verde” – 2008-2011 – 36 meses –
IR: Sandra Beleza
“A comunidade cigana portuguesa: a história demográfica à luz dos padrões de diversidade
genética” – 2007-2010 – 36 meses – IR: Maria João Prata
“Reavaliação com ferramentas genéticas de elevada resolução das origens geográficas e das rotas
de dispersão dos primeiros homens modernos e dos primeiros agricultores da bacia mediterrânea”
– 2007-2010 – 36 meses – IR: Luísa Pereira
“Longevidade em humanos de origem africana - uma abordagem genética” – 2007-2010 – 36 meses
– IR: Luísa Pereira
“Manipulação, in vitro e in vivo, da expressão do Sialyl Lewis X e E-caderina nos tumores da mama
da cadela” – 2007-2010 – 36 meses – IR: Fátima Gartner
91
“Caracterização molecular e funcional da via do mTOR no carcinoma papilar da tireóide” – 20072010 – 36 meses – IR: Ana Sofia Rocha
“MLK3, um novo gene mutado em cancro colorectal com instabilidade de microssatélites” – 20082011 – 36 meses – IR: Raquel Seruca
“Identificação de vias de sinalização mediadas pelo oncogene MUC1 em linhas celulares de
carcinoma gástrico e em células gástricas imortalizadas” – 2008-2011 – 36 meses – IR: Luis Filipe Silva
“No cancro colorectal com instabilidade de microssatélites são os genes BRAF e KRAS novos
marcadores de prognóstico e novas ferramentas terapêuticas?” – 2005-2008 – 36 meses – IR:
Raquel Seruca
“Genes associados à metaplasia intestinal da mucosa gástrica (mucina MUC2 e fucosiltransferase
FUT3): regulação da transcrição e relavância para a adesão do Helicobacter pylori” – 2005-2008 – 36
meses – IR: Leonor David
“Análise funcional dos repressores da caderina-E (Slug, ZEB1 e E12/E47) em carcinomas do
estômago” – 2005-2008 – 36 meses – IR: Fátima Carneiro
“P-caderina no Cancro da Mama: o que regula a sua expressão e qual o seu papel na invasão de
células neoplásicas?” – 2005-2008 – 36 meses – IR: Fernando Schmitt
“Estudo evolutivo e epidemiológico de focos de anemias hereditárias em Portugal” – 2005-2008 –
36 meses – IR: Maria João Prata
“Clarificação da importância do polimorfismo da mucina MUC1 na infecção por helicobacter pylori”
– 2005-2008 – 36 meses – IR: Luís Filipe Silva
“Papel da activação oncogénica do BRAF na carcinogénese da tireoide” – 2005-2008 – 36 meses –
IR: Ana Paula Soares
“Efeitos da infecção por Helicobacter pylori em células epiteliais gástricas” – 2005-2008 – 36 meses
– IR: Céu Figueiredo
“Identificação de mecanismos moleculares subjacentes ao desenvolvimento de cancro gástrico em
famílias portadoras e não-portadoras de mutações germinativas da caderina-E” – 2005-2008 – 36
meses – IR: Carla Oliveira
“Identificação de vias de sinalização envolvidas na regulação do Cdx2 em dois modelos humanos de
diferenciação intestinal e polipose juvenil” – 2005-2008 – 36 meses – IR: Raquel Almeida
“Caracterização molecular genómica e pós-genómica das vias de sinalização RAS/RAF/ERK e
P13K/AKT em tumores agressivos da Tireóide” – 2005-2008 – 36 meses – IR: Ginesa Rostan
92
“Tumores mamários de gata – Análise Patológica, Molecular e Citigenética” – 2005-2008 – 36 meses
– IR: Fátima Gartner
“Caracterização biológica de tumores mamários mistos caninos: histogénese, progressão tumoral e
alterações genéticas” – 2005-2008 – 36 meses – IR: Fátima Gartner
“Mutações germinativas da Caderina-E do tipo "missense" e carcinoma difuso hereditário do
estômago: um modelo para a identificação das vias de sinalização mediadas pela caderina-E
fundamentais na invasão” - 2005-2008 – 36 meses – IR: Gianpaolo Suriano
AGÊNCIA DE INOVAÇÃO
“Teste de susceptibilidade genética para determinação de risco de desenvolvimento de Doença de
Crohn na população portuguesa”, ADI, Programa Ideia – Promotor GENETEST– 2005-2008 – 36
meses – IR: José Carlos Machado
“Desenvolvimento de uma plataforma tecnológica para a produção de anticorpos monoclonais e
seus derivados e seus derivados para terapia anticancerigena” – ADI, Programa IDEIA – Promotor
Biotecnol – 2007-2008 – 18 meses – IR: Fernando Schmitt
MINISTÉRIO DA SAÚDE
“Registo da Deficiência Genética da Metabolização de Tiopurinas na População Portuguesa e
Prevenção Toxicidade em Terapêuticas Citostáticas” – 2006-2008 – 24 meses – IR: Maria João Prata
AGÊNCIA PORTUGUESA DE SEGURANÇA ALIMENTAR
“Avaliação do risco do consumo de sal e da infecção por Helicobacter pylori no desenvolvimento de
carcinoma gástrico e das suas lesões precursoras em Portugal” – 2005-2008 – 36 meses – IR: Manuel
Sobrinho Simões
FUNDAÇÃO CALOUSTE GULBENKIAN
“Caracterização de factores biológicos e estilos de vida com impacto de ocorrência e na forma de
apresentação do cancro – “Lesões da mucosa gástrica em Moçambique e Portugal: “o enigma
Africano” – 2005-2008 – 36 meses – IR: Leonor David
“Utilização clínica dos alvos genéticos do tabaco” – 2006-2009 – 36 meses – IR: Luís Teixeira Costa
“Helicobacter Pylori: da Biologia à clínica” – 2006-2008 – 24 meses – IR: Céu Figueiredo
93
“Irradiação por tinea capitis e risco de cancro” – 2006-2009 – 36 meses – IR: José Teixeira Gomes
“Prevention and early diagnosis of cancer and precancerous lesions of cervix, stomach, breast and
thyroid" - co-financiamento EFTA - 2007-2010 – 36 meses – IR: Manuel Sobrinho Simões
“Mutated suppressor tRNAs as a therapeutic tool for cancer associated syndromes: HDGC as a
model” – 2008-2011 – 36 meses – IR: Carla Oliveira
“Basal-like Breast Cancer: are mammary stem cells new targets for cancer therapy?” – 2008-2011 –
36 meses – IR: Joana Paredes
“miRNAs como alvos moleculares em leucemia humana” 2008-2011 – 36 meses – IR: Helena
Vasconcelos
“Reforço das capacidades institucionais do serviço de Anatomia Patológica do Hospital Central de
Maputo” – 2008-2011 – 36 meses – IR: Manuel Sobrinho Simões
“Apoiar o IPATIMUP para comparticipar nos custos do estudo imunocitoquímico, molecular e
citogenético do carcinoma da tireóide” – 2008-2012 – 48 meses – IR: Manuel Sobrinho Simões
PROJECTOS EM COLABORAÇÃO COM A INDÚSTRIA FARMACÊUTICA
“Diminuição da resistência ao imatinib (mesilato) em modelos de linhas celulares de leucemia
através da diminuição específica de MDR1 com siRNAs” – 2004-2008 – IR: Helena Vasconcelos
“Tumores Estrumais Gastrointestinais: Caracterização Clinico-Patológica e Imuno-Histoquímica e
Identificação de Factores de Agressividade Biológica” – iniciou 2002 - IR: José Manuel Lopes
“Instalação de uma base de dados e banco de tecidos de tumores estromais gastrointestinais e
tumores neuroendócrinos (Regist e REGENE)” – iniciou 2006 - IR: Paula Soares e José Manuel Lopes
“É a via do mTOR relevante na iniciação/progressão dos melanomas e pode ser um alvo terapêutico
nesses tumores? – iniciou 2006 - IR: Paula Soares
“Papel biológico da activação do BRAF na carcinogénese do colon” – iniciou 2004 – IR: Paula Soares
P53 e Resistência a Quimoterapia no cancro da Mama – iniciou 1999 – IR: Fernando Schmitt
“Approaching basal-like breast carcinomas to target theraphy. A project combining the
reinforcement of logistics facilities with translational research” – 2006-2009 – 36 meses – IR:
