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INDEX
INTRODUCTION
SCIENTIFIC OBJECTIVES
EDUCATIONAL OBJECTIVES
SERVICE-ORIENTED OBJECTIVES
INTERNAL SERVICES AND RESOURCES
EXTERNAL SERVICES AND RESOURCES
NETWORKING ACTIONS
TRAINING ACTIVITIES
PHD (DOCTORAL) PROGRAMS
ORGANIZATION OF INTERNATIONAL EVENTS
SUMMARY OF INTERNAL EVALUATIONS
SCIENTIFIC RESEARCH (RESEARCH GROUPS)
CANCER BIOLOGY
CANCER GENETICS
CARCINOGENESIS
TUMOUR MOLECULAR MODELS
POPULATION GENETICS
GENETIC DIVERSITY
GENETICS, EVOLUTION AND PATHOLOGY
SCIENCE DIFFUSION
IPATIMUP DIAGNOSTICS
INTERNAL SERVICES
RECENT PhDs
RESEARCH PROJECTS
SCIENTIFIC PAPERS
MEMBERS OF IPATIMUP AT EDITORIAL BOARDS
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RELATÓRIO DE ACTIVIDADES DE 2010
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INTRODUÇÃO AO RELATÓRIO DE ACTIVIDADES
O ano de 2010 foi marcado por dois acontecimentos majores do processo para criação da Unidade
Orgânica de Investigação da (Fundação) Universidade do Porto, o Instituto de Investigação e
Inovação em Saúde (I3S):
- a apresentação formal da proposta conjunta com o IBMC e o INEB, à Universidade do Porto, para
criação da Unidade Orgânica
- a aprovação da candidatura, promovida pela Universidade do Porto, de “Instalação do instituto de
Investigação e Inovação em Saúde (I3S)”, no âmbito do Concurso “Sistema de Apoio a Infraestruturas Científicas e Tecnológicas – Infra-estruturas Científicas - SAIECT – IEC /2/2010”, Eixo
Prioritário I “Competitividade, Inovação e Conhecimento” do Programa Operacional Regional do
Norte 2007-2013.
O IPATIMUP manteve uma estreita colaboração com o Health Cluster Portugal (HCP) – Pólo de
Competitividade em Saúde, quer isoladamente, quer em articulação com o IPO-Porto (Consórcio
IPATIMUP – IPO) e o Hospital S. João (Protocolo de colaboração).
O IPATIMUP integrou a lista de promotores de um projecto de larga escala a financiar pela Agência
de inovação no âmbito do Sistema de Incentivos à Investigação e Desenvolvimento Tecnológico.
Este projecto tem como objectivo a mobilização de capacidades e competências científicas e
tecnológicas de um vasto conjunto de organizações – empresas, entidades do sistema científico e
tecnológico, e unidades prestadoras de cuidados de saúde – as quais, através do estabelecimento de
parcerias sólidas e funcionais, promoverão a criação de conhecimento e a sua efectiva transferência
e valorização. São promotores, para além do IPATIMUP, Participam como promotores, para além do
IPATIMUP, o IPO-Porto, o Hospital de São João, a Faculdade de Medicina da Universidade de
Coimbra, as Universidades de Aveiro e do Minho, o IMM, o AIBILI, o BIOCANT, os Hospitais da
Universidade de Coimbra, E.P.E., a Critical Health, S.A., a Siemens, S.A., a BIAL, entre outros.
Em 2010, o IPATIMUP realizou a avaliação intercalar de 8 dos 13 Doutorados Contratados no âmbito
do Programa Ciência – Programa de Contratação de Doutorados para o Sistema Científico e
Tecnológico Nacional (Fundação para a Ciência e Tecnologia),
Conforme se poderá ver no relatório relativo à Prestação de Serviços, em 2010 arrancou o IPATIMUP
Diagnósticos, que resultou da fusão das três Unidades de Prestação de Serviços de diagnóstico
existentes em 2009.
O aumento da infra-estrutura material e do número de pessoal contratado e outros colaboradores
tem colocado desafios constantes à organização. O desenvolvimento do Sistema de Informação do
IPATIMUP tem introduzido melhorias significativas nas áreas de gestão de projectos, gestão de
pessoal e gestão de compras. Em 2010, a consolidação das funções de Supervisão Técnica da
Actividade Científica teve efeitos imediatos na gestão de equipamentos e serviços comuns de apoio
à actividade de investigação.
O IPATIMUP iniciou em 2010 um projecto financiado pelo Programa Operacional Regional do Norte,
no âmbito do concurso “Sistema de Apoio a Infra-estruturas Científicas e Tecnológicas – Infraestruturas Científicas - SAIECT – IEC /2/2010”. O projecto – Modelos de Sistemas de Gestão do Risco
na Investigação em Ciências da Vida e da Saúde – visa criar um Sistema de Informação para a Gestão
de Risco que garanta o funcionamento normal, seguro e eficiente de todos os recursos
habitualmente presentes em ambientes laboratoriais de investigação científica em Ciências da Vida e
da Saúde.
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Em Janeiro de 2010, o IPATIMUP acolheu o grupo de NEW Therapies do INEB num dos seus
labotatórios de investigação (com uma área total de 50m2) estimulando deste modo a colaboração
inter-institucional e multidisciplinar, nomeadamente entre o Cancro e a Medicina Regenerativa.
Para além desta iniciativa, o IPATIMUP participu com o INEB como co-promotor no âmbito do
concurso “Sistema de Apoio a Infra-estruturas Científicas e Tecnológicas – Infra-estruturas” para
criar um centro de Bioimagem que sirva o I3S bem como outras instituições ligadas ao sistema de
saúde.
Destacamos ainda o facto de o IPATIMUP ter sido notificado do valor total de financiamento para
2010 relativo ao Financiamento Plurianual/Laboratório Associado da Fundação para a Ciência e a
Tecnologia, através de um email enviado pela FCT em 8 de Fevereiro de 2011, informando que “De
acordo com a disponibilidade orçamental da FCT, o montante aprovado para o financiamento de
2010 foi de 1.227.917,11 Euros, garantindo-se assim que o valor total transferido em 2010 e início de
2011 seja sensivelmente igual ao montante aprovado para 2009.” A FCT tem vindo a calcular este
valor com base no valor de 2005. Em 2010, o IPATIMUP tem o dobro de pessoal contratado e o dobro
de área útil disponível (a obra de ampliação do edifício do IPATIMUP terminou em 2005), em relação
ao que havia tido em 2005.
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Science Outcome
We will highlight here three results related to IPATIMUP scientific publications.
In 2010 researchers from IPATIMUP were authors or co-authored
co
152 scientific papers published
publishe in
international journals, 120 with Impact Factor (IF) ≥ 1. Half (n=64)) of the articles with IF were
published in journals with IF ≥ 3 and about 10% (n=13)
(n=13 in journals with IF ≥ 6. For details see list of
papers.
Papers produced
produc according impact Factor class
In 2010, many of the articles published by researchers IPATIMUP continued to be extensively cited.
Thanks to this effect, the IPATIMUP continued membership in 2010, the group of "most cited
institutions” of the ISI-Web of Knowledge. As shown in the table below IPATIMUP keeps,
keeps for over a
decade, a great number of citations, one of the few Portuguese institutions for research in medicine
and biomedicine to integrate this group of "most cited institutions ".
MOST CITED INSTITUTIONS IN ALL FIELDS
Institution: IPATIMUP
Citation Data (In 5-year Intervals):
5-year Intervals:
2000-2004
2001-2005
2002-2006
2003-2007
2004-2008
2005
2005-2009
2006-2010
# of Papers
47
49
60
52
56
58
53
Times Cited
386
565
525
506
437
515
604
Citations per Paper
8.21
11.53
8.75
9.73
7.80
8.88
11.40
MOST CITED INSTITUTIONS IN CLINICAL MEDICINE
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Institution: IPATIMUP
Citation Data (In 5-year Intervals):
5-year Intervals:
2000-2004
2001-2005
2002-2006
2003-2007
2004-2008
2005-2009
2006-2010
# of Papers
38
42
45
37
41
38
32
Times Cited
365
554
494
432
346
352
421
Citations per Paper
9.60
13.19
10.97
11.67
8.43
9.26
13.16
For the first time, in 2010, IPATIMUP publications and citations were internationally ranked using the
SciVal Spotlight system, a product distributed by Elsevier to the Virtual Library of the University of
Porto. Spotlight is a tool to evaluate the performance of scientific institutions in order to help them
to define research strategies. This tool uses the method of analysis of co-citations to create clusters
of articles (published in five years) and, for a given institution, identifies their skills and compares
them with "market" at the global, regional and national level. Further, it compares institutions for
each skill. IPATIMUP, through the University of Porto, was ranked as Top institution in gastric cancer
and Helicobacter pylori (competency #3) and thyroid carcinoma (competency #6) at global level. See
tables of comparison below.
Legends of the next two spotlight reports.
The columns mean
Fractionalized articles: this is how many articles from the institution (2004-2008) fall within this competency.
These values are fractionalized, meaning that only the fraction of each article that falls within the competency is
counted. Example: if 0.8 of an article falls within this competency, and the remaining 0.2 falls within another
competency, only 0.8 is added to this total.
Total articles: this is how many articles from the institution (2004-2008) fall within this competency. These
values are not fractionalized, meaning that each article counts as 1, even if only a fraction of that article falls
within this competency.
Relative Reference Share (RRS): number of frequently cited articles from the institution, relative to the
institution ranked #1 in this competency. If the institution is ranked #1, the value is compared to the institution
ranked #2 in this competency.
State of the Art (SotA): The recency of the work cited by the institution's articles within this competency,
relative to the average recency for the competency. Positive values indicate the work being cited is more recent
than average.
Citation count: this is the number of times the institution's articles within this competency have been cited. In
other words, this is the total number of citations of the articles from the institution (published in 2004-2008)
that fall within this competency.
Frequently cited articles: the 'highly cited' reference articles used in the model are those that have been most
highly cited during the map year. Older reference articles (those 3 years old or more) need to meet a higher
threshold to be called highly cited than do more recent reference articles. Articles can also not be cited too
many times (over 100 times), to prevent over aggregation in the algorithm around those articles. To meet the
highly cited criteria, an article must thus be:
o Cited fewer than 100 times
o If over 3 years old, cited 5 or more times
o If between 3 and 1 years old, cited the age+1 times
o If 0 years old, cited 3 or more times
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INTRODUCTION
MISSION STATEMET
1. To be a leading health science research institution through internationally competitive science on
molecular pathology and molecular and population genetics.
2. To serve society through science by directing discoveries to the improvement of cancer prevention
and management of cancer patients, and through communicating the significance of the Institution’s
findings to the public.
3. To enjoy a reputation for doing good translational research and for providing appropriate training
conditions, i.e., for successfully translating good science into good clinical practice and for ensuring
good advanced training.
4. As an Associated Laboratory, the IPATIMUP collaborates with the Government in health and
wealth creation, quality of life and public understanding of science.
SCIENTIFIC OBJECTIVES
Besides the specific objectives of each research group, long term objectives of IPATIMUP are the
following:
- To achieve international leadership in research related to the mechanisms involved in geneenvironment interactions in cancerous and precancerous diseases;
- To keep the world-competitive research level on gastric and thyroid carcinogenesis and to achieve
international prominence in research related to breast and colo-rectal cancer;
- To contribute, through the results of its translational research and through partnerships with other
institutions, to the improvement of prevention and early diagnosis of cancer and for the targeted
treatment of cancer patients;
- To improve the quality of scientific production (see WEB) and of the track record of our young
researchers.
- To diversify our traditional approach to cancer research towards other models (e.g. developmental
biology, experimental animal models and regenerative medicine) using the possibilities opened by
the I3S Consortium, the Consortium IPATIMUP – Porto Cancer Institute and the development of the
Tissue Banks of HS João, IPATIMUP and Porto Cancer Institute.
EDUCATIONAL OBJECTIVES
To achieve international prominence in the advanced training of physicians and young scientists in
the setting of the Foundation of Porto University and the future Doctoral Program in Health Sciences
of Porto University;
To contribute for improving the professional training of pathologists and residents in pathology,
geneticists, biologists and technicians;
To contribute, through the training of teachers and their students, for improving the education for
cancer prevention;
To improve the connection in all of these activities with INEB and IBMC.
SERVICE-ORIENTED OBJECTIVES
To keep the international competitive level in the diagnosis of gastric, thyroid, mammary and
colorectal cancer, as well as in the diagnosis of several familial cancer syndromes;
To increase the involvement in the activities of the recently created Health Cluster Portugal (HCP);
To use our diagnostic activities towards the reinforcement of Tissue and Tumour Banks of
IPATIMUP/HS João/Porto Cancer Institute and to consolidate the utilization of the observational
findings in human material as a major trigger to proceed using mechanistic oriented studies.
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INTERNAL SERVICES AND RESOURCES
The IPATIMUP is organized in a way that common facilities, including Cold rooms, -150/-80ºC Freezers
room, Cell culture, Centrifuges’room, Incubator’s room , serve as platforms for sharing of equipment
and other resources among all the Groups. The same holds true for core facilities, including
Sequencing, Proteomics, Real-time PCR, Tissue microarrays, Immunohistochemistry and In situ
hybridization.
All the above facilities are shared whenever necessary with groups of other (national and
international) institutions, namely IBMC and INEB, Porto Cancer Institute, Hospital S. João and
Centre of Medicinal Chemistry (CEQUIMED – UP) of the Faculty of Pharmacy of the University of
Porto.
The small nude mice animal house of IPATIMUP which is located at Hospital S.João and the tumour
banks of neuroendocrine tumours (ReGene) and stromal tumours of the digestive tract (ReGIST) of
IPATIMUP are also shared with the aforementioned institutions.
IPATIMUP has been receiving support from some Portuguese and foreign institutions in the
following fields:
- Confocal microscopy (IBMC/INEB)
- Flow cytometry/Cell sorting (IBMC/INEB)
- Animal models (IBMC/INEB and Institut Pasteur, Paris, France)
- Transgenic animal models (CABD, Sevilla,Spain)
- DNA microarrays (Consortium for Functional Glycomics and CBM, Area Science Park, Trieste, Italy)
- Tissue & tumour bank (Hospital S. João),
- CGH array (Microarray facility, VUmedical centre, Amsterdam, The Netherlands)
- siRNA platform (Max Planck Institute for Infection Biology, Berlin, Germany)
- Genotyping platform (Institut Català d'Oncologia, Barcelona, Spain)
The acquisition of several pieces of equipment is necessary to keep the internal and the external
services and to fulfil the plan of development of IPATIMUP.
EXTERNAL SERVICES AND RESOURCES
IPATIMUP has been providing, since its creation in 1989, scientific and technical services both
nationally and internationally. These services were at first mainly concentrated in diagnostic
anatomic pathology but have been extended to the fields of population and forensic genetics (1991 –
present), molecular pathology (1996- present) and molecular genetics and molecular epidemiology
(1996 – present).
These services are now concentrated in a single Unit , representing a major asset of IPATIMUP in
three aspects: a) Produce valuable material for epidemiology – and pathology-oriented research; b)
Provide an excellent platform for interaction with clinicians (essential for translation research); c)
Contribute to the income of IPATIMUP.
IPATIMUP also provides external services in the fields of Proteomics, Functional genetics (Functional
evaluation of germline missense mutations of E-cadherin for European, north American, south
American and Australian institutions), Genetic epidemiology (Inflammatory diseases of the GI tract,
cardiovascular diseases and neoplastic and preneoplastic diseases, also for institutions throughout
the world), and Molecular pathology (Tissue microarrays, in situ hybridization and “molecular”
diagnosis for therapy selection).
In 2010, IPATIMUP and INEB reinforced their interested on developing new methods for image
analysis and created a Centre devoted to Bioimaging. This centre has an International Advisory
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Board, in which members of INEB and IPATIMUP seat together with the CEO of BIAL and two
International leaders in the area of bioimaging. The centre is a Scientific Platform that works based
on projects which are within the main research lines of the Centre. The focus will be on bioimaging in
the fields of biomaterials, regenerative therapies degenerative diseases and cancer.
IPATIMUP researchers provide consultancy services for the pathology of human tumours from more
than 25 countries (200-300 cases per year), as well as molecular pathology and population/forensic
genetics.
NETWORKING ACTIONS
IPATIMUP’s networking has been described in the reports of each Research Group (not be repeated
here).
To improve internal collaboration among postdocs, in 2010 IPATIMUP created a postdoc forum to
provide structured postdoc input in Institutional matters, to improve critical mass between groups
for research projects, and to pinpoint interesting external collaborators. The periodicity of the
meetings is once a month.
It has also been highlighted the integration of IPATIMUP in the I3S Consortium, Porto Cancer
Institute and Health Cluster Portugal (Vice-presidency), as well as its integration in numerous
international consortia and/or networks (Int Gastric Cancer Linkage Consortium, Eur Union Network
of Excellence for Gastric Cancer, Eur Consortium for Functional Genomics in Infectious Diseases, Eur
Network of Breast Development and Cancer Labs, Int Gastric Cancer Ass).
IPATIMUP researchers continue serving in the Boards of several Int Scientific Societies (Eur Society
of Pathology- President, Eur Society of Cytology, International Academy of Cytology- General
Secretary, European Federation of Cytological Societies, President, Eur Society of Human Genetics,
Eur Helicobacter Study Group- President, Int Network of Glycobiology, ). Prof. Fátima Carneiro has
been elected in 2009 President of the European Society of Pathology (ESP). She is the President of
the ESP in the period 2011-2013.
IPATIMUP members have been involved in the creation, in 1990, of EUROCELLPATH and European
School of Pathology (ESP). Besides organizing courses in Turin and Portugal, IPATIMUP members
were involved in the creation of branches of ESP in Russia (2000), Turkey (2002), Romania (2004)
and Czech Republic (2006). Besides creating the branches, IPATIMUP members have been involved
in running courses in every of the aforementioned cities as well as in Turim.
IPATIMUP members have also been involved in the launching in 2004 (The 7th course will be held on
May 2010) of the Paris Course on Thyroid Pathology of the French Division of IAP.
The following results reflect the networking capacity of IPATIMUP:
-
IPATIMUP members participate in average, per year, as invited speakers in more than 40
international scientific meetings;
-
Researchers from IPATIMUP belong to the Editorial Board of the following 29 international
journals; Acta Cytologica; Advances Anatomic Pathology; Advances in Clinical and
Experimental Medicine; Archives of Pathology Laboratory Medicine; BMC Cancer; Breast
Cancer Research; Cancer Genetic Cytogenetics; Critical Review Oncogenesis; Current
Diagnostic Pathology; Cytojournal; Cytopathology; Diagnostic Cytopathology; Endocrine
Pathology; European J Cancer Prevention; Forensic Science Int: Genetics; Gut Pathogens;
Hereditary Cancer Clinical Practice; Helicobacter; Histopathology; Human Biology; Int J
Surgical Pathology; J Cell and Molecular Medicine; J Pathology; Open Pathology J; Open
Forensic Science J; Pathology Research Practice; Seminars Diagnostic Pathology;
Ultrastructural Pathology; Virchows Archiv.
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TRAINING ACTIVITIES
IPATIMUP is involved in the tutorial (hands on) training of future scientists (fellows with research
initiation grants, Master and PhD students), young physicians (residents and specialists in pathology,
mainly) and lab technicians.
Besides its “own” trainees, IPATIMUP has been involved in the last years in the modular teaching of
the following Graduate Programs: Master Course on Molecular Medicine and Master Course on
Molecular Oncology. Both Master Courses were organized together with the Medical Faculty of
Porto University. From October 2010 on, there will be a Master Course in “Molecular Medicine and
Molecular Oncology”. Organization and teaching of Forensic Genetics MSc, FCUP.