Fernando Schmitt, Manuel Sobrinho Simões e Fátima Carneiro
94
“Uso de populações mistas para estudo da base genética da obesidade e hipertensão: O caso de
Cabo Verde e da população portuguesa das bacias do Tejo, Sado e Rio Guadiana” – GenOHmix” –
2007-2010 – 36 meses – IR: Sandra Beleza
“Expressão da P-caderina: seu efeito nas metásteses do cancro da mama e angiogénese utilizando
modelos animais in vivo” – 2007-2010 – 36 meses – IR: Fernando Schmitt
PROTOCOLOS DE COLABORAÇÃO COM EMPRESAS DE OUTROS SECTORES INDUSTRIAIS E DE
SERVIÇOS
“Criação de um Observatório/Consultório de Risco de cancro familiar e Ambiental” – 2006-2008 – 24
meses – IR: Raquel Seruca
“Desenvolvimento de estudos que identifiquem compostos com propriedades quimioprotectoras
da carcinogênese ou com propriedades inibidoras da invasão de células tumorais” – 2005-2008 – 36
meses – IR: Paula Soares
“Vitamida D como terapia dos carcinomas mamarios de tipo basal:ficçção ou realidade?” – 20072009 – 24 meses; IR: Fernando Schmitt
“Study on the role played by TGF-b dual effect in the progression of papillary thyroid carcinoma” –
2008-2010 – 24 meses – IR: Paula Soares
“DOENÇA DE FABRY: PATOGÉNESE E HISTOPATOLOGIA” – 2007-2009 – 24 meses – IR: Fátima
Carneiro
PROTOCOLOS DE COLABORAÇÃO COM ASSOCIAÇÕES
“Validação do papel xiap na resistencioa da leucemia mielógena aguda à quimioterapia” – 20052008 – 36 meses – IR: Helena Vasconcelos
CONCURSOS E/OU ENQUADRAMENTOS INTERNACIONAIS
“Prevention, diagnosis and molecular characterisation of mismatch repair defect-related hereditary
cancers of digestive systems” – 2006-2009 – 36 meses IR: Raquel Seruca
“Molecular mechanisms of biosynthesis of sialylated cancer-associated mucin carbohydrate
antigens in gastric carcinoma” – 2005-2008 – 36 meses – IR: Celso Reis
“The role of chronic infections in the development of cancer” – 2006-2010 – 48 meses – IR: José
Carlos Machado
95
“Evaluation and Control of Neglected Mucosal Enteric Infections in Childhood” – 2006-2010 – 48
meses – IR: José Carlos Machado
“Mapping of genes predisposing to familial thyroid tumours” – 2006-2009 – 36 meses – IR:
Valdemar Máximo
“Impacts – archive’s tissues: improving molecular medicine research and clinical practice” – 2007 –
2009 – 24 meses – IR: Fátima Carneiro
"Global RNAi approaches to unravel eukaryotic host functions that modulate bacterial infections ERA-NET PathoGenoMics" – 2007-2010 - 36 meses – IR: Céu Figueiredo
“Parasite and host genetic diversity in Helicobacter infections - ERA-NET PathoGenoMics” – 20072010 – 36 meses – IR: Jorge Rocha e José Carlos Machado
“O cancro e as Lesões Pré-Cancerosas do estômago na China” – 2007-2008 – 24 meses – IR: Manuel
Sobrinho Simões
“Prevention and early diagnosis of cancer and precancerous lesions of cervix, stomach, breast and
thyroid" – EEA Grants - 2007-2010 – 36 meses - IR: Manuel Sobrinho Simões
“Discovery of novel cancer serum biomarkers based on aberrant post translational modifications of
O-glycoproteins (O-PTM-Biomarkers) and their application to early detection of cancer” – European
Comission – 2008-2012 – 36 meses – IR: Leonor David
PROJECTOS ESTRATÉGICOS
“Subsídio para a concretização das acções de colaboração com Instituições Norte-Americanas”
(renovação anual) – Fundação Luso Americana para o Desenvolvimento
AGENCIA NACIONAL CIENCIA VIVA
“Autolaboratório” – 2006-2008 – 24 meses – IR: Luís Filipe Santos Silva
“Laboratório Aberto” – 2006-2008 – 24 meses – IR: Luís Cirnes
"Despertar para a Ciência" – 2007-2009 – 24 meses – IR: Luís Filipe Santos Silva
“A Magia da Ciência – 2005-2008 – 36 meses – IR: Luis Filipe Santos Silva
96
UNIVERSIDADE DO PORTO
“Genetic alterations in primary hyperparathyroidism” – 2007-2008 – 12 meses – IR: Paula Soares
“Induction of epstein-Barr(EBV) rectivation in Burkitt Lymphoma cells by anticancer drugs: a study
aiming at identifying inducers and non-induceres of reactivtion to help choosing the safer tratment
options” – 2007-2008 – 12 meses – IR: Helena Vasconcelos
CÂMARA MUNICIPAL DA TROFA
"Despertar para a Ciência" – 2008-2011 – 36 meses – IR: Luís Filipe Santos Silva
PROJECTOS INTERNOS
“Regulation of P-cadherin Expression in Breast Cancer” – 2008-2009 – 12 meses – IR: Doutora Joana
Paredes
“Criação de um Banco de DNA e RNA acoplado ao Banco de Tecidos e Tumores do H. S. João” –
2008-2009 – 12 meses – IR: Profª Fátima Carneiro
“Mapping of genes predisposing to familial thyroid tumours” – 2008-2010 - 24 meses – IR: Doutor
Valdemar Máximo
"Are genetic polymorphisms in inflammatory molecules risk factors for the development of
autoimmune thyroiditis? (This project implies the establishment of a tumour database)" – 2008-2010
– 24 meses – IR: Paula Soares
“Primary hyperparathyroidism - from geneside to bedside” – 2008-2010 – 24 meses – IR: Paula
Soares
“Clinical and functional relevance of Helicobacter pylori vacA intermediate region and CagA tyrosine
phosphorylation motifs” – 2008-2009 – 12 meses – IR: Céu Figueiredo
“The involvement of microRNAs in gastric cancer” – 2008-2009 – 12 meses – IR: Carla Oliveira
“The role of protein quality control in cancer” – 2008-2009 – 12 meses – IR: Joana Correia
“Does P-cadherin expression interfere with E-cadherin function in invasive breast cancer cells?” –
2010-2012 – 24 meses – IR: Fernando Schmitt
“Description and analysis of X-chromosome markers; mutation and recombination” – 2008-2009 –
12 meses – IR: António Amorim
97
“Research launching in fungal models” – 2008-2010 – 24 meses – IR: António Amorim
“Research launching in Aspergillus fumigatus genetics” – 2008-2010 – 24 meses – IR: António
Amorim
“Research launching in biomarkers research” – 2008-2010 – 24 meses – IR: António Amorim
“Description and analysis of genetic polymorphism in micro-ruminants” – 2008-2009 - 12 meses – IR:
António Amorim
“Genetic diversity of Sus scrofa” – 2008-2009 – 12 meses – IR: António Amorim
“Discription and analysis of domestic and wild dog genetic polymorphism” – 2008-2009 – 12 meses –
IR: António Amorim
“Descrição e nálise da distribuição do polimorfismo genético em felines” – 2008-2009 – 12 meses –
IR: António Amorim
“Trajectos evolutivos de residues proteicos em diferentes escalas temporais” – 2008-2009 – 12
meses – IR: António Amorim
“Genes ligados ao sexo na linha germinal masculina” – 2008-2009 – 12 meses – IR: António Amorim
“Study of mTOR pathway in human cancer” – 2008-2011 – 36 meses – IR: José Manuel Lopes
“Pharmacogenetics” – 2008-2010 – 24 meses – IR: António Amorim
“Crypto-Jews and the second Diaspora” – 2008-2010 – 24 meses – IR: António Amorim
“Ethnicity and genetics in Sub-Saharan Africa” – 2008-2009 – 12 meses – IR: António Amorim
“Database for mitochondrial DNA complete control region sequences of the Portuguese
population” – 2008-2009 – 12 meses – IR: António Amorim
IPATIMUP INSTITUIÇÃO PARTICIPANTE
“Uma estratégia para prevenir o cancro gástrico associado a H. pylori, baseada em receptores
específicos para a bactéria-partindo de SAMs para chegar a microsferas de quitosano
funcionalizadas com Gly-R" – 2008-2011 – 36 meses – IR IPATIMUP: Celso Reis – Instituição
Proponente: INEB
“O contributo de factores genéticos e não genéticos para a diversidade fenotipica dos doentes com
fenilcetonúria: um estudo baseado no Programa Português de Rastreio Neonatal" – 2008-2011 – 36
meses – IR IPATIMUP: António Amorim; Instituição Proponente: FMUP
98
“Nanosondas específicas para detecção prematura de células cancerígenas invasoras utilizando o
Cancro Gástrico Difuso Hereditário como modelo” – 2007-2010 – 36 meses – IR IPATIMUP: Raquel
Seruca – Instituição Proponente: INEB
“Dissecção Molecular In Vivo das Vias Morfogenéticas do Fuso Mitótico - Implicações para a
Aneuploidia e o Cancro” – 2005-2008 – 36 meses – IR IPATIMUP: Clara Sambade – Instituição
Proponente: IBMC
“Rastreios de genomica funcional num modelo em Drosophila para o estudo dos mecanismos
moleculares da tumorigénese induzidos por mutaçãoes da Cadherina-E” – 2005-2008 – 36 meses –
IR IPATIMUP: Raquel Seruca – Instituição Proponente: IBMC
“PYLORI L&EPS: Caracterização Estrutural de Lipopolissacarídeos e Exopolissacarídeos de
Helicobacter pylori – Estabelecimento das bases químicas e bioquímicas para o desenvolvimento de
vacinas e para a compreensão dos mecanismos de adesão” – 2005-2008 – 36 meses – IR IPATIMUP:
Céu Figueiredo e Celso Reis – IP: UAveiro
“Avaliação da Epidemiologia da Malária na Republica de Cabo Verde” – 2006-2008 – 24 meses – IR
IPATIMUP: António Amorim – Instituição Proponente: Instituto de Higiene e Medicina Tropical
“Bombas de efluxo em mycobacterium tuberculosis: caracterização molecular dos mecanismos de
efluxo e uso de inibidores de efluxo como novos compostos anti-bacilares” – 2005-2008 – 36 meses
– IR IPATIMUP: Filipe Sansonety – Instituição Proponente: Instituto de Higiene e Medicina Tropical
“O que é, na verdade, um coleho doméstico?” – 2005-2008 – 36 meses – IR IPATIMUP: Jorge Rocha
– Instituição Proponente: Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares
“Aspectos genéticos da actividade física, aptidão física associada à saúde, sobrepeso e obesidade.
Um estudo em gémeos dos 6 aos 20 de idade” – 2006-2009 – 36 meses – IR IPATIMUP: António
Amorim – IP: FCDEP-UP
99
7. TRABALHOS PUBLICADOS
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11.
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14.
Allum WH, Meyer HJ, Garofalo A, Schuhmacher C, de Manzoni G, Degiuli M, Kulig J, van de
Velde C, Roukos D, Barr H, Nowak W, Wittekind C, Sendler A, Park K, Hartgrink H, Haringsma J,
Seruca R. European Union Network of Excellence (EUNE) for Gastric Cancer Steering Group.
Gastric cancer in Europe. Br J Surg 95(4):406-8, 2008. IF - 4,3
Amorim A. A cautionary note on the evaluation of genetic evidence from uniparentally
transmitted markers. Forensic Sci Int Genet. 2(4): 376-378, 2008. IF – 2,0
Araujo R, Coutinho I, Espinel-Ingroff A. Rapid method for testing the susceptibility of
Aspergillus fumigatus to amphotericin B, itraconazole, voriconazole and posaconazole by
assessment of oxygen consumption. J Antimicrob Chemother 62(6):1277-80, 2008 IF – 4.0
Azevedo M, Eriksson S, Mendes N, Serpa J, Figueiredo C, Resende LP, Ruvoën-Clouet N, Haas
R, Borén T, Le Pendu J, David L: Infection by Helicobacter pylori expressing the BabA adhesin
is influenced by the secretor phenotype. J Pathol 215: 308-316, 2008. IF – 5,4
Bajpai S, Correia J, Feng Y, Figueiredo J, Sun SX, Longmore GD, Suriano G, Wirtz D. {alpha}Catenin mediates initial E-cadherin-dependent cell-cell recognition and subsequent bond
strengthening. Proc Natl Acad Sci U S A, 105(47):18331-6, 2008 IF – 9,59
Barber M, Murrell A, Ito Y, Maia AT, Hyland S, Oliveira C, Save V, Carneiro F, Paterson A,
Grehan N, Dwerryhouse S, Lao-Sirieix P, Caldas C, Fitzgerald R: Mechanisms and sequelae of Ecadherin silencing in hereditary diffuse gastric cancer. J Pathol 216:295-306, 2008. IF – 5,4
Barber M, Save V, Carneiro F, Dwerryhouse S, Lao-Sirieix P, Hardwick R, Caldas C, Fitzgerald R:
Histopathological and molecular analysis of gastrectomy specimens from hereditary diffuse
gastric cancer patients has implications for endoscopic surveillance of individuals at risk. J
Pathol 216:286-294, 2008. IF – 5,4
Barros R, Marcos N, Reis CA, De Luca A, David L, Almeida R: Letter to the Editor - CDX2
expression is induced by Helicobacter pylori in AGS cells. Scand J Gastroenterol 8:1-2, 2008 IF –
1,75
Barros R, Pereira B, Duluc I, Azevedo M, Mendes N, Camilo V, Jácobs RJ, Paulo P, Santos-Silva
F, van Seuningen I, van den Brink GR, David L, Freund J-N, Almeida R: Key elements of the
BMP/SMAD pathway co-localize with CDX2 in intestinal metaplasia and regulate CDX2
expression in human gastric cell lines. J Pathol 215: 411-420, 2008. IF – 5,4
Behar DM, Metspalu E, Kivisild T, Rosset S, Tzur S, Hadid Y, Yudkovsky G, Rosengarten D,
Pereira L, Amorim A, Kutuev I, Gurwitz D, Bonne-Tamir B, Villems R, Skorecki K Counting the
founders: the matrilineal genetic ancestry of the Jewish Diaspora. PLoS ONE 3(4): e2062, 2008
-Behar DM, Villems R, Soodyall H, Blue-Smith J, Pereira L, Metspalu E, Scozzari R, Makkan H,
Tzur S, Comas D, Bertranpetit J, Quintana-Murci L, Tyler-Smith C, Wells RS, Rosset S;
Genographic Consortium. The dawn of human matrilineal diversity. Am. J. Hum. Genet. 82:
1130-1140, 2008 IF – 11,0
Cameselle-Teijeiro J, Pardal F, Eloy C, Ruiz-Ponte C, Celestino R, Castro P, Soares P, SobrinhoSimões M. Follicular thyroid carcinoma with an unusual glomeruloid pattern of growth. Hum
Pathol. 39:1540-1547, 2008. IF – 3,0
Canedo P, Castanheira-Vale AJ, Lunet N, Pereira F, Figueiredo C, Gioia-Patricola L, Canzian F,
Moreira H, Suriano G, Barros H, Carneiro F, Seruca R, Machado JC: The interleukin-8-251*T/*A
polymorphism is not associated with risk for gastric carcinoma development in a Portuguese
population. Eur J Cancer Prev 17:28-32, 2008. IF – 4,45
Canedo P, Corso G, Pereira F, Lunet N, Suriano G, Figueiredo C, Pedrazzani C, Moreira H,
Barros H, Carneiro F, Seruca R, Roviello F, Machado JC. The interferon gamma receptor 1
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(IFNGR1) -56C/T gene polymorphism is associated with increased risk of early gastric
carcinoma. Gut 57:1504-1508, 2008. IF – 10,0
Canedo P, Durães C, Pereira F, Regalo G, Lunet N, Barros H, Carneiro F, Seruca R, Rocha J,
Machado JC. Tumour necrosis factor alpha Extended Haplotypes and Risk of Gastric
Carcinoma. Cancer Epidemiol Biomarkers Prev 2008 17:2416-2420, 2008. IF – 4,6
Capellá G, Pera G, Sala N, Agudo A, Rico F, Del Giudicce G, Plebani M, Palli D, Boeing H, Bas
Bueno-de-Mesquita H, Carneiro F, Berrino F, Vineis P, Tumino R, Panico S, Berglund G, Simán
H, Nyrén O, Hallmans G, Martinez C, Dorronsoro M, Barricarte A, Navarro C, Quirós JR, Allen N,
Key T, Bingham S, Caldas C, Linseisen J, Nagel G, Overvad K, Tjonneland A, Boshuizen HC,