PHD (DOCTORAL) PROGRAMS
GABBA (Graduate Program on Basic and Applied Biology Areas) – together with the Medical Faculty,
Sciences Faculty, Institute of Biomedical Sciences (ICBAS) and IBMC. The 1st edition of GABBA took
place in 1996, following the merging into a PhD Program of the two Master Courses on Oncobiology
and Human Genetics that were previously organized at IPATIMUP, with those on Immunology
(ICBAS) and Cell Biology (Medical Faculty). The IPATIMUP holds regularly some of the annual
international meetings, seminars and workshops of GABBA
Molecular Medicine and Molecular Oncology for physicians based upon the merging of the preexisting Master Courses on the same topics – 1st edition in 2007 organized together with the Medical
Faculty, ICBAS, Porto Cancer Institute and IBMC/INEB
Molecular Pathology and Molecular Genetics – 1st edition in 2007, organized together with the same
partners as the aforementioned PhD Program.
Biodiversity Genetics and Evolution PhD Program, FCUP
Biomedicine for MD's – 1st edition in 2008 organized by Gulbenkian and Champalimaud Foundation,
together with IPATIMUP.
IPATIMUP is also involved in the training of residents and specialists of pathology from several
European countries, Brazil and Mozambique (average of 8-10 MDs per year) mainly in cancer
histopathology and cytopathology, and molecular pathology.
IPATIMUP is involved every year in the graduate training of technicians of Higher Education
institutions (Polytechnic Institute of Porto and Private Universities) (average of 6 technicians per
year).
ORGANIZATION OF INTERNATIONAL EVENTS
IPATIMUP has been organizing every year, since 1992 and 1998, respectively, two international
events one focusing on Oncobiology - XVIII Porto Cancer Meeting, and the other on Population
and/or Forensic Genetics.
IPATIMUP INTERNAL EVALUATIONS
We will keep the system we have been using since the early nineties with a couple of alterations
mainly induced by the formation of the Consortia with IBMC and INEB (Consortium I3S) and Porto
Cancer Institute.
The External Advisory Board (EAB) is presently constituted by Prof. Fred Bosman, MD, PhD, who
presides, Prof. Ivan Damjanov, MD,PhD, Prof. Angel Carracedo, Prof. Marc Mareel, MD, PhD and Prof.
Fernando Lopes da Silva, MD, PhD. The EAB of the IPATIMUP made a site visit on March 2011. Prof.
Marc Mareel could not attend this visit. The final report of the EAB has not been delivered yet.
The EABs of IPATIMUP, IBMC and INEB will help the respective Board of Directors to define an EAB
common to the three Institutes under the newly formed I3S.
The Board of Directors will go on paying a particular attention to the scientific productivity of the
different groups, including the public disclosure of all the data (e.g. papers, prizes, …) and the
publication of regular reports on the overall results (see WEB)
We will also continue to evaluate positively (read: to stimulate and reward) intergroup and
interinstitutional collaborations, projects and papers.
The following criteria will be used to evaluate the outcomes:
- Number (weighted by impact factor) of papers published in international peer reviewed journals in
each research field
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- Number of citations obtained in the post-five year period of the publication and their ratio to the
average citation index per paper in each research field
- Number and budget of research projects awarded in national and international context
- Number and value of contracts and patents
- “Prestige” indicators: editorial boards, international prizes, invitations for international
conferences, chairmanships of international scientific boards.
In October 2010, the group leaders reported the board of directors information about the activities
of the post-doc hired within the program Ciencia 2007 from FCT (Portuguese Foundation for Science
and Technology). All Post-doc were evaluated positively by the group leader. One of the eight Postdocs decided to move to another institution although keeping the collaboration with IPATIMUP.
During 2010, the board of directors implemented with the group leaders support an annual
progression report of students and supervisors. This action aims at identifying in early stage
deviations of the students working plan, limitations/deficiencies or problems in the supervision.
These reports were filled online.
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SCIENTIFIC RESEARCH (RESEARCH GROUPS)
Cancer Biology
Objectives
The main objective of the group is to progress in the understanding of the etiopathogenesis of some
types of endocrine and neuroendocrine tumours with a preferential focus in well differentiated
thyroid cancer: papillary carcinoma (classic and follicular variant) and follicular carcinoma. 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; b)
mitochondrial alterations secondary to mitochondrial DNA mutations/deletions or to mutations in
nuclear genes encoding mitochondrial enzymes.
In addition to these basic/translational approach the group has a more basic, scientific interest in
some aspects of cell cycle, tumour-microenvironment interactions and motility/invasiveness
processes in cancer.
Main research topics
1 - Oncobiology of familial and sporadic thyroid tumours with an emphasis on the two major variants
of papillary carcinoma (classic and follicular type) and on the clinico pathologic and molecular
features separating them from follicular carcinoma.
2 - Role of mitochondrial alterations in the etiopathogenesis of sporadic, irradiation-induced and
familial thyroid tumours and on the oncobiology of neuroendocrine tumours (medullary thyroid
carcinoma, pheochromocytoma, paraganglioma, …)
Main Achievements
Translational studies
n the translational field, we have pursued the collaborative project (IPATIMUP-IPO-HSJ) initiated in
the end of 2008 and aiming to perform a thorough clinico-pathological re-evaluation of all the cases
of well differentiated thyroid carcinoma diagnosed and treated in three institutions that showed an
aggressive behavior (see Future Activities). In this frame we have published two papers (SobrinhoSimões M et al, IJSP, 2010)
We do not discard the opportunity to gain access and characterize the unique cases that we receive
as consultation/collaboration. We had the opportunity to publish in 2010, in collaboration with
Joaquin Lado, an exceptional case of a patient with hyperthyroidism due to a FTC bearing an
activating TSHR mutation. The patient presented also a germinative PAX8-PPARgamma
rearrangements, as a mosaicism, and affecting tissues from endodermal and mesodermal origin
(Lado-Abeal et al, ERC, 2010). This constitutes the first report of a germinative PAX8-PPARgamma
rearrangement.
Dissecting molecular pathways
Following our preliminary studies in HEK293 cells exploring signaling pathways activated by
oncogenic BRAF, we have demonstrated in a different cell line (PCCL3), that both RET/PTC and BRAF
can induce STAT3 phosphorylation and transcriptional activation. However, contrarily to what was
described we verified that such activation is dependent on JAKs signaling. Interestingly, expression
arrays of thyroid cells transformed by RET/PTC show an upregulation of IL-6. Altogether these results
lead us to investigate and characterize STAT3 regulation (by MAPK and/or by IL-6/gp130 /JAK
signaling) in PTC.
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Our preliminary results show that STAT3 in thyroid has unexpected growth-suppressive action that
appear to be modulated by the tissue microenvironment. When we implant thyroid cancer cell lines
stably silenced for STAT3 (sh) in nude mouse, we obtain bigger tumors than with the parental cells
expressing STAT3. Also, we saw that pSTAT3 is present in approximately 50% of cases of human PTC,
notably at the periphery of the tumors, in the interface with the stroma, suggesting that this
expression results from the crosstalk between cancer cells and surrounding stromal cells.
The results obtained so far suggest that in thyroid cell lines harbouring the mutant BRAF protein,
Stat3 activation is dependent on gp130/Jak signaling pathway and has a suppressive effect in growth
(these results have been presented as a poster in AACR, Joana Silva, PhD Thesis).
To clarify whether mTOR pathway is over activated in PTC (and if it is related with BRAF mutation)
we have evaluated, the expression levels of upstream (PTEN, pAkt Thr308, pAkt Ser473) and
downstream (pS6 Ser235/236 and p4EBP1 Thr37/46) mTOR pathway proteins. Our results revealed
that in conventional PTC, expression of mTOR pathway proteins has a distinct pattern in the
presence or absence of the BRAF V600E mutation: cPTC cases with BRAF V600E mutation have
higher mTOR pathway activation comparatively to cases without the mutation. We have also treated
thyroid cell lines with different genetic alterations (BRAF, RET/PTC and RAS) with rapamycin and we
verified that cell lines with BRAF mutation show higher sensitivity to the drug (Faustino A,
manuscript in preparation).
Taking into consideration the possible shared etiopathogenic mechanisms (very frequent activation
of BRAF) in thyroid cancer and melanoma we analyzed MTOR pathway in a series of cutaneous
melanoma. In cutaneous melanoma we found a high expression of mTOR pathway proteins whose
expression is related to BRAFV600E. We demonstrated that higher expression levels of some
effectors were associated with worse prognostic parameters, being pS6 Ser235/236 expression
associated with shorter disease-free survival in cutaneous melanomas. We have characterized a
series of ocular melanomas for BRAF, N-RAS and GNAQ mutations and we found that in uveal
melanomas GNAQ mutations are the more prevalent genetic alterations. (Helena Populo, PhD
thesis)
(Papers: Populo H et al, BJO, Mel Res and PCMR).
During 2010 we pursue the work on the establishment of the role of the H-RAS in aneuploidy,
focusing on the role of the two different isoforms (p19 and p21) coded by H-RAS. We consolidated
our data showing that the H-RAS 81C polymorphism is influencing the splicing of the H-RAS gene
towards a higher p21/p19 ratio. Our observations also indicate that the C allele is associated with
increased chromosomal instability and increased centrosome amplification. We have also studied the
role of this polymorphism in cellular behaviour, particularly in cell growth, cell proliferation, cell
death and cell migration. We verified that cells carrying the C allele had increased cell growth and cell
migration rates and less cell death, in comparison to cells carrying the T allele (Castro P Pos-doc
project).
In a previous study we have detected 3 novel germline RET variants (Arg886Trp, Ser649Leu and
Glu511Lys) in sporadic medullary thyroid carcinoma (MTC), all of which were absent in normal
controls. We demonstrated that all the variants have transforming capacity in focus formation
assays, demonstrating their pathogenicity. We observed differences in signaling properties between
RET mutants, which might explain distinct clinical phenotypes and responses to treatment (Prazeres
H, ERC manuscript in revision) (Hugo Prazeres, PhD thesis).
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Primary hyperparathyroidism (PHPT) is a common endocrine disorder characterized by an excessive
autonomous production and release of parathyroid hormone (PTH) by the parathyroid glands that,
in 10% of the cases, are associated with RET mutations as part of MEN2 spectrum. Frequently we are
asked to perform genetic screening of PHPT cases. However the molecular mechanisms underlying
the pathogenesis of sporadic PHPT are incompletely understood being somatic alterations in MEN1
gene and Cyclin D1 protein expression the most frequent. We have characterized a series of PHPT for
germline and somatic alterations of MEN1, RET, CDKN1B gene. We found somatic mutations in MEN1
in two cases and allelic deletions in 50% of the cases showing that MEN1 gene has a relevant role in
the development of sporadic forms of PHPT (manuscript in preparation).
In contrast to the high prevalence of activating mutation or rearrangements in oncogenes no or few
tumor suppressor genes have been identified in the well differentiated thyroid carcinomas (PTC or
FTC). We compared the global gene expression profile in normal versus tumour samples, and
selected the single gene at 2q21, the Low density lipoprotein-related protein 1B (LRP1B), shown to be
down-regulated > than 3 fold. In order to investigate the role of LRP1B in the carcinogenesis of
sporadic thyroid cancer, we further assessed LRP1B inactivation mediated by genomic loss, mRNA
expression, DNA methylation, and microRNAs (miRNAs). In this work we found classical (mutation,
genomic deletion) and novel ways
(DNA-methylation-mediated disruption of an enhancer element and micro-RNA overexpression) in
which this gene is de-regulated at transcriptional and post-transcriptional levels in sporadic thyroid
tumours and cell lines (H Prazeres, PhD thesis) (Paper Prazeres H, et al, Oncogene).
Ethiopathogenesis of radiation induced thyroid cancer
In this item we are following-up a cohort of individuals that suffered epilation by scalp X-ray
irradiation for the Tinea capitis treatment. We have successfully followed-up 26% of the cohort (1135
individuals were observed and 248 individuals deceased). We observed a prevalence of 2.2% of
thyroid cancer (PTC) being 11 cancers diagnosed by us in asymptomatic patients. Basal cell
carcinomas (BCC) have a prevalence of 6.7% (30% of the tumours were multiple BCC), being 21 BCCs
diagnosed by us. Meningiomas were found in 1.0% of the individuals. These figures are 5 to 10 times
higher than those referred for non-irradiated population (Boaventura P, Pos-Doc Project)
(Boaventura P, BJD, 2010)
The results on thyroid pathology, were accepted in Lancet Infectious Diseases, as a letter entitled:
“Head and neck lesions in a cohort irradiated in childhood for tinea capitis treatment”( Boaventura
P, in press).
Mitochondria and cancer
Our work over 2010 intended to establish cellular models of mitochondrial dysfunction caused by
mutations in the mitochondrial DNA (mtDNA) or in nuclear DNA (nDNA)-encoded mitochondrial
proteins. We wanted to demonstrate that these models present the “Warburg effect” and this is
essential for the progression of tumorigenesis.
To achieve our purposes, we have constructed a cybrid cell line with wild-type mtDNA, a cybrid cell
line harbouring a mutation in the mtDNA gene for tRNALeu(UUR) and a cybrid cell line harbouring a
mutation in the mtDNA gene for ND1 subunit of complex I. We have also performed silencing of the
mitochondrial SDHB protein (encoded by the nDNA) using RNA interference in a cybrid cell line with
wild-type mtDNA. Because cybrids with ND1 mutation were only obtained by the end of 2010, the
following results refer only to WT cybrids and tRNALeu(UUR) mutant cybrids.
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We analysed the metabolic phenotype of these cell lines, by assessing the fluxes of glucose, lactate,
glutamate and glutamine across the plasma membrane and the expression of some key enzymes in
bioenergetic pathway. We have concluded that both the SDHB silencing and the mtDNA mutation
alters the cellular metabolism, increasing glycolysis (Lima j and Maximo V).
To assess the influence of the mtDNA mutation and the Warburg effect in tumorigenesis, cybrids
with the mtDNA mutation were analyzed for markers associated to tumourigenesis. Although
mutant cybrids showed a higher population doubling time, they displayed more resistance to
apoptosis and more motility and migration capabilities.
Finally, by injecting both wild-type and mtDNA-mutated cybrids in nude mice, we saw tumour
formation only in mice injected with mtDNA mutated cybrids; in addition in two out of five mice we
could observe invasion and lung metastases, clearly demonstrating the tumourigenic potential of
this specific mutation in vivo. These results suggest that mitochondrial dysfunction, caused either by
mtDNA mutation or SDHB silencing, results in altered cellular metabolism; in addition, cybrids with a
tRNALeu(UUR) mtDNA mutation displayed increased tumourigenic potential (Lima J and Máximo V
project).
To understand the Hürthle cell morphologic phenotype we are evaluating proteins involved in the
mitochondrial fusion (OPA1 and Mitofusin2) and fission process (Fis1 and Drp1) in cases with Hürthle
phenotype (including FHC, PHC and FHA) and cases without the Hürthle phenotype (PTC, FTC and
FVPTC), and we verify that the expression levels of the fission proteins is elevated in the majority of
the tumours with Hürthle phenotype comparing with normal tissue and with the thyroid tumours
without Hürthle phenotype, independently from the lesion histotype (Ferreira A, PhD project).
Networking/Internationalization
NATIONAL COLLABORATIONS
Carlos Palmeira - Mitochondrial Toxicology and Pharmacology Group, Centre of Neuroscience and
Cell Biology, Coimbra, Portugal
Ana Teixeira - Animal Cell Technology Laboratory, Institute of Experimental and Technological
Biology, Oeiras, Portugal
Isabel Torres – Portuguese Institute of Oncology, Porto, Portugal
Teresina Amaro e Cláudia Lobo - Portuguese Institute of Oncology, Porto, Portugal
Cláudio Sunckel – IBMC, Porto, Portugal.
Arnaldo Videira - IBMC, Porto, Portugal.
INTERNATIONAL COLLABORATIONS
José Cameselle-Teijeiro - Universidade de Santiago de Compostela, Spain.
Robert Hofstra - University Medical Center Groningen, Groningen, Holland.
Jacqueline Bromberg and James Fagin – Memorial Sloan Ketering Cancer Centre, NY, USA.
Eugénio Santos – CSIC, Universidad de Salamanca, Spain
Ragnhild Lothe and Rolf Stokheim - Institute for Cancer Research, Oslo, Norway.
Luca Scorrano – University of Genève, Switerzland.
Dillwyn Williams - Strangeways Research Laboratory, University of Cambridge, UK.
Keshav Singh - Roswell Park Cancer Institute, Buffalo, U.S.A.
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Gerry Thomas – Chernobyl Tumour Bank, South West Wales Cancer Institute, Swansea, Wales.
Future Research
Translational studies
We intend to gather the data obtained in the collaborative project involving pathologists, scientists
and clinicians from IPATIMUP, IPO-Porto and H S Joao to progress in the disclosure of biomarkers
with diagnostic, prognostic and therapeutic importance. We are also using high throughput methods
to evaluate the presence of new rearrangements in FVPTC. This part of the work is being done in
Norway by the PhD student Ricardo Celestino, in collaboration with Raghnild Lothe and Rolf
Stockeinhem.
Dissecting molecular pathways
To address the involvement of STAT3 in the signaling activated by mutated BRAF we are
collaborating with Dr Jacqueline Bromberg and Dr. James Fagin (at MSKCC). In this project we are
hypothesizing that STAT3 might indeed play a crucial and novel role in thyroid cancer that primarily
affects the crosstalk with the microenvironment. We intend to establish the role of STAT3 activation
in thyroid carcinogenesis (if growth promoting or growth restraint) and the function of the
microenvironment in the modulation of this effect We are starting to obtain results with the novel
BRAFV600E/STAT3 knockout mouse, that will be determinant to clarify the role of STAT3 in thyroid
carcinogenesis ( Joana Silva, PhD Project ).
To go further in the correlation between BRAF V600E mutation and mTOR pathway activation
(namely in melanoma), we are now comparing the functional effect of BRAF and GNAQ mutations in
MAPK and mTOR pathways activation, cell proliferation and apoptosis.
We are performing transient transfection of HEK293 cells with BRAFWT, BRAFV600E, GNAQWT,
GNAQQ209P and GNAQQ209L vectors. We are also treating melanoma cell lines displaying different
BRAF and GNAQ mutational status with the mTOR inhibitor RAD001(Novartis) and evaluating the
effects in cell growth and in mTOR pathway effectors expression (Helena Populo, PhD thesis and
Alexandra Faustino).
Regarding the project: “S1H-RAS expression and activity regulation: implications in tumourigenesis”
we are studying the silencing of the p19H-RAS isoform by means of siRNA and shRNA. The
preliminary results with siRNA targeting the IDX exon, which is characteristic of the p19H-RAS
isoform, revealed that this isoform appears to have a role in centrosome amplification because in the
cells with silencing the number of centrosomes was augmented. Next, we attempted to silence the
p19H-RAS isoform in 8505C cell line with shRNA. We are performing time-lapse analysis to determine
cell division abnormalities. We are also doing nocodazole treatments to verify whether the spindle
assembly checkpoint was affected (Patricia Castro and Mariline Silva).
Ethiopathogenesis of radiation induced thyroid cancer
Even when matched for age at irradiation, gender and dose, only some of our cohort members
developed radiation related neoplasias. This may due to differences in their radiosensitivity.
Radiation can induce DNA damage that includes single strand breaks (SSB) and double strand breaks
(DSB) and impairment of DNA repair could have a role in the occurrence of radiation-associated
tumours in patients with a history of irradiation. With this in mind we intend to verify if our irradiated
patients that developed neoplasias have DNA repair impairment.
For that we began collecting lymphocytes from some of our cohort members and from the controls.