Peeters PHM, NumansME, Clavel-Chapelon F, Trichopoulou A, Lund E, Jenab M, Kaaks R,
Riboli E, Gonzalez CA: DNA repair polymorphisms and the risk of stomach adenocarcinoma
and severe chronic gastritis in the EPIC-EURGAST study. Int J Epidemiol 37:1316-1325, 2008. IF
– 5,15
Carneiro F, Oliveira C, Leite M, Seruca R: Molecular targets and biological modifiers in gastric
cancer. Semin Diagn Pathol 25:274-287, 2008. IF – 1,66
Carneiro F, Oliveira C, Suriano G, Seruca R: Molecular pathology of familial gastric cancer, with
an emphasis on Hereditary Diffuse Gastric Cancer (HDGC). J Clin Pathol 61:25-30, 2008. IF – 2,4
Carneiro F; Seruca R: Editorial sobre “Importância e caracterização do carcinoma gástrico em
famílias com diagnóstico ou suspeita de síndroma de Lynch”. J Port Gastrenterol 15(2):54-55,
2008. -Cerný V, Mulligan CJ, Rídl J, Zaloudková M, Edens CM, Hájek M, Pereira L. Regional differences
in the distribution of the sub-Saharan, West Eurasian and South Asian mtDNA lineages in
Yemen. Am. J. Phys. Anthropol. 136: 128-137, 2008. IF – 2,27
Coelho M, Alves C, Coia V, Luiselli D, Useli A, Hagemeijer T, Amorim A, Destro-bisol G, Rocha
J Human Microevolution and the Atlantic Slave Trade: A Case Study from São Tomé. Current
Anthropology 49: 134-143, 2008 –
Cole LW, Sidis Y, Zhang C, Quinton R, Plummer L, Pignatelli D, Hughes VA, Dwyer AA, Raivio T,
Hayes FJ, Seminara SB, Huot C, Alos N, Speiser P, Takeshita A, Van Vliet G, Pearce S, Crowley
WF Jr, Zhou QY, Pitteloud N. Mutations in prokineticin 2 and prokineticin receptor 2 genes in
human gonadotrophin-releasing hormone deficiency: Molecular genetics and clinical
spectrum. J Clin Endocrinol &Metabol 93: 3551-3559, 2008 IF – 5,49
Costa JL, Meijer G, Ylstra B, Caldas C. Array comparative genomic hybridization copy number
profiling: a new tool for translational research in solid malignancies. Seminars in Radiation
Oncology 18: 98-104, 2008. IF – 3,78
Costa NR, Mendes N, Marcos NT, Reis CA, Caffrey T, Hollingsworth MA, Santos-Silva
F.Relevance of MUC1 mucin variable number of tandem repeats polymorphism in H pylori
adhesion to gastric epithelial cells. World J Gastroenterol 14(9):1411-4, 2008 IF – 1,77
Costa S, Pinto D, Pereira D, Rodrigues H, Cameselle-Teijeiro J, Medeiros R, Schmitt F.
Importance of TP53 codon 72 and intron 3 duplication 16bp polymorphisms in prediction of
susceptibility on breast cancer. BMC Cancer 8: 32, 2008 IF – 2,7
Costa S, Pinto D, Pereira D, Rodrigues H, Cameselle-Teijeiro J, Medeiros R, Schmitt F. XRCC1
Arg399Gln and RAD51 5’UTR G135C polymorphisms and their outcome in tumor
aggressiveness and survival of Portuguese breast cancer patients. Breast Cancer Res Treat
109: 183-185, 2008. IF – 4,45
Coutinho MF, Lacerda L, Preata MJ, Ribeiro H, Lopes L, Ferreira C, Alves S. Molecular
characterization of the Portuguese patients with mucopolysaccharidosis IIIC: two novel
mutations in the HGSNAT gene. Clin Genet 74:194-5, 2008. IF – 3,18
Crusius JBA, Canzian F, Capellá G, Penã AS, Pera G, Sala N, Agudo A, Rico F, Del Giudice G, Palli
D, Plebani M, Boeing H, Bueno-de-Mesquita HB, Carneiro F, Pala V, Save VE, Vineis P, Tumino
R, Panico S, Berglund G, Manjar J, Stenling R, Hallmans G, Martinez C, Dorronsoro M,
Barricarte A, Navarro C, Quirós JR, Allen N, Key TJ, Binghan S, Caldas C, Linseisen J, Kaak R,
Overvad K, Tjønneland A, Büchner FC, Peeters PHM, Numans ME, Clavel-Chapelon F,
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Trichopoulou A, Lund E, Jenab M, Rinaldi S, Ferrari P, Riboli E, González CA: Cytokine gene
polymorphisms and the risk of adenocarcinoma of the stomach in the European prospective
investigation into cancer and nutrition (EPIC-EURGAST). Ann Oncol 19:1894-1902, 2008. IF –
4,87
Di Palma S, Collins N, Bilous M, Sapino A, Mottolese M, Kapranos N, Schmitt F, Isola J. A
quality assurance exercise to evaluate the accuracy and reproducibility of chromogenic in situ
hybridization for HER2 analysis in breast cancer. J Clin Pathol 61: 757-760, 2008. IF – 2,4
Dufloth R, Arruda A, Heinrich JK, Schmitt F, Zeferino LC. The investigation of DNA repair
polymorphisms with histopathological characteristics and hormone receptors in a group of
Brazilian women with breast cancer. Genetics and Molecular Research 7: 574-582, 2008 -Eriksson B, Kloppel G, Krenning E, Ahlman H, Plockinger U, Wiedenmann B, Arnold R,
Auernhammer C, korner M, Rindi G, Wildi S all other Frascati Consensus Conference
participants, including Lopes JM: Consensus guidelines for the management of patients with
digestive neuroendocrine tumors- well differentiated jejuna-ileal tumor/carcinoma.
Neuroendocrinology 87: 8-19, 2008. IF – 2,29
Ferreira AC, Gomes L, Máximo V, Amil J, Carneiro F, Machado JC, Tavarela-Veloso F. Grim-19
mutations are not associated with Crohn’s Disease. Inflamm Bowel Dis 14:434-435, 2008. IF –
4,7
Ferreira AC, Isomoto H, Moriyama M, Fujioka T, Machado JC, Yamaoka Y. Helicobacter and
Gastric Malignancies. Helicobacter 13 (Suppl 1): 28-24, 2008. IF – 2,4
Gama A, Alves A, Schmitt FC. Identification of molecular phenotypes in canine mammary
carcinomas with clinical implications: application of the human classification. Virchows Arch
453: 123-132, 2008. IF – 2,0
Gama A, Alves A, Schmitt FC. Invasive micropapillary carcinoma in dog (letter). Vet Pathol 45:
600-601, 2008. IF – 1,37
Gama A, Paredes J, Gartner F, Alves A, Schmitt F. Expression of E-cadherin, P-cadherin and Bcatenin in canine malignant mammary tumours in relation to clinicopathological parameters,
proliferation and survival. The Vet Journal 177: 45-53, 2008. IF – 1,75
Goios A, Gusmão L, Rocha AM, Fonseca A, Pereira L, Bogue M, Amorim A. Identification of
mouse inbred strains through mitochondrial DNA single-nucleotide extension. Electrophoresis
29(23): 4795-4802, 2008. IF – 3,6
Goios A, Prieto L, Amorim A, Pereira L. Specificity of mtDNA-directed PCR-influence of NUclear
MTDNA insertion (NUMT) contamination in routine samples and techniques. Int J Leg Med
122: 341-5, 2008 IF – 3,0
Gomes AL, Gouveia A, Capelinha AF, Cruz D, Silva P, Reis RM, Pimenta A, Lopes JM. Molecular
alterations of c-Kit and PDGFRA in GISTs. An evaluation study of a Portuguese series. J Clin
Pathol 61:203-8, 2008. IF – 2,4
Gomes V, Sánchez-Diz P, Alves, C, Gomes I, Amorim A, Carracedo A, Gusmão L. Population
data defined by 15 autosomal STR loci in Karamoja population (Uganda) using AmpF/STR
Identifiler kit. Forensic Science International: Genetics 3: e55–e58, 2008 IF – 2,0
Gouveia AM, Pimenta AP, Capelinha AF, Cruz D, Silva P, Lopes JM: Surgical margin status and
prognosis of gastrointestinal stromal tumor. World Journal of Surgery 32:2375-2382, 2008. IF
– 1,77
Gusmão A, GusmãoL, Gomes V, Alves C, Calafell F, Amorim A, Prata MJ . A Perspective on the
History of the Iberian Gypsies Provided by Phylogeographic Analysis of Y-Chromosome
Lineages. Ann Hum Genet. 72: 215-27, 2008 IF – 2,3
Gusmão L. Genetic characterization of 52 autosomal SNPs in the Portuguese population.