So far we have frozen samples from about 300 individuals, including irradiated individuals with BCC,
PTC, or without pathology, and non-irradiated individuals. To assess the DNA damage and repair we
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18
have been using use the alkaline comet assay, a method recognized as sensitive for measuring DNA
strand breaks. We also intend to use the ¿H2AX assay system, a method more specific for DSB
detection, and that has been previously used in a study of Hiroshima and Nagasaki survivors
(Boaventura P Pos-Doc project and Pereira D)
Mitochondria and cancer
We intend to address a possible role for hypoxia both in the expression of the fission/fusion proteins
as well as in alterations in the mitochondrial network using the XTC.UC1 cell line.
We started also trying to establish a stable XTC.UC1 cell line that lacks Drp1 by shRNA transfection to
access possible differences in metabolism resulting from downregulation/absence of Drp1. We were
also able to find a working antibody for IHC for Mitofusin1 and we verified in our preliminary results
that its expression is lower when compared to the fission proteins and close between Hürthle and
non-Hürthle.
Prizes
Award Prof. Doutor Amândio Sampaio Tavares - SPG
Alvelos MI ,Barbosa E , Teixeira-Gomes J, Soares P. Genetic Alterations in Sporadic Primary
Hyperparathyroidism. Award Prof. Doutor Amândio Sampaio Tavares for the best work presented as
oral communication. XXXV Jornadas Portuguesas de Genética 2010. Braga, Portugal,2010.
Prémio Nacional de Endocrinologia SPEDM/NOVARTIS ONCOLOGY-Ano 2010
Hugo Prazeres, Marta Pinto, Joana Couto, Fernando Rodrigues, João Vinagre, Joana Torres, Vitor
trovisco, Teresa Martins, Manuel Sobrinho-Simões e Paula Soares The lipoprotein receptor LRP1B
suppresses growth, angiogenesis and metastatic potential of tumors generated in vivo by
modulating the extracellular microenvironment composition.
Menção honrosa na categoria de investigação básica clínica SPEDM
Mota F, Soares P, Celestino R, Matthiessen R, Vinagre J, Torres J, Ligeiro D, Pereira P, Seixas D, Castro
S, Pereira J, Fonseca E, Carvalho D.: “Expressão de microRNAs como marcadores de invasão nos
gonadotrofinomas: resultados preliminares”. XIIth congress da Sociedade Portuguesa de
Endocrinologia, Diabetes e Metabolismo (SPEDM), 2010.
Participation in PhD Programs
Programme for Advanced Medical Education – Doctoral Programme for Physicians. Paula Soares,
Valdemar Máximo, Jorge Lima, M Sobrinho-Simões, Patricia Castro.
Programme in Molecular Medicine and Oncology - FMUP. Paula Soares, Valdemar Máximo, Jorge
Lima, M Sobrinho-Simões, Patricia Castro..
13th Edition of the GABBA Doctoral Programme . Paula Soares, Valdemar Máximo, Jorge Lima, M
Sobrinho-Simões, Patricia Castro, Hugo Prazeres, J M Lopes.
PhD programme Ciências da Terra e da Vida - UTAD. Jorge Lima.
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19
Cancer Genetics
Objectives
The Cancer Genetics group is focused on the genetics of three common types of epithelial cancer:
gastric, breast and colorectal.
The group aims at: 1) identifying individuals at increased risk for cancer; 2) identifying clinicopathological features and molecular markers occurring in the setting of familial and sporadic
carcinoma; 3) identifying signaling pathways mediated by genetic and environmental factors pivotal
for tumor development. A special interest is on the identification of the environmental and
epi/genetic factors underlying cancer cell invasion, a topic of crucial importance in cancer control.
The team aims to understand and unravel the molecular and cellular basis of cell invasion, using
cancer as model system. With this basic knowledge the team aims at improving and developing new
strategies for improving the quality of detection and treatment of invasive cancer.
The mortality rate of cancer patients strongly increases when tumor cells are able to invade
neighboring tissues. Because of that, invasion is one of the most (probably the most) appealing
step(s) to develop targets for anti-cancer therapy and new methods to detect invasive cells in an
early stage of disease progression. To design efficient methods for detection of invasive tumor cells
and new therapeutic strategies targeting invasion, it is mandatory to identify key molecular/cell/ECM
players in cancer. Specifically, the group aims to unravel the mechanisms that regulate P-cadherin
and E-cadherin expression, their associated cellular effects and dependent signaling (upstream and
downstream pathways) pivotal for cell invasion. Further, we aim at developing new in vivo models
that do not raise ethical issues to test new tools and new drugs impairing cancer cell invasion or
survival (Drosphila and CAM models).
The Cancer Genetics group collaborates with others namely with groups of Cancer Biology and
Carcinogenesis of IPATIMUP and NEWtherapies from INEB at IPATIMUP.
Specifically in 2010, we aimed at:
Assessing the effect of the fatty acid DHA on Helicobacter pylori growth and colonization in vitro and
in vivo;
Evaluating variation in H. pylori virulence factors on the progression of pre-malignant lesions of the
stomach;
Addressing the role of H. pylori in nuclear and mitochondrial DNA (mtDNA) repair expression and
activities, and in the induction of mutations;
Identifying new molecular mechanisms leading to germline and somatic CDH1 impairment;
Addressing the role of E-cadherin deregulation in gastric cancer progression;
Understanding if bioinformatic analysis of protein structure and conservation is suitable to predict
the impact of CDH1 missense mutations found in hereditary diffuse gastric cancer (HDGC);
Constructing a new model for functional characterization of CDH1 germline missense mutations
found in HDGC families (cellular effects and characterization of E-cadherin/catenin complex by
Proximity Ligation Assay);
Identifying new genes in gastric cancer (GC) progression;
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20
Identifying novel players in Epithelial to Mesenchymal (EMT) transition;
Finding out the genetic and epigenetic mechanisms of CDH3/P-cadherin gene regulation;
Identifying the cellular effects and signaling pathways mediated by P-cadherin overexpression in
breast cancer cells;
Identifying the means by which miRNA-101 modulates E-cadherin expression in gastric cancer;
Identifying novel E-cadherin transcripts with deleterious effect;
Developing new tools for prophylaxis and/or therapeutic intervention in E-cadherin related cancer;
Disclosing the mechanism responsible for mutant E-cadherin expression rescue to the plasma
membrane by the action of Chemical Chaperones (CCs), namely in E-cadherin trafficking and with
molecular partners involved in its regulation;
Determining whether Notch1 constitutes a therapeutic target in E-cadherin related cancer;
Determining whether P-cadherin constitutes a therapeutic target in cancer;
Dissecting the EGFR downstream targets predictive of therapy outcome in gastric, breast and
colorectal cancer patients and assessment of new targeted therapies;
Establishing methodologies to identify cancer cells with stem-like properties at IPATIMUP;
Studying the association between cancer stem cell (CSC) markers and breast cancer subtypes;
Understanding how cancer cells modulate the inflammatory microenvironment and which are the
molecular mechanisms used by these tumor cells to escape immune surveillance.
Main Achievements
Assessment of the effects of DHA on H. pylori growth and colonization in vitro and in vivo
We have demonstrated that DHA decreases H. pylori growth in vitro in a dose-dependent way, and is
able to inhibit H. pylori gastric colonization in vivo. Furthermore, the addition of DHA to standard
treatment resulted in lower recurrence of H. pylori infection in a mouse model. These observations
may pave the way to the evaluation of DHA as a co-adjuvant agent in H. pylori eradication treatment.
Evaluation of the clinical relevance of H. pylori virulence factors on the progression of premalignant lesions of the stomach
Since there are no established predictive markers of progression of gastric preneoplastic lesions, we
have analyzed whether H. pylori virulence factors cagA and vacA could be used as such markers. In a
long-term follow-up study carried out in a province of Spain with a high risk for gastric cancer we
have shown that infection with H. pylori strains cagA-positive, vacA s1, and vacA m1 strains was
associated with progression of gastric preneoplastic lesions (multivariate odds ratio (OR) = 2.28, 95%
confidence interval (CI) 1.13 – 4.58; OR = 2.90, 95% CI 1.38 – 6.13; and OR = 3.38, 95% CI 1.34 – 8.53,
respectively). Infection with strains that are simultaneously cagA-positive and vacA s1/m1 was
associated with progression of gastric precancerous lesions with an OR of 4.80 (95% CI 1.71 – 13.5).
These results suggest that H. pylori genotyping is useful for the identification of patients at high risk
of progression of gastric preneoplastic lesions and who need more intensive surveillance.
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Assessment of the influence of H. pylori in nuclear and mtDNA genetic instability and in cellular
repair pathways
We have shown that H. pylori infection down-regulates the activity and expression of base excision
repair and mismatch repair in vitro (in the AGS cell line infection model) and in vivo (in C57BL/6 mice
infected with H. pylori strain SS1). Furthermore, we have demonstrated that H. pylori induces
genomic instability in nuclear CA repeats in mice, in mtDNA in vitro and in patients with chronic
gastritis. In addition, we have shown that induction of mtDNA mutations is associated with bacterial
virulence. These 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.
Identification of CDH1 germline deficiency in most HDGC families
We found that >70% of CDH1 mutation negative HDGC families, displayed germline monoallelic CDH1
expression or strong downregulation of one of the alleles and demonstrated for the first time that
CDH1 locus is involved in the majority of mutation-negative HDGC families. This result had a clear
impact in the clinical management and diagnosis of HDGC.
In silico analysis to predict the impact of CDH1/E-cadherin gene missense mutations found in HDGC
By bioinformatic analysis we found a positive correlation between the impact predicted by FoldX,
and the in vitro phenotype of the different CDH1 mutations. This analysis was confirmed by other
structure and sequence based predictors. For most of the mutations, when they are found to have
structural impact in silico, they are pathogenic in vitro.
Construction a new model for functional characterization of CDH1 germline missense mutations
found in HDGC families (cellular effects and characterization of E-cadherin/catenin complex by
Proximity Ligation Assay)
We have established a new stable cell model using the Gateway Recombination System. By sitedirected mutagenesis, we have cloned in the entry vector seven missense CDH1 mutations found in
HDGC (T340A, A634V, R749W, E757K, E781D, P799R and V832M). Using Proximity Ligation Assay
(PLA) we analyzed the interaction between E-cadherin and the proteins which compose the
cadherin/catenin cytoplasmic complex and showed that E-cadherin mutations interfere with the
binding of p120- and β-catenins to E-cadherin, leading to its trafficking deregulation.
Finally, five new CDH1 germline missense mutations were found in HDGC patients, and reported to
our laboratory in order to evaluate their pathogenicity through in vitro assays and in silico
bioinformatic analysis. For functional characterization, we performed slow aggregation and matrigel
invasion assays in cells transiently transfected with empty vector pIRES-GFP (Mock) or the vectors
encoding WT, E185V, S232C, L583R, D750N and S853L hE-cadherin. Transfection efficiency was also
controlled by flow cytometry prior to each experiment, to ensure that all conditions had similar
levels of transfection efficiency.
Identification of novel genes involved in gastric cancer (GC)
We identified CPEB, CD44, and C/EBPβ as new genes and interesting markers in GC progression (see
below for details).
Identification of new GC-related genes using Drosophila as model system, molecular
characterization in gastric cancer samples and functional analysis in a chicken in vivo model.
We used a transgenic Drosophila model to screen for novel genes putatively involved in gastric
carcinogenesis. We then evaluated the expression of the most interesting candidates in GC cancer
cell lines and primary tumors by quantitative RT-PCR. We identified six candidates, one of which,
CPEB1 was downregulated in the majority of GC cell lines and primary GC tumors. Furthermore, we
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verified that CPEB1 mRNA expression levels were significantly reduced in 9 Gastric, 7 Colon and 7
Breast Cancer Cell Lines.
Regarding the molecular mechanism leading to CPEB1 downregulation, we verified that there were
no CPEB1 tumor specific mutations associated to its silencing. Instead, alterations were found in the
methylation status of its promoter region. We verified that the methylation profile was significantly
associated with CPEB1 expression both in primary tumors and in GC cell Lines. Furthermore, we
identified the pivotal site at CPEB1 promoter (79th CpG analyzed) that was associated to its mRNA
expression levels.
Using a chick chorioallantoic membrane (CAM) in vivo model system, we uncovered an in vivo antiangiogenic role for CPEB1. By performing a CAM angiogenesis assay, we showed that CPEB1
overexpression in KATOIII GC cells significantly decreased the observed angiogenic response,
confirming a new role for CPEB1, namely in gastric carcinogenesis.
This work has been developed in collaboration with Fernando Casares and Paulo Pereira from
Claudio Sunkel group of IBMC.
Identification of CD44 as a novel molecular marker expressed in sporadic and hereditary GC
We dissected the mRNA splicing pattern of CD44 in normal stomach and GC cell lines (n=9) using
cloning and quantitative mRNA amplification assays and assessed the RNA levels and protein
expression pattern of relevant splicing forms in distinct premalignant and malignant gastric lesions
(sporadic and hereditary). We also explored the association of CD44 and E-cadherin expression. We
observed that exon v6-containing isoforms became increasingly expressed both in gastric
premalignant (hyperplastic polyps, complete and incomplete intestinal metaplasia, low- and highgrade dysplasia) and malignant lesions [cell lines derived from GCs, primary sporadic GCs and
hereditary diffuse GCs (HDGCs)]. Moreover, we verified that whenever E-cadherin expression was
absent, exon v6-containing CD44 isoforms were overexpressed raising the hypothesis of using this
isoform as a marker of early invasive intramucosal carcinoma in HDGC CDH1 mutation carriers that
lack E-cadherin expression in their tumors.
This work has been developed in collaboration with Pedro Granja from the NewTherapies group of
INEB.
Determination of the CCAAT/enhancer binding protein β (C/EBPβ) partnership profile in gastric
carcinogenesis
We have previously found that C/EBPα is downregulated in GC, and that C/EBPβ is overexpressed in
dysplastic lesions and GC. We transfected GC cell lines with a full-length C/EBPα protein, and we
observed a significant decrease in cell proliferation, accompanied by a decrease in Cyclin D1, an
increase in P27 expression, and an increase in expression of the gastric differentiation marker trefoil
factor 1 (TFF1). Noteworthy, C/EBP members form transcriptional protein-complexes with other
transcriptional partners, being cell-phenotype determination directly dependent on the proteins that
are part of the transcriptional complex. Knowing that, we sought to identify novel C/EBPβ interacting
proteins in vitro through co-immunoprecipitation using mass spectrometry-based proteomics
techniques (MALDI-TOF/TOF). We identified members of the heterogeneous nuclear
ribonucleoproteins (hnRNP) family, as interacting proteins of C/EBPβ transcriptional complexes in
our screen. We confirmed the in vitro interaction of C/EBPβ with hnRNPs by reverse
immunoprecipitations. hnRNPs are nuclear ribonucleoprotein-complexes involved in gene
transcription and subsequent post-transcriptional modification of the newly synthesized pre-mRNAs.
Our results suggest that the hnRNP-C/EBPβ interactions may have an important role in the regulation
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of expression of specific genes that are involved in the control of cellular differentiation and
proliferation.
This work is in collaboration with Carcinogenesis group of IPATIMUP.
Identification of novel players in Epithelial to Mesenchymal transition
We generated an in vitro EMT/MET model by supplying or removing TGF-β1 from the culture medium
of a normal mouse mammary epithelial cell line and performed whole RNA-sequencing. The data is
currently under analysis.
Identification of genetic and epigenetic mechanisms of CDH3/P-cadherin gene regulation
We demonstrated that ICI 182,780, a pure antiestrogen, is able to increase CDH3 promoter activity,
as well as to induce on it activating histone epigenetic modifications at putative C/EBP binding sites.
In addition, we also demonstrated that this transcription factor is able to directly activate P-cadherin
transcription in breast cancer cells and that the expression of these two proteins was highly
associated in a series of human breast carcinomas, being both significantly related with high grade
and proliferative invasive breast carcinomas. In addition, we showed for the first time that the
transcription factor C/EBP is able to regulate P-cadherin overexpression in breast cancer cells.
Evaluation of the cellular effects and signaling pathways mediated by P-cadherin overexpression
We found that P-cadherin overexpression, in breast cancer cells with wild-type E-cadherin, promotes
cell invasion, motility and migration, as well as actin cytoskeleton alterations. Moreover, we found
that the overexpression of P-cadherin induces the secretion of matrix metalloproteases, specifically
MMP-1 and MMP-2, which then lead to P-cadherin ectodomain cleavage. Further, we showed that
soluble P-cadherin fragment is able to induce in vitro invasion of breast cancer cells. Since P-cadherin
invasive role seems to be dependent on the presence of E-cadherin in breast cancer cells, we
addressed the biophysical characteristics of P-cadherin and E-cadherin protein-protein interactions,
using in situ proximity ligation assay (PLA), as well as atomic force microscopy (AFM). We also
analysed the transcriptional profile and signaling pathways that are modified when P-cadherin is
overexpressed in a normal E-cadherin cellular context. It was possible to prove that the role of each
cadherin alone is completely distinct from when these are co-expressed in the same cell, conferring
alternative transcriptional programs leading to activation of divergent signaling pathways.
Interestingly, one such pathway is the apoptotic pathway, which showed various genes with altered
expression levels indicating that P-cadherin is a putative cell survival factor in breast cancer cells.
This work has been developed in collaboration with Nuno Santos from IMM and Manuel Santos from
U. Aveiro.
Identification of miRNA-101 as a modulator of E-cadherin expression in gastric cancer
We explored an indirect pathway involving chromosomal abnormalities, a microRNA (miR-101) and a
histone methyltransferase (EZH2), which may contribute to E-cadherin impairment in sporadic
gastric cancer. We confirmed that, independently of the histological type, E-cadherin is frequently
impaired (95%) in our series of sporadic gastric cancer. However, only 30% of the cases harbour
classical inactivation mechanisms. We found that miR-101 expression is downregulated in most of
these cases and proved, for the first time, that this occurs via (micro) deletions at one of the
microRNA-101 loci in chromosome 9p24.1 (miR-101-2 locus). Moreover, 40% of cases showing
decreased levels of miR-101 displayed overexpression of EZH2 (a known target gene of miR-101)
which, in turn, associates with loss or aberrant E-cadherin expression. Conversely, we demonstrated
that depletion of EZH2, by short interference RNA, rescues E-cadherin cell-membrane expression.
Overall, we show that loss of miR-101 with parallel EZH2 upregulation may constitute an additional
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mechanism that can either directly impair E-cadherin expression or may co-exist with classical Ecadherin inactivating mechanisms seen mainly in advanced cancers with intestinal morphology.
Identification of novel E-cadherin transcripts with deleterious effect over the canonical form of Ecadherin
Despite the strong correlation between E-cadherin impairment and malignancy, the cause underlying
its impairment remains unknown in most epithelial cancers. We identified a novel E-cad transcript,
characterized by its tissue specific expression and its functional role in a cancer context.A new E-cad
exon was identified within intron 2 splicing with exon 3 at its canonical splice-site. 5’-RACE and CAGE
analysis pinpointed two potential transcription start sites (TSS) and an ORF. This transcript includes
all downstream canonical exons of E-cad gene, is expected to be translated and was named CDH1a.
CDH1a is specifically expressed in spleen, a non-epithelial tissue and is absent from the stomach
epithelia. In stomach cancer cell lines, it becomes overexpressed. Forced overexpression of CDH1a in
cell lines expressing the canonical E-cad promotes cell invasion and angiogenesis and modifies their
expression pattern as proved by microarray analysis. We identified a novel E-cadherin protein
isoform cis-regulating the function of the canonical form. This finding may enclose a previously
unrecognized mechanism leading to E-cadherin impairment in cancer.
Development of new tools for prophylaxis and/or therapeutic intervention in E-cadherin related
cancer
We generated mini-genes that mimic the endogenous CDH1 transcripts (wild-type and mutant), that
are correctly spliced and expressed, leading to normal E-cadherin protein processing and
localization. This model will be used to test the effectiveness of suppressor tRNAs as a therapeutic
tool.
This work has been developed in collaboration with Ana Paula Pêgo from the NewTherapies group of
INEB and Manuel Santos from U. Aveiro.
Determination of the mechanism responsible for mutant E-cadherin expression rescue to the
plasma membrane by the action of Chemical Chaperones (CCs), namely in E-cadherin trafficking
and with molecular partners involved in its regulation
We have previously shown that it is possible to rescue E-cadherin expression, even in the presence of
E-cadherin mutant forms, by inhibiting the proteasome or by using different Chemical Chaperones
(CCs). Now, using cells stably expressing WT E-cadherin or different HDGC-associated missense
mutations, we show that upon DMSO treatment, not only mutant E-cadherin is restored and
stabilized at the plasma membrane (PM), but also Arf6 and PIPKIγ expressions are altered, both
crucial components of E-cadherin trafficking machinery. We show that modulation of Arf6
expression partially mimics the effect of CCs, suggesting that the cellular effects observed upon CCs
treatment are dependent of Arf6. Further, we show that E-cadherin expression recovery is
specifically linked to Arf6 inhibition and not dependent on endocytosis blockage. Overall, we show
that E-cadherin rescue and stabilization in response to several CCs treatment is dependent on Arf6
downregulation, resulting in the blockage of E-cadherin endocytosis and increased recycling to the
PM. We demonstrate, for the first time, that CCs have a direct influence in the cellular trafficking
machinery and we show that this effect is of crucial importance in the context of juxtamembrane Ecadherin missense mutations (domain where P120 binds to e-cadherin).
Identification of Notch1 as an important therapeutic target in E-cadherin related cancer
We have previously shown that overexpression of mutant human E-cadherin in Drosophila produces
a phenotype characteristic of downregulated Notch. Now, we showed that de novo expression of
wild-type E-cadherin led to a significant decrease in the activity of the Notch pathway. In contrast,
the ability to inhibit Notch-1 signaling was lost in cells transfected with mutant forms of E-cadherin.
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Increased Notch-1 activity in E-cadherin-deficient cells correlated with increased expression of Bcl-2,
and increased resistance to apoptotic stimuli. After Notch-1 inhibition, E-cadherin-deficient cells were
re-sensitized to apoptosis in a similar degree to wild-type E-cadherin cells. We also show that Notchinhibiting drugs are able to significantly inhibit the growth of E-cadherin-deficient cells xenografted
into nude mice. This effect was comparable to the one observed in animals treated with the
chemotherapeutic agent taxol a chemical inducer of cell death.
These findings highlight the possibility of new targeted therapeutical strategies for the treatment of
tumors associated with E-cadherin inactivation.
Identification of P-cadherin as a therapeutic target in cancer
We tested the therapeutic role of the bacterial protein azurin in P-cadherin overexpressing cells (in
vitro and in vivo). The ongoing experiments concerning the cellular effects of treating different
breast cancer cell models (with distinct levels of P-cadherin expression) with azurin showed that this
peptide downregulates the specific expression of P-cadherin, and does not affect E-cadherin
expresssion. We also saw that azurin is able to inhibit P-cadherin-induced cell invasion.
This work has been developed in collaboration with the group of Arsenio Fialho- IBB-IST.
Dissection of the EGFR downstream targets predictive of therapy outcome in gastric, breast and
colorectal cancer patients and assessment of new targeted therapies
In colon, siRNA technology was used as a first approach to inhibit MAPK, PI3K or both signaling
pathways in cell lines harboring genetic alterations responsible for resistance to anti-EGFR therapy
(KRAS, BRAF and PI3K activation). The signaling molecules selected to be silenced were MEK1, MEK2
and PIK3CA and the CRC cell lines used included HCT116, SW480, RKO and HT29. Cellular
proliferation/viability, cell cycle and apoptosis were monitored and, at the moment the most
effective target was shown to be PIK3CA. Proteins from the MAPK and PI3K pathways (downstream
of MEK1/2 and PI3K), phosphorylated and total forms, are also being investigated.
In GC, we characterized a series of 63 gastric carcinomas with high levels of microsatellite instability
(MSI) for we aimed to determine the frequency of gene mutations in members of EGFR pathway-Epithelial Growth Factor Receptor (EGFR), KRAS, BRAF, PIK3CA and MLK3. Within all alterations
found, deletions of the A13 repeats of EGFR were common (47.6%), suggesting this molecular event
as an important biomarker for stratification of GC patients for treatment with EGFR inhibitors. KRAS,
PIK3CA and MLK3 genes occurred in 17.5%, 14.3% and 3.2%. No BRAF or EGFR hotspot mutations were
identified. Results from this study are expected to bring new insight into the use of EGFR
pharmacological inhibitors as anticancer therapy in GC.
In breast cancer we demonstrated that basal-like subtype of breast cancer showed a high frequency
of PTEN losses which can explain the failure of anti-EGFR therapy in this aggressive type of breast
cancer, since loss of PTEN is one of the mechanisms of resistance to TKI.
Establishment of methodologies to identify cancer cells with stem-like properties at IPATIMUP
We were able to establish already three different methods: i) Aldehyde dehydrogenase activity
(ALDEFLUOR assay); ii) FACS analysis of stem cell surface markers; and iii) the culture of mammary
cells in anchorage independent conditions (mammosphere assay). All these methods were optimized
and applied to a large series of breast cancer cell lines.
Furthermore, using a series of breast cancer cell lines, we show that P-cadherin enriched populations
(by genetic manipulation or by sorting) have a high mammosphere forming efficiency (MFE), as well
as a higher expression of CD44, CD24 and CD49f CSC markers. Interestingly, on an extensive tissue
microarray series, we have seen that the worst disease-free and overall survival is found in patients
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26
with the combination of P-cadherin expression with either CD24 or CD44 markers. When compared
with Luminal cell lines, Basal-like cells have a greater ALDEFLUORbright subpopulation and the Pcadherin positive subfraction of these cell lines is enriched in stem cell activity (MFE and 3D growth).
Interestingly, P-cadherin also confers resistance to X-ray induced DNA damage, supporting a role of
this molecule in the maintenance of another CSC property.
Identification of cancer stem cell markers in breast cancer subtypes
Using a series of 467 invasive breast carcinomas and 7 breast cancer cell lines, we analysed the
expression of CD44, CD24 and ALDH1, in order to evaluate their distribution among the distinct
molecular subtypes, using different methods of evaluation: immunohistochemistry and flow
cytometry. The results led us to conclude that the described CD44+CD24-/low and the ALDH1+ stemlike phenotypes identify cancer stem cells with distinct levels of differentiation, being the former
profile more related with tumors which origin is possibly related with primitive mammary stem cells,
whereas the last one seems to be a marker of tumors deriving most likely from luminal committed
progenitors. These findings constitute an initial alert about the need to better explore the
paramount method and biomarkers that identify breast cancer stem cells within the distinct
molecular subtypes, since it is pivotal to translate the “cancer stem cell” concept to the clinical
practice.
Dissection of how cancer cells modulate the inflammatory microenvironment and which are the
molecular mechanisms used by these tumor cells to escape immune surveillance
In one hand we detected an increase of the levels of IL-6, IL-8 upon co-cultured of CRC cells with
monocytes. On the other hand, CRC cells in presence of dendritic cells resulted in a reduction of IL-6
secretion. Although very preliminary these data support the existence of an interaction between CRC
cells and different types of immune cells and also points towards an effect of CRC cells on the
modulation of the tumoral inflammatory microenvironment by regulating cytokine secretion.
This work has been developed in collaboration with Mário Barbosa from the NewTherapies group of
INEB.
National Collaborations
Alexandre Carmo, Cell Activation and Gene Expression, IBMC, Porto;
Ana Paula Pêgo, NEWTherapies group, INEB, Porto;
Arsénio Fialho, IBB-Instituto Superior Técnico (IBB/IST/UTL), Lisboa;
Fátima Baltazar, Life and Health Sciences Research Institute (ICVS), University of Minho, Braga;
Isabel Palmeirim, Department of Medicine, University of Algarve, Faro;
João Taborda Barata, Instituto de Medicina Molecular (IMM), FMUL, Lisboa;
Manuel A. Santos, Department of Biology and CESAM, University of Aveiro, Aveiro;
Manuel Coimbra, Departament of Chemistry, University of Aveiro, Aveiro;
Maria Oliveira, NEWTherapies group, INEB, Porto;
Mário Barbosa, NEWTherapies group, INEB, Porto;
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Nuno Azevedo, Department of Chemical Engineering, Faculty of Engineering, University of Porto,
Porto;
Nuno C. Santos, Unidade de Biomembranas, Instituto de Medicina Molecular (IMM), FMUL, Lisboa;
Paulo Pereira, Group of Biology of Ageing, IBILI, Coimbra;
Paulo Pereira, Molecular Genetics, IBMC, Porto;
Pedro Granja, NEWTherapies group, INEB, Porto;
Peter Jordan, Instituto Nacional Ricardo Jorge, Lisboa.
International Collaborations
Australia
Amanda Charlton, Department of Pathology, The Children's Hospital at Westmead, Sydney
Georgia Chenevix-Trench, NHMRC Senior Principal Research Fellow, The Queensland Institute of
Medical Research, Brisbane.
Belgium
Marc Mareel, Laboratory of Experimental Cancer Research, Department of Radiotherapy and
Nuclear Medicine, Ghent University Hospital, Ghent;
Marc Bracke, Laboratory of Experimental Cancer Research, Ghent University Hospital, Ghent.
Brazil
Dulciene Queiroz, Laboratory of Research in Bacteriology, Faculdade de Medicina, Universidade
Federal de Minas Gerais, Belo Horizonte.
Canada
David Huntsman, British Columbia Cancer Agency, Vancouver.
Costa Rica
Vanessa Ramirez, Departments of Pathology and Gastroenterology, Calderón Guardia Hospital
San José.
Denmark
Lene J Rasmussen, University of Copenhagen, Copenhagen.
Finland
Lauri A Aaltonen, Tumor Genomics Research Group, Department of Medical Genetics, Biomedicum
Helsinki, University of Helsinki.
France
Alex Duval, INSERM, Hôpital Saint-Antoine, Paris;
Eliette Touati, Institute Pasteur, Paris.
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Germany
Thomas Meyer, Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin;
Federico Canzian, German Cancer Research Center (DKFZ), Heidelberg;
Thomas Schulz, Institute of Virology, Medical School Hannover.
Holland
Bauke Ylstra, Microarray Core Facility (MAF) of the VU University Medical Center/ Cancer Center
Amsterdam;
Beatriz Carvalho, Dept Pathology, VU Univ. Medical Center, Amsterdam;
Leen-Jan van Doorn, DDL Diagnostic Laboratory, Voorburg;
Marjolijn Ligtenberg and Han van Krieken, Radboud University Nijmegen Medical Centre, Nijmegen;
Robert Hofstra, Department of Medical genetics, University of Groningen, Groningen.
Ireland
Steffen Backert, School of Biomolecular and Biomedical Sciences, University College Dublin, Dublin.
Israel
Yosef Yarden, Weismann Institute, Rehovot.
Italy
Franco Roviello, Dept Surgery and Oncology, University of Siena, Siena;
Remo Sanges, Cluster in Biomedicine, Trieste.
Spain
Gema Moreno-Bueno, Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM),
Instituto de Investigaciones Biomédicas 'Alberto Sols' CSIC-UAM, Madrid;
Jorge F. Cameselle-Teijeiro, Department of Pathology, Complexo Hospitalar Universitario de Vigo
(CHUVI), Vigo;
José Palacios, Servicio de Anatomía Patológica, Hospital Virgen del Rocío, Sevilla;
Luis Serrano, Systems Biology, CRG, Barcelona;
José Luis Skarmeta, Centro Andaluz de Biología del Desarrollo, Sevilla;
Fernando Casares, Centro Andaluz de Biología del Desarrollo, Sevilla;
Carlos Gonzalez, Unit of Nutrition, Environment and Cancer, Catalan Institute of Oncology (IDIBELLICO), Barcelona;
Gabriel Capellá, Catalan Institute of Oncology (IDIBELL-ICO), Barcelona.
Sweden
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Ola Söderberg, Department of Genetics and Pathology, University of Uppsala, Uppsala.
UK
Göran Landberg, Breakthrough Breast Cancer Research Unit, Paterson Institute for Cancer Research
(PICR), University of Manchester, Manchester;
Robert B. Clarke, Breast Biology Group, Paterson Institute for Cancer Research (PICR), University of
Manchester, Manchester;
Elia Stupka, Univ. College of London Cancer institute, London;
Carlos Caldas, Cambridge Research Institute Li Ka Shing Centre, Cambridge;
John Atherton, Nottingham Digestive Diseases Centre NIHR Biomedical Research Unit, School of
Clinical Sciences, University of Nottingham, Nottingham;
Jorge Sérgio Reis-Filho, The Breakthrough Breast Cancer Research Centre, Institute of Cancer
Research, London.
USA
Gregory Lauwers, Department of Pathology, General Hospital, Boston;
Kevin Haigis, Molecular Pathology Unit of the Massachusetts General Hospital, Boston;
David Mooney, Lab of Cell and Tissue Engineering, School of Engineering and Applied Sciences
(SEAS), Harvard University, Cambridge.
Future Research
Elucidate the mechanisms underlying the inhibitory effect of DHA on H. pylori growth and gastric
colonization;
Clarify the influence of H. pylori on the cell-cell tight junctional complex, and explore the functional
consequences and signaling pathways associated with tight junction dysfunction in this context;
Study the upstream and downstream signaling leading to aberrant C/EBPβ expression in gastric
cancer, namely the influence of TGFbeta signaling;
Molecular characterization of novel CDH1 transcripts target effectors and associated signalingpathways to understand their functional and clinical relevance;
Analyze new forms of intronic regulation at the cadherin family of genes loci;
Identify novel players in EMT/MET and its function in cancer and metastasis;
Identification of novel microRNAs associated pathways involved in E-cadherin impairment;
Determine whether the CD44v6 (+) sub-population in 3D cultures shows enhancement of invasive,
proliferation, apoptosis-resistance and stemness features;
Determine whether the CD44v6-targeting peptides do allow specific targeting to variant of receptor;
We will dissect the molecular mechanisms responsible for the recognition/regulation of E-cadherin
and its HDGC-associated mutants;
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30
Determine whether HDGC associated E-cadherin mutations interfere with the membrane trafficking
and/or half-life of E-cadherin;
Study the expression and activity of specific E-cadherin trafficking regulators and determine if they
are differently regulated in the context of HDGC associated E-cadherin missense mutations;
Test tRNA suppression as a therapeutic approach to HDGC;
Dissect the signaling pathways responsible for angiogenesis blockade by CPEB1 in GC;
Test CPEB1 regulation by predicted Transcription Factors in GC;
Validate other interesting candidate genes in tumors in GC;
Study the regulatory relationship between E-cadherin and P-cadherin in breast cancer, its cellular
consequences and associated signaling pathways;
Test whether P-cadherin expression is a determinant of cancer stem cell activity in breast cancer and
a marker of tumors deriving most likely from luminal committed progenitors;
Verify the therapeutic value of P-cadherin as a molecular target to impair breast cancer cell invasion
and metastization, which may have important implications for the development of new /specific
therapeutics for these invasive cancers;
Verify the cellular effects mediated by bacterial derived peptides in P-cadherin overexpressing cells
(in vitro and in vivo);
Identify the transcription factors that underlie cancer stem phenotype and P-cadherin expression;
Establish 3D cultures and radiotherapy resistance assays at IPATIMUP;
Study whether P-cadherin expression is a response to hypoxia in the tumor microenvironment,
acting as a cancer cell survival factor;
Use the expression of the tight junction proteins claudins (1,3,4 and 7), in order to identify the new
breast cancer subtype: the Claudin-low subtype, and to study their association with breast cancer
stem cell markers;
Study the cellular effects mediated by VitD d in breast cancer progression and identify the underlying
molecular mechanisms;
Study the role of CK2 in the regulation of PI3K- PTEN pathway in breast cancer;
Determine the expression profile of distinct subtypes of breast cancer;
We will determine in CRC cell lines the phosphorylation of 46 kinase phosphorylation sites upon
silencing of MEK1/2 and/or PI3K. Proteins with major impact will be further analysed;
We will start analyzing the effects of a panel of MEK1/2 and PI3K/mTOR inhibitors (e.g. AZD6244,
BEZ-235) in CRC cell lines. In parallel, colon primary cultures will be established and the drugs also
tested in these cells;
To proceed with in vitro studies using co-cultures of K-RAS and B-RAF mutant CRC cells and their
isogenic knockouts and immune cells, in order to establish the importance of MAPkinase pathway
activation on immune cell modulation by CRC cancer cells;
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Verify the functional role of PI3K modulation, in EndMT transdifferentiation using biomimetic in vitro
models and siRNA assays.
Prizes
Fernando Schmitt- "Educator of the Year 2011" da Papanicolaou Society of Cytology, USA.
Céu Figueiredo- Prize for best oral presentation (Peleteiro B, Lopes C, Figueiredo C, Lunet N). Salt
intake and gastric cancer risk according to Helicobacter pylori infection, tumour location and
histological type. Enrico Anglesio. XXXV Meeting of the Group for Epidemiology and Registration of
Cancer of Latin Languages Countries. Toledo, Spain. May 2010.
Joana Paredes - Premio Centro Oncológico de Galicia “José Antonio Quiroga y Piñeyro”, Real
Academia de Medicina e Cirugia de Galicia, A Coruña, Spain.
Gianni Corso. Merit Award ASCO Cancer Foundation® 2011 Gastrointestinal Cancers Symposium San
Francisco CA “Oncogenic mutations in MAPK cascade as novel molecular biomarkers for treatment
of gastric cancer patients with EGFR inhibitors”.
Joana Paredes
• “P-cadherin and invasion (breast cancer cell model)”. Oncobiology module, GABBA (Graduate
Program in Areas of Basic and Applied Biology) PhD Program, at IPATIMUP, Porto, Portugal.
• “P-cadherin and invasion (breast cancer cell model)” Oncobiology module, Gulbenkian PhD
Program of Advanced Medical Formation, with Champalimaud Foundation participation, at
IPATIMUP, Porto, Portugal.
• “Stem Cells: their association with Cancer". PhD Program on Molecular and Environmental Biology,
CBMA-Minho University, Braga, Portugal.
Joana Caldeira
Drosophila as an In Vivo Model to Study Cancer. “Gulbenkian Doctoral Programme for Physicians –
Oncobiology module, 2010” 10th January, 2010 (IPATIMUP, Porto, Portugal)
Drosophila as an In Vivo Model to Study Cancer. “GABBA Programme – Oncobiology module, 2010”
20th April, 2010 (IPATIMUP, Porto, Portugal)
Joana Correia
Participated in the module of Oncobiology for the Doctoral program of Gulbenkian: “Programa de
Formação Médica Avançada”
Participated in the Oncobiology module for the Graduate Program in Areas of Basic and Applied
Biology (GABBA), of the University of Porto
Participated in the module of “General introduction to basic laboratory techniques”, of the Doctoral
Program in Health Sciences, form the Faculty of Medicine, University of Coimbra
Sofia Fernandes
Novel Therapeutic Strategies for Colorectal Cancer. “Gulbenkian PhD Programme of Advanced
Medical Formation, Oncobiology module, 2010” 10-14 January, 2010 (IPATIMUP, Porto, Portugal)
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32
Raquel Seruca
Responsible for the Oncobiology module, GABBA (Graduate Program in Areas of Basic and Applied
Biology) PhD Program, at IPATIMUP, Porto, Portugal.
Responsible forthe Oncobiology module, Gulbenkian PhD Program of Advanced Medical Formation,
with Champalimaud Foundation participation, at IPATIMUP, Porto, Portugal.
Céu Figueiredo
Helicobacter pylori infection and susceptibility to gastric carcinoma. Oncobiology module, GABBA
(Graduate Program in Areas of Basic and Applied Biology) PhD Program. IPATIMUP, Porto, Portugal.