Forensic Sci Int Genet Supplement Series 1(1):358-360, 2008. IF – 2,0
Horta R, Barreto F, Marques M, Rebelo M, Reis JC, Lopes JM, Amarante J: Epithelialmyoepithelial parotid carcinoma after kidney transplantation. ecancermedicalscience 82,
2008. doi: 10.3332/ecancer.2008.92.--
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Jenab M, McKay JD, Ferrari P, Biessy C, Laing S, Capella Munar GM, Sala N, Peña S, Crusius JB,
Overvad K, Jensen MK, Olsen A, Tjonneland A, Clavel-Chapelon F, Boutron-Ruault MC, Kaaks
R, Linseisen J, Boeing H, Bergmann MM, Trichopoulou A, Georgila C, Psaltopoulou T, Mattiello
A, Vineis P, Pala V, Palli D, Tumino R, Numans ME, Peeters PH, Bueno-de-Mesquita HB, Lund E,
Ardanaz E, Sánchez MJ, Dorronsoro M, Navarro Sanchez C, Quirós JR, Hallmans G, Stenling R,
Manjer J, Régner S, Key T, Bingham S, Khaw KT, Slimani N, Rinaldi S, Boffetta P, Carneiro F,
Riboli E, Gonzalez C: CDH1 gene polymorphisms, smoking, Helicobacter pylori infection and
the risk of gastric cancer in the European Prospective Investigation into Cancer and Nutrition
(EPIC-EURGAST). Eur J Cancer 44:774-780, 2008 IF – 4,45
Karam R, Carvalho J, Bruno I, Graziadio C, Senz J, Huntsman D, Carneiro F, Seruca R, Wilkinson
MF, Oliveira C: The NMD mRNA surveillance pathway downregulates aberrant E-cadherin
transcripts in gastric cancer cells and in CDH1 mutation carriers. Oncogene. 27: 4255-4260,
2008. IF – 6,4
Kocjan G, Bourgain C, Fassina A, Hagmar B, Herbert A, Kapila K, Kardum-Skelin I, KlobovesPrevodnik V, Krishnamurthy S, Koutselini H, Majak B, Olszewski W, Onal B, Pohar-Marinsek Z,
Shabalova I, Smith J, Tani E, Vielh P, Wiener H, Schenck U, Schmitt F. The role of breast FNAC
in diagnosis and clinical management: a survey of current practice. Cytopathology 19: 271-278,
2008. IF – 1,2
Labouriau R, Amorim A. Human fertility increases with marital radius. Genetics 178: 601 -603,
2008 IF – 4,56
Labouriau R, Amorim A. Comment on "An association between the kinship and fertility of
human couples" Science 322 (5908): 1634, 2008 IF – 26,37
Lima-Ramos V, Pacheco-Figueiredo L, Costa S, Pardal F, Silva A, Amorim J, Lopes JM, Reis RM.
Role of TP53 codon 72 polymorphism in susceptibility, overall survival and adjuvant therapy
response in gliomas. Cancer Genetics and Cytogenetics 180:14-19, 2008.IF – 1,55
Lima-Rodrigues M, Valle-Fernandes A, Lamas N, Cruz A, Baltazar F, Milanezi F, Nunes R, Reis
RM, Pedrosa J, Castro AG, Almeida A. A new model of laryngitis: neuropeptide,
cyclooxygenase, and cytokine profile, Laryngoscope. 118(1):78-86, 2008 . IF – 2,0
Longatto-Filho A, Duarte M, Schmitt FC. Lymphangiogenesis: from the pig embryos to cancer.
J Bras Patol Med Lab 44: 215-220, 2008.-Longatto-Filho A, Pinheiro C, Ferreira L, Scapulatempo C, Alves VA, Baltazar F, Schmitt F.
Peritumoural, but not intratumoural, lymphatic vessel density and invasion correlate with
colorectal carcinoma poor-outcome markers. Virchows Arch 452: 133-138, 2008. IF – 2,0
Lunet N, Bastos J, Cumaio F, Silva P, Dias E, Barros H. Recall of drug utilization depends on
subtle structural questionnaire characteristics. Pharmacy world & science : PWS 30: 175-81,
2008 IF – 0,76
Macedo FYB, Baltazar F, Almeida PR, Távora F, Ferreira FV, Schmitt FC, Brito GA, Ribeiro R.
Cyclooxygenase-2 expression on ifosfamide-induced hemorrhagic cystitis in rats. J Cancer Res
Clin Oncol 134: 19-27, 2008. IF – 2,36
Macedo FYB, Baltazar F, Mourão LC, Almeida PR, Mota JM, Schmitt FC, Ribeiro RA. Induction
of COX-2 expression by acrolein in the rat model of hemorrhagic cystitis. Exp Toxicol Pathol
59: 425-430, 2008. IF – 1,3
Maia CJ, Santos CR, Schmitt F, Socorro S. Regucalcin is expressed in rat mammary gland and
prostate and down-regulate by 17B-estradiol. Mol Cell Biochem 311: 81-86, 2008. IF – 1,7
Maia CJ, Socorro S, Schmitt F, Santos CR. STEAP1 is over-expressed in breast cancer and
down-regulated by 17B-estradiol in MCF-7 cells and in the rat mammary gland. Endocrine 34(13):108-16, 2008. IF – 2,57
Maia CJB, Socorro S, Schmitt F, Santos CRA. Characterization of oligoadenylate synthetase-1
expression in rat mammary gland and prostate: effects of 17-estradiol on the regulation of
OAS1g in both tissues. Mol Cell Biochem 314: 113-121, 2008. IF – 1,76
Mangas M, Nogueira C, Prata MJ, Lacerda L, Coll MJ, Soares G, Ribeiro G, Amaral O, Ferreira C,
Alves C, Coutinho F, Alves S. Molecular analysis of mucopolysaccharidosis type IIIB in
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65.
66.
67.
68.
69.
70.
71.
72.
73.
74.
75.
76.
Portugal: evidence of a single origin for a common mutation (p.R234C) in the Iberian
Peninsula. Clin Genet 73:251-6, 2008 IF – 3,18
Marchio C, Iravani M, Natrajan R, Lambros MB, Savage K, Tamber N, Fenwick K, Mackay A,
Senetta R, Di Palma S, Schmitt FC, Bussolati G, Ellis IO, Ashworth A, Sapino A, Reis-Filho JS.