April 2010.
Participation in Master Programs
Joana Paredes
• “Mechanisms of Cellular Communication” and “Cell adhesion, invasion and metastisation”. PostGraduation course on Fundamentals of Genetics, Development and Neoplasia, ICVS, Minho
University, Braga, Portugal.
• “Progressão Tumoral: Angiogénese, Invasão e Metastização”. Oncobiology course, Universidade
Católica Portuguesa, Porto, Portugal.
• “Cancer Stem Cells: implications for cancer biology and therapy”. Advanced Course on
Oncobiology, CNC, Faculdade de Medicina da Universidade de Coimbra, Coimbra, Portugal
Raquel Seruca
• “ E-cadherin mediated pathways”. Advanced Course on Oncobiology, CNC, Faculdade de Medicina
da Universidade de Coimbra, Coimbra, Portugal
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33
Carcinogenesis
Objectives
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).
Main Achievements
Our main achievements follow two lines of action: one on the molecular mechanisms involved in the
development of gastric intestinal metaplasia (IM) and the second, where we identified new
mechanisms involved in interaction between glycosylation and infection by Helicobacter Pylori and
also on glycosylation modifications in cancer. The two lines are cross fertilizing since IM is a paradigm
of modifications of the glycoproteome and it’s a model where regulatory mechanisms start to be
understood – a first step was given by showing that MUC2 mucin is a major carrier of the sialyl-Tn
antigen in IM, which strongly suggests, in view of our previous work, that the CDX2 master gene,
involved in IM development, can be in fact a major regulator of whole glycoprotein modifications.
After identification of BMP2/4, through Smad4, as major players in initiating gastric IM (2008,2009)
we have in 2010 contributed with three publications that support the lack of reversibility of IM in the
clinical setting and demonstrate that CDX2 auto-regulates its own promoter which can explain the
stability of IM phenotype (Barros R et al, Biochem Soc Trans 2010; Barror R et al, Scand J
Gastroenterol 2010; Barros R et al, Gut in press).
We participated in two epidemiologic studies that showed that salt intake does not have an impact
on IM development and also on the evaluation of sensitivity of methods to detect past H. pylori
infection (Peleteiro B et al, Cancer Causes and Control 2010; Pintalhao M et al, Nutr Cancer 2010).
We proceeded with previous work on glycan receptors relevant for H.pylori adhesion (Magalhães A
et al, Braz J Med Biol Res 2010; Magalhães A et al, Expert Rev Proteomics 2010) and clarified the
genetic variation of the FUT2 enzyme, responsible for the “secretor” glycosylation determinant for
adhesion of BabA+ H.pylori (Silva LM et al, Glyconj J 2010).
Proximity ligation assays were used for the first time for in situ identification of glycopeptide
compounds and MUC2 intestinal mucin was shown to be the carrier of the cancer-associated sialyl-Tn
antigen in intestinal metaplasia and gastric carcinomas (Conze T et al, Glycobiology 2010). Two
review papers highlight ours and others observations on the relevance of N- and O-glycosylation as
cancer biomarkers (Pinho SS et al, Cell Mol Life Sci in press; Reis CA et al, J Clin Pathol 2010).
The enzymatic pathways involved in the biosynthesis of cancer-associated Sialyl-Lex and sialyl-Lea in
gastric cancer cells was clarified and enzymes ST3Gal III, ST3Gal IV and FUT5 were identified as major
players (Carvalho AS et al, Int J Biochem Cell Biol 2010).
We identified glycan binding protein Galectin-3 overexpression in intravascular tumour cell
populations as a crucial event for canine mammary tumour metastases (de Oliveira JT et al,
Glycobiology 2010).
Our involvement in an EU funded project for detection of cancer serum biomarkers generated mass
spectrometry identification of several new potential targets with cancer-associated glycoforms in
the serum of breast cancer patients. Peptides from these targets, covering potential O-glycosylation
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34
sites, were printed in microarrays and glycosylated with recombinant enzymes to generate different
glycopeptides. Serum from cancer patients is currently being searched for the presence of
antibodies to the glycopetide targets identified. On the same line of action different mucin-based
glycopeptides were printed on the microarrays, and are also being used to immunize mice to obtain
glycopeptide specific antibodies. A glycan dependent monoclonal antibody for MUC16 mucin was
already obtained and is currently under final characterization for publication – we have evidence
suggesting it will be a promising alternative to CA125 assay for ovarian cancer detection.
Faculty of Health Sciences of the University of Copenhagen – Ulla Mandel and Henrik Clausen. This
collaboration has been fundamental for characterization of carbohydrate antigens and
glycosyltransferases using unique monoclonal antibodies. We are collaborating with this group for
building glycopeptides arrays in the context of the European project. One PhD student of the group
(Lara Silva) is doing a joint PhD thesis. We regularly collaborate in pos-graduate teaching activities at
the University of Copenhagen – PhD Glycobiology Course.
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 the field.
INSERM, Strasbourg – Jean-Noel Freund. This collaboration is essential for the study of CDX2
regulation in intestinal metaplasia using animal models. A PhD thesis (Rita Barros) was completed
between our two groups.
Umea University, Sweden – Thomas Borén. This collaboration has contributed for establishing
H.pylori adhesion assays. A PhD thesis (Ana Magalhães) is being completed between our two groups.
Consortium for Functional Glycomics – The Scripps Research Institute, CA, USA - James Paulson. This
collaboration (Celso Reis is a member of the Consortium) has provided the use of resources of the
Consortium (funded by the NIH), including Microarray analysis and knock-out mice.
University of Uppsala - Ola Soderberg. This collaboration has allowed the successful establishment of
Proximity-Ligation assays for identification of glycopeptide 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.
Institut Pasteur, France - Eliette Touati. This collaboration is essential for the study of Helicobacter
Pylori using animal models. A PhD thesis (Joana Gomes) is being developed between the two groups.
Osaka University and RIKEN, Japan – Naoyuki Taniguchi. This collaboration is essential for the study
of N-glycosylation in cancer, by providing access to unique resources including monoclonal
antibodies and due to the recognized expertise of the Japanese group in the field.
Utrecht University Clinic of Companion Animals, The Netherlands –This collaboration is important for
the study of dog mammary tumours. A PhD thesis (Joana Oliveira) is being co-supervised by Prof.
Gerard Rutteman.
Biocenter Oulu, Oulu Centre for Cell-Matrix Research, Department of Medical Biochemistry and
Molecular Biology, University of Oulu, Finland. - Aki Manninen. This collaboration is very promising
for the assessment of galactan efficacy in vitro and also in vivo in a metastasis assay conducted in
nude mice.
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Future Research
We aim to expand our knowledge on CDX2 regulation by generating animal models as proof-ofprinciple for BMP involvement in in vivo models and will clarify new regulatory interactions (eg SOX2
and MEX3A). We aim to apply our glycobiology expertise into getting synthetic
carbohydrates/analogs for inhibiting adhesion of Helicobacter Pylori to gastric cells and to achieve
identification of glycopeptides for serum detection of cancer at early stages. A wider understanding
of cancer associated modifications in the serum glycoproteome will be pursued. N-glycosylation of Ecadherin and its putative relevance for cadherin dysfunction in cancer will be explored using cell lines
models and clinical samples. We aim to clarify the role mediated by carbohydrate-Galectin-3
interaction in regulation of tumour progression and metastasis.
The group aims to clarify mechanisms involved in transdifferentiation of gastric mucosa. We will
continue to search regulatory mechanisms involved in CDX2 regulation and expression in gastric IM
lesions, characterized by transdifferentiation to an intestinal phenotype. Specifically, we will extend
recent findings on the involvement of SOX2 as a CDX2 repressor in the stomach and also regulated
by the BMP pathway. We will also extend recent findings in three dimension cultures, showing that
CDX2 expression is also regulated post-transcriptionally by the protein MEX3A. This protein
sequesters RNA molecules impairing their translation, in that way regulating protein levels.
Furthermore, we will continue studying the involvement of the BMP pathway in CDX2 regulation and
IM onset (previously published) by generating a mouse model overexpressing the BMP pathway in
the stomach and evaluating the gastric phenotype with the expectation that IM lesions will develop.
The group aims to characterize the role of glycans for H.pylori adhesion/infection and to discover
novel anti-adhesion therapeutic strategies based on synthetic carbohydrates/analogs. Several
approaches will be used: 1) Cell lines genetically manipulated for glycosyltransferases expression and
mice knocked-out for glycosyltransferases, with glycan profiles characterized by
immunohistochemistry and mass spectrometry, are being used to identify glycans relevant for
H.pylori adhesion/infection and also for induction, upon adhesion/infection, of new
glycosyltransferases repertoires; 2) We will continue the development of novel strategies for
inhibition of H. pylori adhesion and infection. This approach is being developed within an on-going
collaboration with Dr. Cristina Martins from INEB, funded by FCT. In this project we are developing
and testing Chitosan microspheres with synthetic carbohydrates receptors for inhibition of H. pylori
adhesion, using the models described above.
The group will participate in defining the serum glycoproteome of cancer patients and in production
of glycopeptide arrays, with the aim of generating serum tests for cancer diagnosis. a) Validation of
the identified glycopeptides will be performed by Western-blotting using Proximity Ligation (PLA)
assays; b) Several cancer-associated glycopeptides identified by mass spectrometry are currently
being tested on glycopeptides arrays; c) Mucin-based glycopeptides (based of recombinant MUC2,
MUC5AC and MUC6 mucins) are being produced chemoenzymaticaly and printed on the arrays to
screen serum from patients with gastritis, intestinal metaplasia and gastric carcinomas. This
approach aims at evaluating auto-antibodies to specific glycopeptides in the serum of the patients.
The group will generate glycopeptide specific monoclonal antibodies with increased specificity for
cancer-associated mucin glycoforms. a) Recombinant MUC2, MUC5AC and MUC6 proteins are being
produced and glycosylated in vitro with glycosyltransferases to produce cancer-associated
glycoforms of the mucins. These mucin glycoforms are being used to immunize mice in order to
generate cancer-specific monoclonal antibodies; b) A MUC16 GalNAc glycosylated glycoform was
used to immunize mice and a monoclonal antibody was produced and is being extensively
characterized.
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36
The group will use the glycobiology expertise to evaluate the role of E-cadherin glycosylation in
cancer cell behaviour. We will genetically manipulate cancer cell lines by transfecting specific
glycosyltransferases and evaluate the E-cadherin glycosylation modifications and its impact in cancer
cell biology. By using mass spectrometry we will characterize the different N-glycans structures
attached to E-cadherin; we will evaluate the biological role of each E-cadherin N-glycan structure in
cancer by transfecting cancer cell lines with mutant forms of E-cadherin for potential N-glycosylation
sites and evaluating its consequences on cancer cell behaviour (in vitro and in vivo). We will further
validate the findings by analysing the pattern of expression of specific glycosyltransferases and their
products in a set of human gastric carcinoma cases displaying E-cadherin dysfunction but without
genomic alterations.
The group aims to clarify and interfere with the mechanisms involving sialic-acid mediated galectin-3
functionality. We will try to clarify if posttranslational sialic-acid masking (by
sialidases/sialyltransferases) of galactose residues, that act as ligands for galectin-3, can be a
modulator of cyclic adhesion/de-adhesion of cancer cells. To interfere with the system we will both
manipulate sialidases activity to regulate ligand exposure and use galactan as a competitor for
galectin-3 binding in in vivo nude mice models, using a highly metastatic canine mammary tumour
cell line.
Programa Doutoral de Medicina e Oncologia Molecular of the Medical Faculty of the Universisty of
Porto . Raquel Almeida, Celso Reis, Leonor David.
Programa Doutoral em Patologia e Genética Molecular do Instituto de Ciências Biomédicas Abel
Salazar . Raquel Almeida, Celso Reis, Fátima Gärtner, Leonor David.
PhD program GABBA (Graduate program in areas of Basis and Applied Biology) of the University of
Porto . Raquel Almeida, Celso Reis, Leonor David, Salomé Pinho.
Programa doutoral para médicos das Fundações Gulbenkian e Champalimaud . Raquel Almeida, Celso
Reis, Leonor David.
Mestrado de Bioquímica da Faculdade de Ciências da Universidade do Porto . Leonor David.
Supervision of Rita Pinto on “Cancer glycoproteome alterations: is there a role for CDX2?”.
Mestrado em Oncologia do Instituto de Ciências Biomédicas Abel Salazar . Celso Reis. Supervision of
Diana Campos on “Biomarkers for early detection of gastric cancer based on autoantibodies
signatures”. .
Mestrado em Oncologia do Instituto de Ciências Biomédicas Abel Salazar. Fátima Gärtner.
Mestrado em Análises Clínicas e Saúde Pública da Universidade Católica Portuguesa . Raquel
Almeida, Hugo Osório, Celso Reis.
Mestrado em Biotecnologia, Universidade de Aveiro . Fátima Gärtner (Thesis supervision)..
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37
Tumor Molecular Models
Objectives
The major research interest of the group is to decode the molecular models beneath the initiation,
progression and resilience of epithelial tumors. Our focus are cell membrane proteins which are key
factors in these processes with relevance on cell-cell cross talk and external stimuli integration. MUC1
glycoprotein constitutes our elective target due to the multiple functional roles and the frequent
alterations of the molecule observed in several tumor types. We aim to identify the relevance of
MUC1 in oncogenic signaling and drug resistance phenotype of cancer (stem) cells. The long-term
objective is to develop MUC1 comprehensive models critical for the development of new diagnostic
and/or therapeutic strategies that effectively overcome current limitations on tumor detection and
therapy.
Main Achievements
Team:
Besides the PI (Filipe Santos Silva) the group is now composed by Natália Costa (PhD Student),
Andreia Sousa (PhD student) and Cristina Teixeira (research trainee).
At this phase of consolidation we invested mainly on the formation of master degree students
integrated in one-year projects. The students with best performance applied to PhD individual grants
or have been recruited to research project grants. In September 2010, Joana Castro got her Masters
in Cell and Molecular Biology from Faculty of Sciences and Technology of the University of Coimbra
with the thesis “Characterization of the involvement of cancer stem cells in gastric cancer resistance
to chemotherapy”. In December 2010, Cristina Teixeira got her Masters in Biology with the thesis
“Chemoresistance in Pancreatic Cancer Stem Cells”. Andreia Sousa has been selected to the PhD
program in Medicine and Molecular Oncology - Medical Faculty of the University of Porto and got a
PhD grant from FCT (ref# SFRH/BD/73410/2010) with the thesis “Relevance of MUC1 splice variants
for pancreatic cancer stem cells phenotype”. Both PhD students (Andreia Sousa and Natália Costa)
have FCT grants (SFRH/BD/36961/2007 and SFRH/BD/73410/2010) in the area of Health Sciences in
collaboration with Prof. Michael Anthony Hollingsworth from Eppley Cancer Institute, University of
Nebraska Medical Center.
Projects:
Research activity has been supported by our FCT projects: “Identification of signaling pathways
mediated by MUC1 oncogene in gastric carcinoma cell lines and immortalized gastric cells” (ref#
PTDC/SAU-OBD/65616/2006) and “Development of a medical information system about Hereditary
Breast and Colorectal cancer” (ref#HMSP-IDSIM/SIM/0013/2009); and collaborative project:
“Development of siRNA-loaded nanoparticles to circumvent chemoresistance in cancer stem cells"
(PTDC/EBB-BIO/099672/2008).
We submitted two new research project proposal: “Biology of pancreatic cancer stem cells - the
relevance of MUC1 protein” ref# PTDC/SAU-ONC/121933/2010 and “Information and Communication
Technologies on Biomedical Education - A brave new virtual world” ref# PTDC/CPE-CED/119313/2010,
to the FCT “Call for proposals for scientific research and technological development projects in all
scientific domains – 2010”. We collaborate with Dr. Sandra Rocha from Chemical Engineering Group –
Faculdade de Engenharia da Universidade do Porto (FEUP) in the preparation of the new research
project proposal “Nanoparticles for cancer chemoprevention by bioactive natural compounds”
ref#PTDC/QUI-BIQ/117648/2010.
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38
We have been part of the European consortium that prepared and submitted the proposal
“Specialized nanosystems for cancer therapy” to the EUROPEAN call FP7-NMP-2010-LARGE-4 –
Development of nanotechnology-based systems for detection, diagnosis and therapy for cancer
(Cancer Systems). Within this process we gather experience and contacts for future applications to
international agencies, which will reduce our dependency on national funding. We further reinforce a
multidisciplinary network of collaborations, renovating and establishing new international and
national collaborations (listed bellow), in order to successfully tackle the different aspects of our
research plan.
Workshop organization
We have been selected to host a Harvard Medical School Portugal Program Workshop – Visualizing
molecular and cellular processes with 3D animation. Porto. June 2010.
Research - MUC1 signaling in gastric cancer
MUC1 is a major component of the stomach mucus layer that modulates interactions between the
epithelium and external factors. MUC1’s highly conserved cytoplasmic domain (MUC1-CD) has been
recently reported to be involved in cell signaling processes in different tumor models. Using coimmunoprecipitation/immunoblotting and Proximity Ligation Assay (PLA) we prove that MUC1-CD
directly binds ERK1/2, EGFr and Beta-catenin. Furthermore siRNA assays showed that MUC1
conditions the expression levels and phosphorylation of ERK1, ERK2 and EGFR. These observations
proved an extensive involvement of MUC1 in gastric cancer signaling pathways namely EGF/MAPK
and beta-Catenin pathways. These findings were presented at “Meeting on Protein Phosphorylation
and Cell Signaling - 30 Years of Tyrosine Phosphorylation”. San Diego, USA.
We also began to characterize the impact of MUC1 in gastric tumors biology using in vivo models.
Tumorigenicity assays in nude mice showed that MUC1 down-regulation (siRNA) conditions tumors
growth rate.
Research - Cancer Stem cells and drug-resistance phenotype
We have been characterizing the pancreatic cancer stem cells (CSC) and evaluating their possible
involvement in drug-resistance phenotype. Using a panel of different pancreatic cancer cell lines
(Panc1, HPAFII, Capan2), we observed that the CSC sub-population dimension was inversely related
with the cell line differentiation grade. Furthermore increased drug-resistance to Gemcitabine, 5-FU
and Doxorubicin is associated with lower differentiation grade. The chemoresistance of CSC was
studied in Capan 2 in CSC (CD133+) and non-CSC (CD133-) sub-populations. for Capan 2 and hTERTHPNE cell lines with gemcitabine, a standard drug for pancreatic cancer treatment. It was possible to
see that CD133+ subpopulation is more resistant than the respective CD133- subpopulation in Capan 2
cell line (p=0.054). This observation is in agreement with CSC hypothesis that this subpopulation is
responsible for the resistance to current therapies.
In order to analyze the possible involvement of the apoptotic pathways in this chemoresistant
phenotype, PARP, Bcl-XL and Caspase3 proteins expression levels were studied. An increased level of
inactive Caspase3 was detected in Capan 2 CD133+ subpopulation. This observation may indicate a
reduction in Caspase3 activation with a consequent impact on apoptosis.
We showed that pancreatic cancer cell line S2-013 previously treated with cisplatin expressed higher
levels of CD133 cell surface marker and higher chemoresistance which could be due to the detected
overexpression of Bcl-2 in the putative CSC enriched population. To understand if the membrane
protein CD133 was directly involved in chemoresistance RNAi technology was used to knock-down
CD133 expression. No differential chemoresistance was observed upon CD133 silencing, indicating
that this protein itself is not directly responsible for chemoresistance phenotype.
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39
Michael Anthony Hollingsworth. Eppley Cancer Center – University of Nebraska Medical Center.
MUC1 involvement in signaling pathways.
Prof. Hollingsworth is also the co-supervisor of PhD Students Natália Costa and Andreia Sousa.
Angie Rizzino. Department of Biology and Microbiology - University of Nebraska Medical Center.
Embryonic stem cells biology.
Christopher Heeschen. Stem Cells and Cancer Group – Centro National de Investigationes
Oncologicas (CNIO).
Pancreatic cancer stem cells.
Francisco Real. Epithelial Carcinogenesis group - Centro National de Investigationes Oncologicas
(CNIO).
Pancreatic cancer carcinogenesis.
George D. Jones. Radiation and oxidative stress Group– University of Leicester.
Characterization of Drug-resistance phenotypes.
Paula Alves. Animal Cell Technology Group - ITQB – Universidade Nova de Lisboa.
Bioreactors - large-scale expansion of pancreatic cancer stem cells.
Manuel Coelho, Chemical Engineering Group – Faculdade de Engenharia da Universidade do Porto
(FEUP).
Nanotechnology in chemotherapy and chemoprevention.
Michele Ouellette. Department of Biochemistry and Molecular Biology - University of Nebraska
Medical Center.
Immortalization of pancreatic and gastric normal cells (h-TERT).
Patricia Mesquita. Instituto Nacional de Recursos Biológicos, I.P. (INRB/MADRP).
On-going collaborative project on MUC1 transcriptional regulation in bovine endometrium cells by
the maternal hormones progesterone and estrogen and by the embryo - a crucial process on
implantation.
Future Research
MUC1 - gastric cancer cells.
The group will be involved in further characterization of MUC1-mediated oncogenic signaling
pathways in gastric cancer cells. Considering our results showing the involvement of MUC1-CD in
oncogenic signaling pathways of gastric cancer cells, we aim to evaluate how MUC1 variability
(VNTR) and post-translational modifications (e.g. phosphorylation) may condition these signaling
pathways.
MUC1 - pancreatic cancer stem cells
Considering the results obtained to date we envision MUC1 oncoprotein as an elective target to
tackle pancreatic cancer resilience to current therapies. We think that MUC1 expression levels,
alternative splicing variability and post-translational modifications conditions either intracellular
signaling as well as the cross talk between PCSC (stem cells niche effect) and consequently the
differentiation and cell survival processes. We will evaluate MUC1 expression levels, alternative
splicing variants, and post-translational modifications in PCSC and their impact on oncogenic
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40
signaling pathways. We will further characterize the impact of MUC1 in the drug-resistance
phenotype of PCSC.
MUC1 - new diagnostic and therapeutic tools
On the long run we plan to extend collaborations with other groups that will be focused on the
development and validation of new diagnostic and therapeutic tools design upon MUC1 relevance to
cancer cells biology. The ongoing colaboration with FEUP group is focused on the screening of
MUC1-functionalized nanoparticles efficacy in tumor cells/toxicity in normal cells.
Prizes
Honorable mention at 11th Ciencia en Accion - Science Short Documentaries
We received an honorable mention at 11th Ciencia en Accion Meeting with the documentary “In Vivo
– Cervix Cancer Prevention”. Santiago de Compostela. October 2010.
Supervisor of a PhD Student (Andreia Sousa - SFRH/BD/73410/2010) from the PhD Program of
Biomedicine - Faculty of Medicine of the University of Porto.
. Filipe Santos Silva.
Supervisor of a PhD Student (Natália Costa - SFRH/BD/27669/2006) from the PhD Program of
Biomedicine - Faculty of Medicine of the University of Porto.. Filipe Santos Silva.
PhD program GABBA (Graduate program in areas of Basis and Applied Biology) - University of Porto.
Filipe Santos Silva (lecturing at Oncobiology Module).
PhD program for Medical doctors - Gulbenkian and Champalimaud Foundations. . Filipe Santos Silva
(lecturing at Oncobiology Module).
Santos Silva F. “The Gastric microbioma – biodiversity in humans". Science Café – a Meeting between
scientists and politicians, celebrating the International year of Biodiversity. Promoted at national
parliament by Ciência Viva – National Agency for Science and Technology. Lisboa, Portugal. 2010.
Co-supervisor of the research program of a Biology student (Cristina Teixeira) from the Biology
masters course from University of Porto. On December 2010, Cristina Teixeira, obtained the Masters
in Biology, with the thesis “Chemoresistance in Pancreatic Cancer Stem Cells”.
Supervisor of the research program of a Biology student (Joana Castro) from the Cell Biology
masters course from University of Coimbra. On September 2010, Joana Castro, obtained the Masters
in Cell and Molecular Biology, with the thesis “Characterization of the involvement of cancer stem
cells in gastric cancer resistance to chemotherapy”.
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41
Population Genetics
Objectives
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,
conservation and management of domesticates and laboratory animals as well as food quality
assessment.
Main Achievements
Genetic characterization of NE Portugal communities of Jewish descent
The analyses of the male lineages from NE Portugal communities of Jewish descent demonstrated a
(surprising) level of diversity and a distinctive genetic profile with clear Near East affiliation.
Genetic characterization of Portuguese Gypsies communities - the autosomal portait
From the point of view of the autosomal genome, Portuguese Gypsies showed a reduction in
diversity when compared with the host population and with other Roma communities, in a E-W
gradient (in agreement with migration route); despite a strong drift, all Roma samples analysed
clustered together and were clearly distinguished from each host population
Genetic characterization of Portuguese Gypsies communities - the paternal lineages
The analysis of Y-chromosome lineages revealed an ancestral component, shared by all Roma
groups, reflecting their origin in India, but also a substantial admixture with the non-Gypsy
population from Iberia. This introgression from the host population is higher than observed in other ,
more Eastern European Roma groups, a unexpected finding, given their late arrival to Iberia.
Genetic characterization of Portuguese Gypsies communities - the spectrum of pathological
mutations
All patients of Gypsy origin share the same mutation (c.117delC-alpha; p.R40GfsX23 at the BCKDHA
gene), causing the neonatal severe form of maple syrup urine disease. These results are of medical
relevance since carrier tests and prenatal diagnosis can be offered to families at risk, particularly
because the carrier frequency was estimated at 1.4% among the healthy Portuguese Gypsies from the
South.
Malaria associated genetic traits in Cabo Verde
Analysis of pyruvate kinase-encoding gene (PKLR) and adjacent regions (chromosome 1q21) showed
evidence of malaria selective pressure
Uniparental markers in Populations from Southwest Iberia with Past Malaria Endemicity
An enrichment of sub-Saharan and Near East lineages was found, attributable to Sub-Saharan slaves
influx and intense Mediterranean trade.
X chromosome population profilings
X-chromosome specific markers were used to characterize population samples from Azores and
Portuguese mainland, using microsatellites and SNPs; significant differences among Azorean islands
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42
and between them and continental Portugal were found whereas there were no significant
heterogeneities between mainland regions.
Assessment of individual interethnic admixture proportions
A PCR multiplex involving 48 ancestry-informative insertion-deletion polymorphisms (INDELs) was
developed, able of efficiently measure the proportions of three different ancestries (sub-Saharan
African, European, and Native American), especially suited for Latin America substructured
populations.
Identification of species by the analysis of variable-length sequences
.A new method, based upon a PCR multiplex analysis of variable-length sequences containing
multiple insertion/deletion variants showed to be able to discriminate 93.3% of eukaryotic species
from 18 taxonomic groups. A computational platform was also developed and a profiling kit for
discrimination of 10 mammalian species was successfully validated on highly processed food
products with species mixtures and proved to be easily adaptable to multiple screening procedures
routinely used in molecular biology laboratories.
Development of molecular tools for dog identification, discrimination from wolf, and sex
identification
PCR based multiplexes amenable to successfully genotype severely degraded samples were
developed using autosomal and X-linked microsatellites. These tools proved to be able to perform
highly discriminating individualization, sex identification as well as to distinguish domestic dog form
wolf.
Identification of transcriptional changes in response to X chromosome dosage
Expression analysis in adult 40,XX and 39,XO mice identified several genes on the X chromosome
overexpressed in XX females, including those reported as escaping X inactivation, as well as new
candidates. Our results support the prediction that the mouse inactive X chromosome is largely
silent, while providing a list of the genes potentially escaping X inactivation in rodents. Genes
deregulated in XO mice are good candidates for further study in an involvement in Turner Syndrome
phenotype. Our study also exposed several autosomal genes involved in mitochondrial metabolism
and in protein translation which are differentially expressed between XX and XO mice.
Identification of Y-chromosome genes essential for sperm production in humans
We have shown that one of the primate-specific Y-linked ribosomal protein genes, RPS4Y2, has
restricted expression in testis and prostate, in contrast with its X-linked homologue. Our results
suggest that one of the Y-linked copies of the ribosomal protein S4 is preferentially expressed during
spermatogenesis and might be important for germ cell development and thus for male fertility.
Patterns of Genetic diversity demonstrate high indoor dispersion capability of Aspergillus
fumigatus
Analysis of genetic diversity among strains from 19 medical units of the same hospital showed no
correlation with the presence of high-efficiency particulate air filters or any other air filtration
system. In addition, the most prevalent strains were recovered from water samples, which indicates
that water plays an important role in the fungus indoor dispersion.
Y chromosome lineages help to clarify East African demographic history
We identified a new Y-SNP apparently specific to Nilotic groups, as well as the associated haplotypes.
The detection of a new haplogroup is important to differentiate Nilotes from other groups, helping
to trace migration and admixture events that occurred in Eastern Africa, at the fringe of Bantu
expansion.
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43
General derivation of the sets of pedigrees with identical kinship coefficients
Some pedigrees share the same identity-by-descent (IBD) probabilities and are therefore
indistinguishable using unlinked autosomal markers. We have derived the mathematical framework
for the complete sets of pedigrees with the same IBD partitions, considering kinships linking any pair
of non-inbred individuals, whether they are related just maternally or paternally, or both.
Incidence of maple syrup urine disease in Portugal
Maple syrup urine disease is an autosomal recessive disorder of branched-chain amino acids
metabolism with a worldwide frequency of 1/185,000 live newborns. Based on the review of the
cases diagnosed by tandem mass spectrometry, an incidence of 1/86,800 live newborns was
estimated in Portugal, indicating that the disease is more frequent than reported in most
populations.
Implications of the heterogeneity of frequency distributions of pharmacogenetically relevant
polymorphisms
Genotyping of vitamin K epoxide reductase complex 1 (VKORC1) and GSTM3, a member of the
glutathione S-transferase family in various populations from Europe, Africa and South America has
shown that, due to the extensive differences in allele frequencies at both these loci, and the high
degree of admixture in Brazil, specific cancer risks and drug administration dosage must be
evaluated at an individual basis.
The origin and age of the c.156_157insAlu BRCA2 mutation
This mutation has so far only been reported in hereditary breast/ovarian cancer (HBOC) families of
Portuguese origin. We screened for this rearrangement 5,443 suspected HBOC families from several
countries. Apart from Portuguese families it was detected only in one proband living in France and in
four individuals requesting predictive testing living in France and in the USA, all being Portuguese
immigrants. Haplotype analysis allowed a time estimate for the founder event at 558 +/- 215 years
ago.
Evolutionary constraints of the Conserved Oligomeric Golgi (COG) complex in vertebrates
Using protein distances and dN/dS ratios as a measure of the rate of evolution, we showed that all
COG subunits are evolving under strong purifying selection, although COG1 seems to evolve faster
than the remaining proteins. This suggests that COG subunits are evolutionary constrained to
maintain the interactions between each other, as well with other partners involved in vesicular
trafficking
Evolution and functional diversification of phosphomannomutases (PMM)
Two PMM enzymes exist in humans: PMM2 presents PMM activity, and its deficiency causes a
Congenital Disorder of Glycosylation; PMM1 can also act as glucose-1,6-bisphosphatase in the brain
after stimulation with inosine monophosphate and thus far has not been implicated in any human
disease. We established that duplication occurred early in vertebrate evolution and identified the
most probable sites that evolved to distinct functional specificities.
Identification of Candida glabrata mutations related to resistance to antifungal treatment
We report the first case of Candida glabrata-disseminated candidiasis with the acquisition of
echinocandin resistance following anidulafungin treatment. The initial isolates recovered were
susceptible to echinocandins. However, during 27 days of anidulafungin treatment, two resistant
strains were isolated: the resistant peritoneal fluid isolate exhibited a Ser663Pro mutation in position
1987 of FKS2 HS1, whereas the resistant blood isolate displayed a phenylalanine deletion (Phe659).
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44
Analysis of current data analysis strategies used in MS-based proteomics
We reviewed the most accepted algorithms for analysis of proteomics data and we have detected a
high degree of redundancy on algorithm development in computational proteomics in recent years.
Functional blockade of a5ß1 integrin induces scattering and genomic landscape remodeling of
hepatic progenitor cells
Cells treated with a specific antibody against a5ß1 integrin exhibited cell spreading and scattering,
over-expression of liver stem/progenitor cell markers and activation of the ERK1/2 and p38 MAPKs
signaling cascades, in a similar manner to the process triggered by HGF/SF1 stimulation. Gene
expression profiling revealed marked transcriptional changes of genes involved in cell adhesion and
migration, as well as genes encoding chromatin remodeling factors. These responses were
accompanied by conspicuous spatial reorganization of centromeres, while integrin genes conserved
their spatial positioning in the interphase nucleus.
Virtual expert mass spectrometrist: iTRAQ tool for database-dependent search, quantitation and
result storage
We developed the first tool that can integrate multiple high throughput quantitative iTRAQ
experiments and perform statistical analysis of the result. A novel aspect of the algorithm is that it
can correct signals that are saturated. The proposed saturation correction could be used for many
other purposes.
Susceptibility to five antifungals of Aspergillus fumigatus strains isolated from cystic fibrosis
patients
The work intended to evaluate the susceptibility to azole and non-azole antifungals of 159 isolates of
A. fumigatus collected from cystic fibrosis patients under azole antifungal therapy. The susceptibility
of the recurrent isolates was in agreement with the susceptibility of the first isolate identified (100 %
of essential agreement). Even after azole exposure, several recurrent A. fumigatus strains were
detected in the following sputum samples. The development of resistance of A. fumigatus to the
antifungals seems to be rare among cystic fibrosis patients.
Ancestry informative markers (AIMs)
Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Belém, Pará, Brazil
Sidney Emanuel Batista dos Santos
Expression and regulation of mammalian sex chromosomes genes
Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, UK
Nabeel A Affara
Division of Stem Cell Biology and Developmental Genetics, MRC National Institute for Medical
Research, London,UK
Julien Bauer
Dept. Biochemistry, Dept. Pathology, University of Cambridge, UK
Carole A Sargent, Peter J Ellis
Bioinformatics
Novo Nordisk, Copenhagen, Denmark (Albrecht Grulher)
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45
BMB, SDU, Odense, Denmark (Ole N Jensen)
Johns Hopkins University, USA (Akhilesh Pandey)
CIC bioGUNE, Spain (Manuel S. Rodriguez)
Population and Forensic Genetics
Genomics Medicine Group, Institute of Legal Medicine, CIBER for Rare Diseases (CIBERER), Univ.
Santiago de Compostela, Spain (Angel Carracedo)
Pharmacogenetics
Divisão de Farmacologia, Coordenação de Pesquisa, Instituto Nacional de Câncer, Rio de Janeiro, RJ,
Brasil
(Guilherme Suarez-Kurtz)
Genome-wide structural variation
Wellcome Trust Sanger Institute, Cambridge, UK
Matt Hurles
Genetics of male infertility
Department of Pathology & Immunology
Washington University School of Medicine, MO, USA
Don Conrad
X chromosome inactivation
Department of Biochemistry and Molecular Biology
Penn State University College of Medicine, PA, USA
Laura Carrel
Mammalian genomics
Department of Molecular and Cell Biology
University of Connecticut, CT, USA
Rachel O’Neill
X-chromosome markers: population genetics and forensics
Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences,
University of Copenhagen, Denmark
NielsMorling
Repeat instability in Machado-Joseph disease
Center of Excellence in Neuromics
Notre-Dame Hospital, Montréal, Canada
Guy A. Rouleau
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46
Genetics of admixed populations
Laboratório de Diagnósticos por DNA
Universidade do Estado do Rio de Janeiro
Elizeu Fagundes de Carvalho
Future Research
Intra- and inter-specific evolutionary analysis of genomic structural variants
Genomic rearrangements (with a special focus on inversions) will be analyzed in humans (when
polymorphic) and in Lemuridae (when they are present/absent) in congeneric species. Their
evolutionary role will be analyzed both as recombination blockers and as speciation drivers.
Persistence of archaic haplotype blocks in modern humans
The release of Neanderthal genome allowed us to compare its sequences with modern humans. A
special search in X –chromosome sequence stretches of putative Neanderthal origin will be
performed.
Evolutionary and functional analyses of coevolving sites
Phylogenies (and phenotype effects) are currently analyzed at a site-by-site basis (i.e. positions are
assumed to vary independently at a protein and to have an effect independent of the rest of the
sequence). We will analyze both DNA and protein sequences in an evolutionary and functional
perspective, combining the classical approach of detecting the co-occurrence of protein residues or
nucleotides in sequence alignments, with new methodologies developed in-house.
Comparative and evolutionary study of NAD metabolic pathways
We will use a combination of computational and molecular approaches to study the evolution of
enzymes related to NAD metabolism across species. These enzymes are implicated in a wide variety
of diseases, ranging from cardiovascular to neurodegenerative disorders, and are attractive targets
for the development of anticancer drugs, diabetes treatment and even novel therapeutics for
parasitic diseases.
Cross-species comparisons of genes escaping X inactivation
The characterization of genes escaping X inactivation in different species is a promising strategy to
unveil new mechanisms of escape. Indeed, it is plausible that dosage compensation has found
different solutions throughout mammalian evolution. We will compare the epigenetic profile of the
inactive X chromosome of several species occupying key positions in the mammalian phylogeny in
order to allow the comparison of distantly related as well as more recently diverged species.
Genetic determinants of male fertility
Although environmental factors may contribute to male subfertility, the complexity of pathways
involved in spermatogenesis implies that an appreciable number of genes should play a role. Most of
the efforts to understand the genetic basis of impaired spermatogenesis have been focused on the Y
chromosome. We will perform a genome-wide search for structural variants in individuals with
azoospermia in order to evaluate the contribution of presently unknown genetic defects to severe
spermatogenic impairment and discover yet unidentified genetic determinants of male fertility.
Demographic history of communities of crypto-Jewish origin
We will use a combination of genealogical/demographic historical reconstruction, through the study
of the available archives (birth, death, marriage and Inquisition processes) and a population genetics
approach, using markers with different modes of transmission allowing the simultaneous tracing of
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47
paternal, maternal and biparental lines of the NE Portuguese Jewish communities and those that
went to exile after the Expulsion. The genealogical reconstructions and the coalescence of genetic
data will be used to characterise the founder’s gene pool, the origin and the timeline of
introgressions, as well as extinctions, and the evolution of inbreeding.
Gene overlap in vertebrates : origin, maintenance and evolution
The origin, maintenance and evolution of overlapping gene pairs in vertebrates is analyzed by a
series of comparative genomic and transcriptional analysis complemented and validated with
experimental assays performed in distinct vertebrate species. Using the COG8/PDF overlapping gene
pair in rodents and mammals (but not in other vertebrates), we have already verified that the gain
and loss of start, stop or regulatory signals are the forces that drive the process of gene overlap.
Consequences
of
gene
duplication:
pseudogeneization,subfunctionalization
or
neofunctionalization of paralogs
The metallothionein family is composed of proteins involved in metal detoxification and oxidative
stress protection. We have found two inactivating mutations with polymorphic frequencies in
human populations in a conserved family member. We explore
the tolerance to the
pseudogeneization event in humans, in the context of the high number of surviving paralogs that
can provide physiological compensation to the loss.
Origins and dispersion of European Roma populations
We intend to conclude the study already performed for Y-chromosome and autosomal markers with
the characterization of maternal lineages through the sequencing of mtDNA.