Genomic and immunophenotypical characterization of pure micropapillary carcinomas of the
breast. J Pathol 215: 398-410, 2008. IF – 5,4
Marcos NT, Magalhães A, Ferreira B, Oliveira MJ, Carvalho AS, Mendes N, Gilmartin T, Head
SR, Figueiredo C, David L, Santos-Silva F, and Reis CA: Helicobacter pylori induces b3GnT5 in
human gastric cell lines, modulating expression of the SabA adhesin ligand sialyl-Lewis x. J Clin
Invest 118: 2325-2336, 2008. IF – 2,88
Marques M, Magro F, Cardoso H, Carneiro F, Portugal R, Lopes J, Costa Santos C: Infliximabinduced lupus-like syndrome associated with autoimmune hepatitis. Inflamm Bowel Dis
14:723-725, 2008. 5- Ferreira AC, Gomes L, Máximo V, Amil J, Carneiro F, Machado JC, TavarelaVeloso F: GRIM-19 mutations are not associated with Crohn's disease. Inflamm Bowel Dis
14:434-435, 2008. IF – 4,7
Martinho O, Gonçalves A, Moreira MA, Ribeiro LFJ, Queiroz GS, Schmitt FC, Reis RM,
Longatto-Filho A. KIT activation in uterine cervix adenosquamous carcinomas by KIT/SCF
autocrine/paracrine stimulation loops. Gynecol Oncol 111: 350-355, 2008.IF – 2,6
Martins P, Schmitt F, Almeida H, Frazao JM. Evaluation of parathyroid gland angiogenesis in
chronic kidney disease associated with secondary hyperparathyroidism. Nephrol Dial
Transplant 23(9):2889-94, 2008 IF – 3,16
Martins S, Coutinho P, Silveira I, Giunti P, Jardim LB, Calafell F, Sequeiros J, Amorim A. Cisacting factors promoting the CAG intergenerational instability in Machado-Joseph disease.
Am J Med Genet B Neuropsychiatr Genet 147B: 439-46, 2008 IF – 4,2
Matos P, Oliveira C, Velho S, Gonçalves V, da Costa LT, Moyer MP, Seruca R, Jordan P. BRaf(V600E) cooperates with alternative spliced Rac1b to sustain colorectal cancer cell
survival. Gastroenterology 135(3):899-906, 2008 IF – 11,67
Máximo V, Lima J, Soares P, Silva A, Bento I, Sobrinho-Simões M. GRIM-19 in Health and
Disease. Adv Anat Pathol 15:46-53, 2008. IF – 3,0
Milanezi F, Carvalho S, Schmitt FC. EGFR/HER2 in breast cancer: a biological approach for
molecular diagnosis and therapy. Expert Rev Mol Diagn 8: 417-434, 2008. IF – 3, 1
Morais P, Magina S, Ribeiro MC, Rodrigues M, Lopes JM, Thanh HT, Wehnert M, Guimarães H:
Dermatopatia restritiva – relato de um caso e breve revisão da literatura. Trabalhos da
Sociedade Portuguesa de Dermatologia e Venereologia 66: 619-628, 2008.-Moutinho C, Mateus A R, Milanezi F, Carneiro F, Seruca R, Suriano G: EGFR structural
alterations in gastric cancer. BMC Cancer 8: 10, 2008 IF – 2,7
Paredes J, Correia AL, Ribeiro AS, Milanezi F, Cameselle-Teijeiro J, Schmitt FC. Breast
carcinomas that co-express E- and P-cadherin are associated with p120-catenin cytoplasmic
localisation and poor patient survival. J Clin Pathol 61: 856-862, 2008.IF – 2,4
Pereira F, Carneiro J, Amorim A.. Identification of Species with DNA-Based Technology:
Current Progress and Challenges. Recent Pat DNA Gene Seq. 2(3):187-200, 2008 -Pereira F, Carneiro J, Soares P, Maciel S, Nejmeddine F, Lenstra JA, Gusmão L, Amorim A.. A
multiplex primer extension assay for the rapid identification of paternal lineages in domestic
goat (Capra hircus): Laying the foundations for a detailed caprine Y chromosome phylogeny.
Mol Phylogenet Evol. 49(2): 663-8, 2008 -Pereira F, Soares P, Carneiro J, Pereira L, Richards MB, Samuels DC, Amorim A.Evidence for
variable selective pressures at a large secondary structure of the human mitochondrial DNA
control region. Mol Biol Evol 25(12): 2759-70, 2008. IF – 6,4
Pereira L, Gonçalves J, Bandelt H-J. Mutation ‘C11994T’ in the mitochondrial ND4 gene is not
a cause of low sperm motility in Portugal. Fertil Steril 89: 738-741, 2008. IF – 3,16
104
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80.
81.
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83.
84.
85.
86.
87.
88.
89.
90.
Pereira R, Fondevila M, Phillips C, Amorim A, Carracedo A, Gusmão L
Genetic
characterization of 52 autosomal SNPs in two sub-Saharan African populations. Forensic Sci
Int Genet Supplement Series 1:361-363, 2008 IF – 2,0
Pico A, Castillo A, Vargas C, Amorim A, Gusmão L Genetic profile characterization and
segregation analysis of 10 X-STRs in a sample from Santander, Colombia. Int J Legal Med. 122:
347–351, 2008 IF – 3,0
Pinheiro C, Longatto-Filho A, Scapulatempo C, Ferreira L, Martins S, Pellerin L, Rodrigues M,
Alves VA, Schmitt F, Baltazar F. Increased expression of monocarboxylate transporters 1, 2
and 4 in colorectal carcinomas. Virchows Arch 452: 139-146, 2008. IF – 2,0
Pinto M, Wu Y, Mensink RG, Cirnes L, Seruca R, Hofstra RM. Somatic mutations in mismatch
repair genes in sporadic gastric carcinomas are not a cause but a consequence of the mutator
phenotype. Cancer Genet Cytogenet. 180: 110-4, 2008 IF – 1,55
Plockinger U, Couvelard A, Falconi M, Sundin A, Salazar R, Christ E, Herder WW, Gross D,
Knapp WH, Knigge UP, Kulke MH, Pape UF all other Frascati Consensus Conference
participants, including Lopes JM: Consensus guidelines for the management of patients with
digestive neuroendocrine tumors- well differentiated appendix and goblet cell carcinoma.
Neuroendocrinology 87: 20-30, 2008. . IF – 2,29
Prazeres HJ, Rodrigues F, Soares P, Naidenov P, Figueiredo P, Campos B, Lacerda M, Martins
TC. Loss of heterozygosity at 19p13.2 and 2q21 in tumours from familial clusters of nonmedullary thyroid carcinoma. Fam Cancer 7:141-149, 2008 IF – 2,2
Preto A, Figueiredo J, Velho S, Ribeiro A, Soares P, Oliveira C, Seruca R. BRAF provides
proliferation and survival signals in MSI colorectal carcinoma cells displaying BRAF(V600E) but
not KRAS mutations. J Pathol. 214:320-327, 2008. IF – 5,4
Prieto L, Alonso A, Alves C, Crespillo M, Montesino M, Picornell A, Brehm A, Ramírez JL,
Whittle MR, Anjos MJ, Boschi I, Buj J, Cerezo M, Cardoso S, Cicarelli R, Comas D, Corach D,
Doutremepuich C, Espinheira RM, Fernández-Fernández I, Filippini S, Garcia-Hirschfeld J,
González A, Heinrichs B, Hernández A, Leite FP, Lizarazo RP, López-Parra AM, López-Soto M,
Lorente JA, Mechoso B, Navarro I, Pagano S, Pestano JJ, Puente J, Raimondi E, RodríguezQuesada A, Terra-Pinheiro MF, Vidal-Rioja L, Vullo C, Salas A. 2006 GEP-ISFG collaborative
exercise on mtDNA: reflections about interpretation, artefacts, and DNA mixtures. Forensic
Sci Int Genet 2(2):126-33, 2008 IF – 2,0
Quental S, Macedo-Ribeiro S, Matos R, Vilarinho L, Martins E, Teles EL, Rodrigues E, Diogo L,
Garcia P, Eusébio F, Gaspar A, Sequeira S, Furtado F, Lança I, Amorim A, Prata MJ. Molecular
and structural analyses of maple syrup urine disease and identification of a founder mutation
in a Portuguese Gypsy community. Mol Genet Metab. 94(2):148-56, 2008. IF – 2,55
Ramage J, Goretzki PE, Manfredi R, Komminoth P, Ferone D, Hyrdel R, Kaltsas G, Kelestimur F,
Kvols L, Scoazec JY, Garcia MIS, Caplin ME, all other Frascati Consensus Conference
participants, including Lopes JM: Consensus guidelines for the management of patients with
digestive neuroendocrine tumors- well differentiated colon and rectum tumor/carcinoma.
Neuroendocrinology 87: 31-39, 2008. IF – 2,29
Rocha AS, Paternot S, Coulonval K, Dumont JE, Soares P, Roger PP.Cyclic AMP inhibits the
proliferation of thyroid carcinoma cell lines through regulation of CDK4 phosphorylation. Mol
Biol Cell.19:4814-4825, 2008. IF – 6,4
Rodrigues M, Vitó I, Santos R, Paiva J, Pontes P, Silva P, Carneiro F: Establishment of a Tumour
Bank: The experience of the Department of Pathology of Hospital S.João (Porto, Portugal).
Cell and Tissue Bank 2008 Jul 2. -Saleiro S, Barbosa M, Souto Moura C, Almeida J, Ferreira S: Epithelioid
hemangioendothelioma – a rare pulmonary tumour. Revista Portuguesa de Pneumologia
14:421-425, 2008 -Sánchez-Diz P, Alves C, Carvalho E, Carvalho M, Espinheira R, García O, Pinheiro MF, Pontes L,
Porto MJ, Santapa O, Silva C, Sumita D, Valente S, Whittle M, Yurrebaso I, Carracedo A,
Amorim A, Gusmão L; GEP-ISFG (The Spanish and Portuguese Working Group of the
105
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104.
105.
106.
International Society for Forensic Genetics). Population and segregation data on 17 Y-STRs:
results of a GEP-ISFG collaborative study. Int J Legal Med. 122(6):529-33, 2008. IF – 3,0
Saraiva AL, Gärtner F, Pires MA. Expression of p63 normal canine skin and primary cutaneous
glandular carcinomas. Veterinary journal 177: 136-40, 2008 IF – 1,75
Saranga S, Prista A, Nhatumbo L, Beunen G, Rocha J, Blangero S, Maia J. Heritabilities of
somatotype components in a population from rural Mozambique. Am J Hum Biol 20: 642-646,
2008. IF – 1,8
Schmitt FC, Longatto-Filho A, Valent A, Vielh P. Molecular techniques in cytopathology
practice. J Clin Pathol 61:258-267, 2008. IF – 2,4
Silva F, Carvalho S, Milanezi F, Schmitt FC. Carcinoma da mama de tipo basal. Acta Med Port
21: 387-392, 2008.-Simões-Correia J, Figueiredo J, Oliveira C, van Hengel J, Seruca R, van Roy F, Suriano G.
Endoplasmic reticulum quality control: a new mechanism of E-cadherin regulation and its
implication in cancer. Hum Mol Genet. 17(22):3566-76, 2008 IF – 7,8
Simpson PT, Reis-Filho JS, Lambros MBK, Jones C, Steele D, Mackay A, Iravani M, Fenwick K,
Dexter T, Jones A, Reid L, Da Silva L, Shin SJ, Hardisson D, Ashworth A, Schmitt FC, Palacios J,
Lakhani SR. Molecular profiling pleomorphic lobular carcinomas of the breast: evidence for a
common molecular genetic pathway with classic lobular carcinomas. J Pathol 215: 231-244,
2008. IF – 5,4
Soares H, Maia A, Campos M, Dória S, Lopes JM, Fontoura M: Clinicopathological features of
45,X/46,Xidic(Y) mosaicism and therapeutic implications:case report. São Paulo Medical
Journal 126: 297-299, 2008.-Soares-Vieira JÁ, Billerbeck AEC, Iwamura ESM, Mendonça BB, Gusmão L, Otto P . Population
and mutation analysis of Y-STR loci in a sample from the city of São Paulo (Brazil). Genet Mol
Biol 31:651-656, 2008. IF – 0,48
Sobrinho-Simões M, Máximo V, Rocha AS, Trovisco V, Castro P, Preto A, Lima J, Soares P.
Intragenic mutations in thyroid cancer. Endocrinol Metab Clin North Am 37:333-362, 2008 IF –
2,1
Steinmuller T, Kianmanesh R, Falconi M, Scarpa A, Taal B, Kwekkeboom DJ, Lopes JM, Perren
A, Nikou G, Yao J, Delle Fave GF, O'Toole D: Consensus guidelines for the management of
patients with liver metastases from digestive (neuro)endocrine tumors: Foregut, Midgut,
Hindgut, and Unknown Primary. Neuroendocrinology 87:47-62, 2008. IF – 2,29
Timonera E, Eloy C, Paiva ME, Lopes JM, Asa S, van der Kwast: Composite adenomatoid tumor
and myelolipoma of adrenal gland: report of two cases. Archives of Pathology and Laboratory
Medicine 132:265-267, 2008. IF – 1,8
Toscanini U, Gusmão L, Berardi G, Amorim A, Carracedo A, Salas A, Raimondi E. Y
chromosome microsatellite genetic variation in two Native American populations from
Argentina: Population stratification and mutation data. Forensic Sci Int Genet. 2(4):274-280,
2008. IF – 2,0
Trindade E, Pissarra S, Carneiro F, Amil Dias J: Esofagite eosinofílica: causa de disfagia
persistente. ENDOnews 22:11-12, 2008.-Trovisco V, Couto JP, Cameselle-Teijeiro J, de Castro IV, Fonseca E, Soares P, Sobrinho-Simões
M. Acquisition of BRAF gene mutations is not a requirement for nodal metastasis of papillary
thyroid carcinoma. Clin Endocrinol (Oxf). 69:683-685, 2008. IF – 3,37
Valbuena C, Carvalho E, Bustorff M, Ganhão M, Relvas S, Nogueira R, Carneiro F, Oliveira JP:
Kidney biopsy findings in heterozygous Fabry disease females with early nephropathy.
Virchows Arch 453: 329-338, 2008. IF – 2,0
van Krieken JH, Jung A, Kirchner T, Carneiro F, Seruca R, Bosman FT, Quirke P, Fléjou JF, Plato
Hansen T, de Hertogh G, Jares P, Langner C, Hoefler G, Ligtenberg M, Tiniakos D, Tejpar S,
Bevilacqua G, Ensari A: KRAS mutation testing for predicting response to anti-EGFR therapy
for colorectal carcinoma: proposal for a European quality assurance program. Virchows Arch
453:417-431, 2008. IF – 2,0
106
107. Velho S, Moutinho C, Cirnes L, Albuquerque C, Hamelin R, Schmitt F, Carneiro F, Oliveira C,
Seruca R. BRAF, KRAS and PI3KCA mutations in colorectal serrated polyps and cancer: primary
or secondary genetic events in colorectal carcinogenesis ? BMC Cancer 8: 255, 2008 IF – 2,7
108. Viana-Pereira M, Lopes JM, Little S, Milanezi F, Basto D, Pardal F, Jones C, Reis RM: Analysis of
EGFR overexpression, EGFR gene amplification and the EGFRvIII mutation in Portuguese highgrade gliomas. Anticancer Research 28:913-920, 2008. IF – 1,4
109. Vieira DS, Dufloth RM, Schmitt FC, Zeferino LC. Carcinoma de mama: novos conceitos na
classificação. Rev Bras Ginecol Obstet 30: 42-47, 2008. -110. Woo MM, Salamanca CM, Miller M, Symowicz J, Leung PC, Oliveira C, Ehlen TG, Gilks CB,
Huntsman D, Auersperg N. Serous borderline ovarian tumors in long-term culture: phenotypic
and genotypic distinction from invasive ovarian carcinomas. Int J Gynecol Cancer 18(6):123447, 2008 IF – 1,4
107
REVISTAS CIENTÍFICAS
INTERNACIONAIS
COM MEMBROS DO
IPATIMUP
NOS SEUS EDITORIAL
BOARDS
Acta Cytologica (SCI PRINTERS & PUBL INC)
Advances in Anatomic Pathology (LIPPINCOTT WILLIAMS & WILKINS)
Advances in Clinical and Experimental Medicine (AKADEMIA MEDYCZNA
WE WROCŁAWIU)
Archives of Pathology and Laboratory Medicine (COLLEGE OF
AMERICAN PATHOLOGISTS)
Breast Cancer Research (BIOMED CENTRAL LTD)
Cancer Genetics and Cytogenetics (ELSEVIER SCI IRELAND LTD)
Critical Review in Oncogenesis (BEGELL HOUSE, USA)
Current Diagnostic Pathology (CHURCHILL LIVINGSTONE)
Cytojournal (BIOMED CENTRAL)
Cytopathology (BLACKWELL PUBLISHING LTD)
Diagnostic Cytopathology (WILEY-LISS)
Endocrine Pathology (BLACKWELL PUBLISHING LTD)
European Journal of Cancer Prevention (LIPPINCOTT WILLIAMS &
WILKINS)
Forensic Science International (ELSEVIER SCI IRELAND LTD)
Gut Pathogens (BIOMED CENTRAL)
Helicobacter (BLACKWELL PUBLISHING LTD)
Hereditary Cancer in Clinical Practice (UICC GLOBAL CANCER CONTROL)
Histopathology (BLACKWELL PUBLISHING LTD)
Human Biology (WAYNE STATE UNIVERSITY PRESS)
International Journal of Surgical Pathology (WESTMINSTER PUBL INC)
Journal of Cellular and Molecular Medicine (CAROL DAVILA UNIV PRESS)
Journal of Pathology (JON WILEY & SONS LTD)
The Open Pathology Journal (BENTHAM OPEN)
Pathology Research & Practice (URBAN & FISCHER VERLAG)
Seminars in Diagnostic Pathology (W B SAUNDERS CO)
Ultrastructural Pathology (TAYLOR & FRANCIS INC)
Virchows Archiv (SPRINGER)
108
NÚCLEO DE AMIGOS
DO
IPATIMUP
Amorim Inv. e Participações
Astrazeneca Produtos Farmacêuticos Lda
Banco BPI, SA
Bayer Portugal, SA
BES
Bial - Portela & C.ª, SA
Fundação Millennium BCP
GlaxoSmithKline Prod. Farmacêuticos, Lda
Merck Sharp & Dohme, Lda.