MicroRNAs as co-regulators of branched chain a-ketoacid dehydrogenase complex
We will explore the role of miRNAs in the regulation of branched chain amino acids metabolism,
particularly through branched chain a-ketoacid dehydrogenase (BCKD) complex repression. We will
also investigate how miRNA regulation might contribute to the phenotypic variability associated to
dysfunction of the BCKD complex underlying the condition known as maple syrup urine disease.
Genetic diversity and resistance to anti-fungal therapy
The acquisition of antifungal resistance will be studied through the analysis of mutations at both
target enzymes of antifungal drugs and the transcription factors that activate efflux pumps. Gene
diversity studies will be carried in Candida spp. and Aspergillus spp.
Archaeogenetics of domesticates and wild relatives
The studies in animal domestication that have been carried out in extant populations will be
extended to archaeological materials (ancient DNA). We expect to develop methods for species
identification (particularly needed for distinction of Capra from Ovis) and to test the hypothesis of
local (Iberian) domestication events.
mtDNA variation in health and disease (with a special emphasis on deletions)
The causes and consequences of mitochondrial DNA deletions in animal cells will be explored,
namely at somatic and germinal levels, tissue specificity and senescence.
Evolution of nuclearly transferred mitochondrial DNA sequences (NUMTs)
NUMTs are insertions of mitochondrial DNA (mtDNA) sequences into the nuclear genome that are
thought to occur continuously through evolution. They are of relevance in evolutionary and
population genetics because (a) they are mitochondrial sequences that have been kept under
different evolutionary constraints; (b) they allow studying insertions occuring at different times; and
(c) they present insertion polymorphism in human populations. We aim to study NUMTs in an
_________________________________________________________________________________________________________________________________
48
evolutionary perspective by typing them in human populations and comparing evolutionary
mechanisms with the ones observed in inbred mice strains.
Microphylogeography: Language as a genetic barrier
At the North-Eastern extreme of the Portuguese territory two different languages coexist
(Portuguese and Leonese dialects); this rare phenomenon allows us to address the origin of the
people from the region, to assess the micro-geographic substructure and to evaluate the degree of
population exchanges across the Portuguese-Spanish border. Furthermore we expect to shed light
upon the relations between cultural traits and mating behavior, and the role of gender in the specific
transmission of the language.
Genetic history of sub-Saharan and Amerindian populations
We will continue the study of these populations with the aim of reconstructing their demographic
history. In both cases the extant populations’ gene pools has been profoundly remodeled by recent
expansions and admixtures; we intend to use genetic markers with distinct mode of transmission to
infer the original (pre-Bantu expansion and pre-Columbian) genetic profiles of these populations.
Mathematical modeling of kinship
We intend to continue the development of the generalized mathematical framework to sex-linked
transmission, as well as the inference of kinship between any pair of individuals from their genetic
profile.
Genetics of neurodegenerative disorders
We will study the role of genes involved in replication, repair and recombination on repeat instability
of expanded alleles of Machado-Joseph disease. SNPs within 92 candidate genes will be analysed in
138 patients for whom the expanded repeat size of the transmitting parent is also available.
Characterization of Daphnia longevity genes
We will determine life span in Daphnia spp., and the genetic diversity in lineages of D. magna and D.
longispina with different life spans will be characterized. The longevity-related genes will be
validated by gene sequencing and comparative genomics, and functional assays will be used to
quantify expression and activity of these genes under a wide range of growth conditions.
The paradox of d-globin gene conservation
Hemoglobin A2 (a2d2) is assumed to be physiologically unimportant because normally it accounts for
less than 3% of the total adult hemoglobin. However, d-globin gene shows much less genetic
diversity than ß-globin duplicate (approximately 97% of hemoglobin molecules). We intend to clarify
its evolutionary history among humans and other primates and thus to solve the paradox of its
surprising conservation through detailed and unbiased haplotype analysis, expression and structural
studies.
Bioinformatics
Bioinformatics related research lines will be continued in association with (and from now on oriented
by) the new Research Group lead by Rune Matthiesen
Pharmacogenetics, lifestyle and dietary adaptations: insights from genetic diversity patterns
A screening for a battery of genesthat might play a role in the metabolism and in the taste of
compounds contained in many foods will be performed. Besides AGXT, putatively implicated in a coadaptation to meat-rich diets, and copy number variation of the human amylase gene, a series of
drug metabolizing enzymes will be also studied. Through the comparative analysis of populations of
contrasting lifestyles, we hope to obtain a better understanding on the geentic events associated
with diet changes that have accompanied the Neolithic emergence.
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49
Programa Doutoral em Biologia. Antonio Amorim.
Programa GABBA UP. Antonio Amorim.
Programa Doutoral em Ciências Forenses, FMUP. Gusmão L.
Genética Forense FCUP. Antonio Amorim.
Genética Forense FCUP. Maria Joao Prata.
Genética Forense FCUP. Leonor Gusmao.
Genética Forense FCUP. Cintia Alves.
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50
Genetic Diversity
Objectives
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 a detailed
characterisation of worldwide genetic diversity for the uniparental markers, and the design of
studies to investigate complex phenotypes, namely fertility, longevity and cancer. 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 that are being proposed by integrative
computational analyses.
In order to accompany the advances of the current genomic era, we will begin the screening of
genome-wide chips at a population level, taking advantage of the powerful links between
anthropology, bioinformatics, population genetics and clinical genetics that the group has already
established for the uniparental markers.
Main Achievements
Population Genetics
Population genetics depends largely on excellent sample datasets. The international collaborations
secured these, to such an extent that we are conducting research in Europe, North Africa, East
Africa, Sahel, Arabian Peninsula and, in 2011, in Asia. Our group was also successful in upgrading to
the new high-resolution population genetic studies, and the main lines of research are conducting to
several publications in peer review journals with a high impact factor. Namely, the group leader
participated in an international study led by the collaborator Doron Behar aiming to disclose the
history of the Jewish Diaspora; the results showed that the joint analyses of the three sets of
markers at high-resolution (~650K genome-wide SNPs, complete mtDNA and Y-chromosome)
revealed features which would not be disclosed otherwise; this manuscript was published in Nature
(Behar et al. 2010). We coordinated and published work informative to unravel the colonisation of
North Africa, showing that maternal haplogroups arriving there in the last 45 thousand years (ka)
displayed a main expansion in the time frame of the Late Pleistocene, around 20 ka, with a weak
Neolithic signal of a recent population expansion in the last 5 ka (Pereira et al. 2010, BMC Evol Biol),
and a moderate sub-Saharan input mainly due to the trans-Saharan slave trade led by Arabs (Harich
et al. 2010, BMC Evol Biol). We provided information for the genetic characterization of the various
population groups in the African Sahel, showing that Tuaregs living there have maternal lineages
involved in the post-Glacial Maximum expansion from Iberia refugia towards Europe and North
Africa and paternal lineages traced to the Near Eastern Neolithic expansion (Pereira et al. 2010, Eur J
Hum Genet), and that no substantial exchanges occurred between nomadic pastoralists and
sedentary farmers in the Lake Chad Basin and emergence of pastoralism might have been an earlier
and/or a demographically more important event than the introduction of sedentary agriculture in
this part of Africa (Cerny et al. in press, Mol Biol Evol). In the Arabian Peninsula, we confirmed that
the post-Last Glacial Maximum period of the past 20,000 years, during which climatic conditions
were becoming more hospitable, has been a significant period of time in the formation of the extant
genetic composition and population structure of this region (Cerny et al. 2011, Mol Biol Evol),
contributing to the settlement of Socotra and genetic exchanges with East Africa (Musilova et al. in
press, Am J Phys Anthropol).
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51
Clinical Genetics
In an application to mitochondrial clinics, we used detailed phylogenetic trees for human mtDNA,
combined with pathogenicity predictions for each amino acid change, to evaluate selection on
mtDNA-encoded protein variants. Protein variants with high pathogenicity scores were significantly
rarer in the older branches of the tree. The measured effect of selection increased exponentially with
increasing pathogenicity score. We found no measurable difference in this measure of purifying
selection in mtDNA across the global population, represented by the macro-haplogroups L, M and N.
We obtained a list of all possible single amino acid variations for the human mtDNA encoded
proteins, with their predicted pathogenicity scores and our measured selection effect, to be used as
a tool for assessing novel protein variations which are often reported in patients with mitochondrial
disease of unknown origin, or for assessing somatic mutations acquired through aging or detected in
tumors. These results are under revision (Pereira et al., Am J Hum Genet).
Bioinformatics
In a Bioinformatics approach, we developed a free online calculator named PopAffiliator
(http://cracs.fc.up.pt/popaffiliator) for individual population affiliation in the three main population
groups, Eurasian, East Asian and sub-Saharan African, based on genotype profiles for the common
set of short tandem repeats (STRs) used in forensics (Pereira et al. in press, Int J Legal Med). Because
of their sensitivity and high level of discrimination, STRs are currently the method of choice in routine
forensic casework and data banking, usually in multiplexes up to 15–17 loci, being surveyed
worldwide. The PopAffiliator calculator performs affiliation based on a model constructed using
machine learning techniques. The model was constructed using a data set of approximately 15,000
individuals collected for this work. The accuracy of individual population affiliation is approximately
86%, showing that the common set of STRs routinely used in forensics provide a considerable
amount of information for population assignment, in addition to being excellent for individual
identification. The team element Nuno Silva presented his Master Degree thesis on “Improvement of
an autosomal STR online database and evaluation of human worldwide genetic diversity”. He
analysed worldwide data for 13 STRs deposited in an online database of allele frequency data
developed by us (Strdna-db; 190 populations and 69,229 individuals) and in the online PopAffiliator
tool comprising genotype profiles (43 populations and 11,181 individuals), intending to understand
how informative these markers used in forensics could be to unravel human demographic history.
Inter-population comparisons indicate a significant level of population structure, with a global FST
value of 4.3-5.0% for both datasets, thus in agreement with levels inferred in non-forensic studies.
This agreement further extends to the pattern of within-population diversity, which shows a
decrease from sub-Saharan African to American populations, in accordance with the recent African
origin of modern humans. Actually, the geographic distance to East Africa explains 55% of the
decrease in genotype diversity, a pattern that could be explained by a series of founder effects
during the expansions out-of-Africa. Our results show that extensive datasets from forensics can be
used to address population genetics’ questions, and the statistical methods used provide reliable
results as they account for the particularities and limitations of those markers.
Funding
We were successful in securing a Post-doc grant for Pedro Soares (SFRH/BPD/64233/2009), who
returned to Portugal after a PhD at University of Leeds, and a PhD grant to Nuno Miguel Monteiro da
Silva (SFRH/BD/69119/2010). We were successful in achieving funding from FCT, in the last call of FCT
projects: PTDC/CS-ANT/113832/2009 - “Genetic and chronological characterisation of the European
settlement by modern humans in the Upper Palaeolithic” 173.000 euros for three years, beginning 1st
March 2011. We gained experience in applying for funding from international agencies: (1) an NIH SF
424 (R&R) application in June 2010, together with Dr. David C. Samuels from the Center for Human
Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University
_________________________________________________________________________________________________________________________________
52
Medical Center, Nashville, TN, USA; (2) an EU FP7-HEALTH-2011-single-stage collaborative project in
November 2010, coordinated by Dr. Anavaj Sakuntabhai from Institut Pasteur, Paris, France; (3) an
EUROTAST - Marie Curie ITN proposal in December 2010/January 2011, coordinated by Dr. Thomas
Gilbert. FCT opened a call for Projects in All Fields in December 2010, to which we submitted two
projects as main applicants and one project as collaborators.
Characterisation of the Neolithic in the Great Mediterranean
Collaboration with Martin Richards (Institute of Integrative & Comparative Biology, Faculty of
Biological Sciences, University of Leeds, UK), Vincent Macaulay (Department of Statistics, University
of Glasgow, UK) and João Zilhão (Department of Archaeology, University of Bristol, UK)
Characterisation of the settlement of Europe in the Upper Palaeolithic
Biological Sciences, University of Leeds, UK) and Vincent Macaulay (Department of Statistics,
University of Glasgow, UK)
Characterisation of the pre-history of Southeast Asia
Biological Sciences, University of Leeds, UK) and Vincent Macaulay (Department of Statistics,
University of Glasgow, UK)
Characterisation of the settlement of the Arabian Peninsula
Collaboration with Farida Alshamali, (Dubai Police General Headquarters) and Viktor Cerny (Institute
of Archaeology of the Academy of Sciences of the Czech Republic, Prague)
Complete mtDNA databases and genome-wide screenings applied to population genetics
Collaboration with Doron Behar (Rappaport Faculty of Medicine and Research Institute, Technion
and Rambam Medical Center, Haifa, Israel).
Complete mtDNA databases and its application in clinical genetics
Collaboration with David C. Samuels (Center for Human Genetics Research, Department of Molecular
Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN, USA)
Autosomal markers and worldwide population structure
Collaboration with Mathias Currat and Estella Poloni (Départment d’Anthropology et d’Ecologie,
Université de Geneve, Switzerland)
Impact of human genetics on the outcome of infection and infectiousness to mosquitoes
Collaboration with Anavaj Sakuntabhai and Richard Paul from (Institut Pasteur, Paris, France)
Future Research
Population genetics
In the year of 2011, we will publish data obtained so far for the complete mtDNA genome screening,
in order to address the following questions of human history:
a) Improvement of the Out-of-Africa model, by applying updated mutation rates and several
statistical methods to complete sequences of haplogroup L3 (70 new and 299 published), aiming to
optimise the time estimation for the out-of-Africa migration;
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53
b) Evaluation of the Neolithic genetic influence in the Great Mediterranean – we are finishing 300
complete mtDNA sequences in Near East and Europe, belonging to haplogroups J and T;
c) Investigation of the settlement of Europe in the Upper Palaeolithic – we are finishing 300
complete mtDNA sequences in Near East and Europe, belonging to haplogroup U
d) Settlement of Arabian Peninsula and remnants of the out-of-Africa migration: we are finishing 90
complete mtDNA sequences in Near East and Europe, in the roots of haplogroups N*, M* and L*.
We will develop SNaPshots for typing Y-chromosome SNPs informative in typical haplogroups from
the various geographic regions we are investigating. The paternal information will complement the
results we obtained for the maternal component of the population.
In the new era of genomics, it is becoming essential to add information from genome-wide
screenings, which are revealing minutia genetic relatedness/admixture aspects in neighbouring
populations, which can have been erased by genetic drift in the uniparental markers. We will screen
2,500,000 loci (Omni 2.5 Illumina array) in around 150 individuals in several populations from the
Sahel region, complementing the results we are obtaining for mtDNA and Y-chromosome.
The post-doc Pedro Soares conducted his PhD on the study of Southeast Asia pre-history. At least at
the mtDNA level, this geographic region is the less characterised. His supervisor Martin Richards
collected an extensive dataset of biological samples in this region, which is available to our group to
continue investigation. Pedro applied a FCT project in the December 2010 – February 2011 call, to
conduct this investigation. We will enlarge sample collection (to Macau, Laos and Cambodia), and
characterise complete mtDNA lineages, Y-chromosome and genome-wide SNPs. We will complement
these studies on Asian pre-history with investigation of the Portuguese maritime expansion imprint
in the gene pool of those populations, by sampling auto-declared descendents of Portuguese. We
are celebrating in 2011 the 500 years of the arrival of Portuguese sailors in Southeast Asia.
Clinical genetics
The know-how on phylogenetics and statistical analyses of extensive genetic datasets will be applied
to investigate some clinical aspects:
a) Giving mitochondrial DNA phylogenetics expertise to the non-specialist, by developing user
friendly computer tools. We initiated already some steps of this complex online tool, as the
evaluation of mtDNA selection and the development of a computer tool mtDNA GeneSyn. We will
work now on: developing a new algorithm to construct Phylogenetic Trees from mitochondrial DNA
(mtDNA) sequences, overcoming serious limitations of existing ones; automating the process of
constructing Phylogenetic Trees and provide a user friendly interface to the user; using (MultiRelational) Data Mining techniques to extract informative patterns from mtDNA sequences; testing
the phylogenetic approach in clinical data, helping to establish more informative diagnoses for
mitochondrial diseases. This project will be performed in collaboration with David C. Samuels, Rui
Camacho and Nuno Fonseca, and the project was submitted to FCT in the December 2010 – February
2011 call.
b) Genomics and complex traits. As genomics is now in a boom phase, applying genome-wide
screenings to enlarged population sets is in the order of the day. We will analyse data from the
Illumina 660WQuadv1 beadchip, containing 657,366 SNPs (single nucleotide polymorphisms) in 400
individuals with mild dengue infections and 200 individuals with severe dengue cases. These results
were obtained by our collaborators from the Institut Pasteur, and we will help in the analyses to
detect association.
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54
Bioinformatics
a) We will develop an online tool to give mitochondrial DNA phylogenetics expertise to the nonspecialist, as referred in the previous section.
b) We are automating the founder analysis developed by Martin Richards and Vincent Macaulay in
2000. This analysis allows to estimate the time for migration of lineages from a source to a sink
populations. This method is now done by hand by a few experts. This work is being performed by the
Master student in Informatics and Computing Engineering (Faculty of Engineering, University of
Porto) Marco Alves.
c) We are evaluating selection on mtDNA-encoded protein variants and calibrating the mutation rate
in several mammalian species, such as chimpanzee, dog, mouse, rat, cow and orca. This work is being
performed by the Master student in Bioinformatics (University of Minho) Diogo Abrantes.
PhD Program in Biomedical Research - Faculty of Medicine, University of Coimbra. Luisa Pereira
presented a seminar “Genetic lineages of human foundations: contribution of the second genome”
at the Advanced course on Translational bigenomics – from the bench to the bedside. .
Biodiversity, Genetics and Evolution - Faculty of Sciences, University of Porto. Luisa Pereira
supervised the thesis “Improvement of an autosomal STR online database and evaluation of human
worldwide genetic diversity”. Student: Nuno Miguel Monteiro da Silva.
Human Evolution and Biology - Faculty of Sciences and Technology, University of Coimbra. Luisa
Pereira presented a seminar “A portrait of humans as a young species – a mitochondrial DNA”.
Human Evolution and Biology - Faculty of Sciences and Technology, University of Coimbra. Luisa
Pereira was examiner of the thesis “Estudo da variabilidade genética associada à persistência da
lactase em Portugal e em diversas populações africanas”. Student: Sara Daniela Verde da Veiga Pires.
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55
Genetics, Evolution and Pathology
Objectives
Our major research goal is to study the evolutionary forces that shaped the current patterns of
human genetic diversity and their implications in health and disease. Our research is focused both on
population history and on the analysis of the origin, evolution and spread of specific genetic variants
involved in human disease and human adaptation. Most of our scientific activities are structured
around the following three major, interconnected, areas: 1) genetic structure and history of African
and African-derived populations; 2) evolutionary history of adaptive traits with special emphasis on
proteolysis processes; and 3) study of admixed populations as models to understand the genetic
basis of complex traits with anthropological relevance or biomedical interest. During the reporting
period, we focused on the following goals: i) to assess levels and patterns of genetic variation in
southern Angola and Mozambique; ii) to characterize the evolutionary history of a null allele
associated to severe alpha-1-antitrypsin (SERPINA1) deficiency; iii) to describe the activity of a serine
protease inhibitor gene previously shown be under positive selection (SERPINA2); iv) to explore
additional signatures of selection among other human serine protease inhibitors genes, namely on
SERPINB and WFDC gene clusters; v) to characterise the genetic structure and admixture dynamics
of the Cape Verde Archipelago population and to evaluate the role of genetic ancestry explaining the
phenotypic variation in skin pigmentation observed in the archipelago.