Mota Engil, SGPS, SA
Novartis Farma - Prod. Farmacêuticos, SA
SAG GEST - Soluções Automóvel Globais, SA
Sanofi-Aventis
Sonae SGPS, SA
Unicer
109
ANEXOS
110
111
112
Porto Cancer Meeting
XVII Edition
“100th Reunión de la Territorial del Noroeste de la Península
Ibérica”
Pathology of the digestive system
April 11-13, 2008
Will be held at IPATIMUP, from 11th to 13th April 2008.
PROGRAMME
Friday, 11th April
09:00 Registration
10:15 Welcome Session
10:30 Case presentations* (maximum number-15).
13:00 Lunch
14:00 Case presentations* (maximum number-15).
16:30 Coffee break
Slide Seminar *
Paula Chaves (Institute of Oncology, Lisbon, Portugal)
Afonso Fernandes (Medical Faculty & H.Sta Maria, Lisbon,
Portugal)
Isabel Fonseca (Institute of Oncology & Medical Faculty,
Lisbon, Portugal)
17:00
Gregory Lauwers (Harvard Medical School & Massachusetts
General Hospital, Boston, USA)
Elizabeth Montgomery (Johns Hopkins University,
Baltimore, USA)
Lawrence Bugart (Abbott Northwest Hospital, Minneapolis,
USA)
18:30 Closing
21:00 Meeting Dinner
Saturday, 12th April
Barrett’s adenocarcinoma.
09:00 Elizabeth Montgomery (Johns Hopkins University,
Baltimore, USA)
Differentiation markers in gastric carcinogenesis with
09:45 emphasis on mucin and mucin glycosylation.
Leonor David (IPATIMUP & Medical Faculty, Porto, Portugal)
Gastric dysplasia and gastric polyps.
10:30 Gregory Lauwers (Harvard Medical School & Massachusetts
General Hospital, Boston, USA)
11:15 Coffee break
Molecular pathology of gastric cancer.
11:45 Fátima Carneiro (IPATIMUP & Medical Faculty/H.S.João,
Porto, Portugal)
12:30
Refractory sprue and cryptic T cell lymphoma.
Marie Robert (Yale University, New Haven, USA)
13:15 Lunch
113
14:15
Dysplasia and cancer in inflammatory bowel disease.
Joel Greenson (University of Michigan, Ann Arbor, USA)
KRAS and BRAF oncogenic mutations in MSS colorectal
carcinoma progression.
15:00
Raquel Seruca (IPATIMUP & Medical Faculty, Porto,
Portugal)
Tumor budding and methylation/MSI in colorectal cancer.
15:45 Lawrence Burgart (Abbott Northwest Hospital, Minneapolis,
USA)
16:30 Coffee break
17:00
Pancreatic neuroendocrine tumours.
Audrey Lazenby (University of Nebraska, Lincoln, USA)
Pancreatic cystic tumours.
17:45 Gregory Lauwers (Harvard Medical School & Massachusetts
General Hospital, Boston, USA)
EUS FNA of pancreato-biliary tract.
18:30 David Lewin (Medical University of South Carolina,
Charleston, USA)
Sunday, 13th April
Gastrointestinal stromal tumours (GIST) and their
09:00 mimickers.
Joel Greenson (University of Michigan, Ann Arbor, USA)
09:45
Allograft rejection in liver transplantation.
Augusta Cipriano (University Hospital, Coimbra, Portugal)
10:30
Early hepatocellular carcinoma and its precursors.
John Hart (University of Chicago, Chicago, USA)
11:15 Coffee break
Slide Seminar *
Maria José Brito (Hospital Garcia de Orta, Almada, Portugal)
Marie Robert (Yale University, New Haven, USA)
Joel Greenson (University of Michigan, Ann Arbor, USA)
11:45
John Hart (University of Chicago, Chicago, USA)
Audrey Lazenby (University of Nebraska, Lincoln, USA)
David Lewin (Medical University of South Carolina,
Charleston, USA)
13:15 Adjourn
* The clinical histories and the representative images of the cases to be
presented in the first day (Sessions of Case Presentations, also devoted
to Pathology of the Digestive System), should be sent to the Secretariat
(e-mail: [email protected]) before March 21, 2008. These cases as
well as those of the two Slide Seminars will be available online (sites of
the Portuguese Society of Pathology and Portuguese Society of
Cytology.
Supported by GABBA Program, FCT, FLAD, Porto City Hall and
Novartis Oncology
114
Portugaliæ Genetica
11th edition
27-28 March 2008
PROGRAMME
Thursday, 27
09:00Registration
The origins of genome complexity. (Michael Lynch, Indiana
09:30
University Bloomington)
11:00Coffee break
11:30 Inbred mice as an evolutionary model. (Ana Goios, IPATIMUP)
New insights from the natural mutant mouse leaner. (Isabel Alonso,
12:00
IBMC)
MtDNA and Y-STRs heterogeneity in chimpanzee subspecies.
12:30
(Leonor Gusmão, IPATIMUP)
13:00Lunch break
Comparative genomics for the study of development, evolution and
15:00
genetic diseases. (José L. Gómez-Skarmeta, Pablo de Olavide Uni.)
16:00 X&Y, a long lasting genomic affair. (Alexandra Lopes, IPATIMUP)
Detecting natural selection on the human genome: the case of
16:30
innate immunity. (Luís Barreiro, Institut Pasteur)
17:00Coffee break
17:30Poster session
Friday, 28
Macroevolutionary implications of compensatory pathogenic
09:30
deviations. (Fyodor Kondrashov, University of California)
11:00Coffee break
A comparative approach to the evolution of mitochondrial DNA.
11:30
(Filipe Pereira, IPATIMUP)
The genetic basis of adaptation to new environments in sexually
12:00
reproducing species. (Henrique Teotónio, IGC)
12:30 Protein evolution of homeobox genes. (Jorge Vieira, IBMC)
13:00Lunch break
Regulatory variation and evolution in humans. (Manolis
15:00
Dermitzakis, Sanger Center)
An outsider’s view of comparative genomics. (Luís Costa,
16:00
IPATIMUP)
16:45Coffee break
17:30 Applied Biosystems
18:00Close session
115
XII EQUINOX CONFERENCE
XII CONFERÊNCIA DO EQUINÓCIO
20 de Outubro de 2008
IMPACTO SOCIAL DAS EPIDEMIAS / ENDEMIAS
COORDENAÇÃO: José Pacheco Pereira
10h00
Jorge Torgal
11h00
Intervalo
11h30
Manuel Villaverde Cabral
13h00
Almoço de trabalho
14h00
José Pacheco Pereira
116