Main Achievements
i) We characterized genetic structure of 19 Bantu-speaking groups from Mozambique and Angola
using a multilocus approach based on 14 newly developed compound haplotype systems
(UEPSTRs). We showed that the observed patterns of genetic variation revealed high levels of
genetic homogeneity between major populations from Angola and Mozambique, with two main
outliers: the Kuvale from Angola and the Chopi from Mozambique. Our observation of low levels
of genetic divergence across the studied groups is difficult to reconcile with an early split
between East and West Bantu-speaking groups, favoring dispersal models that emphasize the
close relationship between populations from western and eastern savanna areas located
southerly to the African rainforest. ii) We applied a genetic evolutionary approach to a clinical
study of severe SERPINA1 deficiency caused by the Q0Ourém allele and we demonstrated that its
segregation in several families could not be explained by recent consanguinity and that Q0Ourém
had a single origin – probably in the Middle Ages. iii) We performed a series of comparative
studies for SERPINA2 and SERPINA1, which combined experimental assays carried out in
transduced cell lines with phylogenetic-based tests of selection. All together, our results reinforce
the hypothesis of SERPINA2 being a functional protein and not strictly a genomic redundancy. iii)
In the SERPINB cluster, we identified a full-length SERPINB11 variant encoding a non-inhibitory
SERPIN as the putative candidate of selection. Since its frequency could be significantly correlated
with the pathogen burden per geographic area we suggested a selective advantage of SERPINB11
linked to an innate immunity function. In the WFDC cluster, we identified long-range haplotypes
linked to potentially advantageous alleles consistent with positive selection centered on WFDC8
(Europeans) and on SPINT4 (Africans). For WFDC8, the most likely candidate variant targeted by
selection was rs7273669A, which may down-regulate gene expression by abolishing the binding
site of two transcription factors. For SPINT4, the probable candidate was a haplotype
configuration [Ser73+98A] (rs6017667A-rs6032474A) that may simultaneously affect protein
function and gene regulation. We proposed an event of short-term balancing selection for
WFDC8, because the candidate variant haplotype had already started to accumulate neutral
_________________________________________________________________________________________________________________________________
56
variations; for SPINT4, we suggested an ongoing selective sweep because the candidate variant
had a star-shaped genealogy, indicating a recent increase in frequency. We propose that major
selection pressures driving adaptation in WFDC genes may be related to innate immune functions
in the reproductive tract, with possible repercussions for fertility levels. iii) We pursued with the
characterization of the admixture structure of the Cape Verde archipelago and its implications for
understanding the genetic architecture, evolution, and genotype-phenotype correlations that
underlie normal morphologic variation, such as pigmentary traits. We have characterized 697
Cape Verdeans with 1,199,187 single nucleotide polymorphisms and applied and compared
genotype-based and ancestry-based association approaches for skin and eye color in these
individuals. We identify one major locus for eye color, and four major loci for skin color which act
in an additive and semidominant manner, and together explain about half of the overall estimated
genetic variation. Our results indicate that Afro-European pigmentary variation uses a different
set of genes from those used within Europe, suggest that both coding and regulatory variations
provide a genetic explanation for the relationship between eye and skin color, and highlight the
potential and the pitfalls of using allele distribution patterns as indicators of phenotypic
differences.
Susana Seixas - Invited speaker at National Human Genome Research Institute at the National
Institutes of Health (NHGRI/NIH). Lecture: “An evolutionary perspective into the world of serine
protease inhibitors”.
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57
Science Diffusion
The activities of scientific diffusion remain as one of the primary functions of IPATIMUP.
In 2010, the Scientific Diffusion and Continuous Education Unit was reorganized in two Units, the
Science Diffusion Unit and the Public Awareness of Cancer Unit.
The activities may be summarized as follows:
- Continuation of the protocol with the Education Department of Porto City Hall – Program “Porto de
Crianças”;
- Participation at the Day (Week to be more precise) of the University of Porto with “hands on
experience” for the public at large.
- Continuation of the protocol with the National Agency “Ciência Viva” for the Program “Ciência Viva
em Férias”. Students from the last years of Portuguese secondary schools come to work at an
IPATIMUP lab, in very small groups, for two weeks during Summer. We receive about 30 students
each year.
- Visits to IPATIMUP of classes (usually divided in two halves) of students from secondary schools by
appointment – two days a year: IPATIMUP’s Day and Science Day.
- Continuation of an annual multidisciplinary conference on Science, Culture & Society (Equinox
Conference) for the public at large.
- Project “Junior’s University” under the patronage of Porto University providing week stays of
students in IPATIMUP to develop small projects.
- Project “Open Lab” (Laboratório Aberto) implemented in a partnership with the National Agency
Ciência Viva (financial support) and Porto City Hall (Provider of the building and of part of its
equipment) meant for the experimental “teaching” of sciences. The Open Lab is constituted by two
big labs and other logistic facilities at the Centre of Teaching Resources of Porto’s City Hall, located
200m from IPATIMUP. The average number of students from primary and secondary schools that
work in the Open Lab is about 2800 per year.
Projects (multimedia and special education areas):
a) “Prevention and early diagnosis of cancer and precancerous lesions of cervix, stomach, breast and
thyroid – CancerMobile” (Funded by EEA),
b) “Development of a medical information system about Hereditary Breast and Colorectal cancer” (Funded by Harvard Medical School Portugal Program),
c) “Development of a model of inclusive education of science in a population visually impaired
students”- (Funded by Gulbenkian Foudation).
Development of products:
a) MICe –Virtual Microscope –Educational software,
b) Eureka Sessions - Experimental protocols,
c) In Vivo - Short Documentaries about Cancer Prevention.
Workshop organization
We have been selected to host a Harvard Medical School Portugal Program Workshop – Visualizing
molecular and cellular processes with 3D animation. Porto. June 2010.
Conferences and Meetings
Santos Silva F. “The Gastric microbioma – biodiversity in humans". Science Café – a Meeting between
scientists and politicians, celebrating the International year of Biodiversity. Promoted at national
parliament by Ciência Viva – National Agency for Science and Technology. Lisboa, Portugal. March
2010.
Ribeiro N, Marcos NT, Carvalho L, Santos Silva F. “In Vivo – Cervix Cancer Prevention”- Science Short
Documentaries. 11th Ciencia en Accion. Santiago de Compostela. October 2010.
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58
Carvalho L, Silva J, Santos Silva F. “Research and Science Outreach at IPATIMUP”. EUROSKILLS - The
European Championship of Professions. Lisboa. December 2010.
Santos Silva F. Development of a medical information system about hereditary breast and colorectal
cancer. Harvard Medical School Portugal Program – 1st Annual retreat . Porto, Portugal. 2010.
Santos Silva F. Dialogical approaches on science communication – Health Sciences. 11th International
Conference on Public Communication of Science and Technology. New Delhi, India. December 2010.
Prizes
Honorable mention at 11th Ciencia en Accion - Science Short Documentaries with the documentary
“In Vivo – Cervix Cancer Prevention”. Santiago de Compostela. October 2010.
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59
IPATIMUP Diagnostics
1. Introduction
In 2010 the three diagnostic Units of IPATIMUP went through an important reorganization process
with the objective of creating a single diagnostic Unit henceforth called IPATIMUP Diagnostics (Fig.
1). As a direct and immediate
mediate consequence of this process a lot of effort was put on leveling
processes, resources and standards of quality among the three departments of IPATIMUP
Diagnostics – Pathology, Genetic Diagnosis, and Parentage testing and Genetic Identification.
The general goals of the aforedescribed fusion were the following:
•
•
•
•
•
To increase flexibility in human resources management.
To increase the capacity to reduce variable costs (consumables and services
acquisition).
To create a single transversal strategy of negotiation
negotiation with health care institutions.
To optimize occupation of laboratory space and boost the creation of synergies
between the three pre-existing
pre
units.
To homogenize the existing quality management and quality control plans among the
three departments.
In parallel a new Commercial department was created with the objectives of increasing the visibility
of IPATIMUP Diagnostics, and increasing our capacity to talk with health care institutions and health
care providers, both at national and international levels.
le
Figure 1: Organigram of IPATIMUP Diagnostics
2. Exams
_________________________________________________________________________________________________________________________________
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60
Pathology
Total
11746
1249
9663
639
195
Total
2406
1662
406
338
Histology
Cytology (includes 2854 cases of FNA cytology)
Molecular Pathology
Consultations
Diagnostic Genetics
Tumour mutation screening
Genetic Diagnosis - Complex
Genetic Diagnosis - Simple
Parentage testing and
Genetic Identification
Total
Genetic Characterizations (including lineage markers)
Parentage investigations and genetic profile comparisons
(sample/individual)
170
72
98*
3. Consultations
Figure 2 – World map indicating the origin and number of consultations during 2010.
4. Training, lectures and other activities
4.1 Pathology
Name
Period
Training
Current situation
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61
Dr. César Augusto Alvarenga, PhD student, Instituto
de Patologia de Campinas, Campinas, São Paulo,
Brazil
12/09/2009 23/07/2010
Anatomical Pathology and
Cytopathology
Concluded
Dr.ª Paula Itagyba Paravidino, Master student,
Instituto de Patologia de Campinas, Campinas, São
Paulo, Brazil
12/09/2009 23/07/2010
Cytopathology
Concluded
Dra. Fabíola Couto Fernandes, Pathology Resident,
Hospital Central de Maputo, Mozambique
08/01/2010 29/01/2010
Cytopathology
Concluded
Drª. Lidiane de Araújo Lima, Pathology Resident,
Universidade Federal do Rio Grande do Norte, Natal,
RN, Brazil
01/06/2010 31/07/2010
Cytopathology
Concluded
Dr. Silvio Constantino do Valle, Pathology Resident,
Instituto Nacional do Câncer, Rio de Janeiro, Brazil
01/12/2010 31/01/2011
Cytopathology
Concluded
Dr Lucas Hoffman, Pathology resident, Pontifícia
Universidade católica de Campinas, Campinas, Brazil
01/09/2010 31/10/2010
Surgical Pathology and
Cytopathology
Concluded
Dra. Adriana Oliveira, Pathology Resident, Santa Casa
de São Paulo, São Paulo, Brazil
01/11/2010 31/12/2010
Surgical Pathology and
Cytopathology
Concluded
Dra. Sofia Teixeira, Endocrinology resident, Hospital
de Santo António, Porto, Portugal
01/12/2010 28/02/2011
Aspiration Cytology
Ongoing
Training
Current situation
Dr. Cheila Ribeiro, Graduate student, Universidade do 09/2009 –
Minho, Braga, Portugal
09/2010
Genetic Diagnosis
Concluded
Dr. Maria João Pina, Graduate student, ESTSP, Porto,
Portugal
02/2010 –
03/2010
Genetic Diagnosis
Concluded
Dr. Hélder Rocha, Graduate student, ESTSP, Porto,
Portugal
03/2010 –
04/2010
Genetic Diagnosis
Concluded
Dr. Ana Antunes, Pneumology resident, Centro
Hospitalar de V. N. Gaia, Portugal
04/2010 –
07/2010
Molecular Pathology
Concluded
Dr. Maria João Pina, Graduate student, ESTSP, Porto,
Portugal
02/2010 –
03/2010
Genetic Diagnosis
Concluded
Dr. Yolanda Roa, Pathologist, Hospital Calderon
Guardia, San Jose, Costa Rica
06/10
Molecular Pathology
Concluded
Dr. Lúcia Águas, Oncology resident, Hospital S. João,
Porto, Portugal
10/2010 –
Molecular Pathology
Ongoing
Dr. Ana Justino, Graduate student, ESTSL, Lisboa,
Portugal
12/2010 –
Genetic Diagnosis
Ongoing
4.2 Diagnostic Genetics
4.2.1 Training
Name
Period
4.2.2 Invited talks
Machado JC. Genética: onde estamos uma década após a associação do NOD2 com a doença
de Crohn. GEDII (Grupo de estudo da doença inflamatória intestinal) 2010. Porto, Portugal,
Janeiro de 2010.
Machado JC. Hereditary and familial non hereditary gastric cancer. Rabin Medical Center
Gastroenterolgy Symposium. Tel-Aviv, Israel, Abril de 2010.
_________________________________________________________________________________________________________________________________
62
-
-
Machado JC. Genetic susceptibility to gastric carcinoma and its clinical implications. 3rd Joint
Conference German Society for Hygiene and Microbiology (DGHM) ans Association for
General and Applied Microbiology (VAAM). Hannover, Alemanha, Março de 2010.
Machado JC. EGFR e cancro. 6º Simpósio Nacional de Cancro Digestivo. Albufeira, Portugal,
Outubro de 2010.
Machado JC. Genética na clínica actual e no futuro. Quando pedir, o que retirar de facto dos
resultados genéticos, perspectivas futuras. 18ª Jornadas de Cardiologia dos Hospitais da
Zona Centro. Viseu, Portugal, Novembro de 2010.
4.3 Parentage testing and Genetic Identification
4.3.1 Invited talks
Amorim A. A Genética Forense já não é só para homens…. Curso Pos-Graduado UERJ, 26
Março. Rio de Janeiro, Brazil. 2010.
Amorim A, Garcia O. Casos complejos de Paternidad y otros vínculos biológicos. La
interpretación de incompatibilidades: alelos silentes y mutaciones. Curso Interpretacion
estadistica de resultados de los analisis de ADN; 17-19 Mayo. Buenos Aires, Argentina . 2010.
Amorim A. Genética Forense no-humana . III REUNION MERCOSUR DE GENETICA FORENSE
/JORNADAS LATINOAMERICANAS DE GENETICA FORENSE, 19-20 Mayo. Buenos Aires,
Argentina. 2010.
Amorim A. Forensic geneticists and sociologists: Can we talk?. Risky profiles: Societal
dimensions of forensic uses of DNA analysis, 2-3 July . Goethe University Frankfurt am Main,
Germany. 2010.
Amorim A, Celso Mendes C, Oliveira S. Estatística DNA . III Seminário de DNA e Laboratórios
Forenses; 21-24 Set. Brasilia, Brasil. 2010.
Amorim A. DNA forense não humano. III Seminário de DNA e Laboratórios Forenses; 21-24
Set. Brasilia, Brasil. 2010.
Amorim A. O DEVER DE EXPLICAR E A OBRIGAÇÃO DE COMPREENDER: condições de
melhoria do uso da Genética Forense. I Simpósio DNA, Genética e Justiça. Escola da
Magistratura do Estado do Rio de Janeiro. 31/05. Rio de Janeiro, Brasil. 2010.
Gusmão L. Polimorfismos do DNA: Aplicações em estudos de ancestralidade e em genética
de populações e forense. Programa de Pós-Graduação em Biociências da UERJ
(Universidade do Estado do Rio de Janeiro). Rio de Janeiro, Brasil. 2010.
Gusmão L. Características gerais do cromossoma Y, tipos de polimorfismos e aplicações em
Genética Forense. Universidade de Aveiro, Portugal, 29 de Maio de 2010.
Gusmão L. Marcadores de cromossoma X em investigação de parentesco. Universidade de
Aveiro, Portugal, 29 de Maio de 2010.
Gusmão L. Ejercicio Control Calidad 2009. III CURSO INTERNACIONAL TEÓRICO-PRACTICO
EN GENETICA DE POBLACIONES Medellín, 4 e 5 de Outubro. Colômbia . Medellín, Colômbia.
2010.
Gusmão L. Marcadores ligados a los cromosomas sexuales y relaciones biológicas complejas.
Simposio Paternidades y Relaciones Biologicas Complejas. XI Congresso Colombiano de
Genética Humana. Medellín, Colombia, October 6, 2010.
Gusmão L. Marcadores ligados a los cromosomas sexuales en la práctica forense. Simposio
Genética Forense. XI Congresso Colombiano de Genética Humana. Medellín, Colombia,
October 7, 2010.
Gusmão L. Los marcadores sexuales en las pruebas de filiación. III Simposio Internacional.
Pruebas de Filiación: Un enfoque Legal. XI Congresso Colombiano de Genética Humana.
Medellín, Colombia, October 8, 2010.
Gusmão L. Genética Poblacional e Implicaciones Forenses. VIII Jornadas Anuales de la
Sociedada Argentina de Genética Forense. Rosario, Argentina. 2010.
4.3.2 Participation in Master Programs
Forensic Genetics Masters Course, Faculty of Sciences of University of Porto, Portugal.
_________________________________________________________________________________________________________________________________
63
4.3.3 Projects
Collaboration in FCT project “Mothers and fathers after the "biological truth"? Gender, inequalities
and parental roles in the cases of investigation of paternity”, PIHM/PI/0020/2008.
5. Quality Control
5.1 Pathology
•
Date of Institution 19-01-1998
The Quality Control System was done through the informatics systems Sislab and the results
published in the Unit’s Quality Manual 2009. The main findings, compared with the last 3 years, were:
2007
2008
2009
2010
Total nº of cases
13.214
14.099
10.883
11.746
Cases reviewed
670
465
501
470
2007
2008
2009
2010
Identification of speciman, archive and macroscopy
0.45%
0.01%
3.9%
1.06%
Diagnosis
0.0%
0.01%
0.2%
0.2%
Coding
0.0%
0.0%
0.5%
0.0%
Discordant values:
In 2010 the “turn-around time” (TAT) was the following:
-
Histological Exams:
Cytological Exams:
Screening cytologies:
87,12% of reports are sent in 2 working days
97,60% of reports are sent in 2 working days.
99,85% of reports are sent in 7 working days.
The main results for the Gynecological Citology quality control analysis were:
2007
2008
2009
2010
Total cases
7.299
7370
5129
6733
Reviewed cases
1438
1368
1013
1253
Concordance between
cytotechnician
pathologist
Discordance between
cytotechnician
pathologist
and
and
2007
2008
2009
2010
1313
1223
896
1150
(91, 3%)
(89, 4%)
(88, 5%)
(91.78%)
125
145
117
103
(8, 6%)
(10, 6%)
(11, 5%)
(8.22%)
The total amount of unsatisfactory cases for analysis was 0.59% (0,75% in 2009).
ASCUS/ACG were diagnosed in 155 cases with a ASCUS/Lesion reason of 2,57 (2,67 in 2009).
Apart from participating, with concordance, in all CAP Proficiency Tests, we continue to positively
participate in external quality control programs for imuno-histochenical techniques of UK-NEQAS
and the Quality Program of the Brazilian Society of Pathology (PIQ). All these activities are registered
according to our procedure PR MED-05.
5.2 Diagnostic Genetics
Participation in the pilot KRAS European Quality Assurance Program with a genotype score ≥ 90%.
_________________________________________________________________________________________________________________________________
64
Participation in the Regional KRAS EQA scheme 2010 with a genotype score ≥ 90%.
These
data
can
be
consulted
http://kras.eqascheme.org/info/public/eqa/previous_participants.xhtml
at
5.3 Parentage testing and Genetic Identification
Participation in the 2010 Quality Control Exercise (Paternity and Forensics) of the GHEP-ISFG (Spanish
and Portuguese Group of the International Society for Forensic Genetics). Certificates can be
accessed through the website www.ipatimup.pt.
In 2010 this quality control program consisted of three exercises: Practical Kinship study, Theoretical
Kinship study and a Forensic module.
Participation in other GHEP-ISFG collaborative exercises during 2010 included:
- Collaborative exercise on DNA mixture interpretation;
- Collaborative exercise on autosomal SNP genotyping.
6. Publications
• Albergaria A, Ribeiro AS, Pinho S, Milanezi F, Carneiro V, Sousa B, Sousa S, Oliveira C,
Machado JC, Seruca R, Paredes J, Schmitt F. ICI 182,780 induces P-cadherin overexpression
in breast cancer cells through chromatin remodelling at the promoter level: a role for
C/EBPb in CDH3 gene activation. Hum Mol Genet 19: 2554-2566, 2010.
• Gomes V, Alves C, Amorim A, Carracedo A, Sánchez-Diz P, Gusmão L (2010) Nilotes from
Karamoja, Uganda: haplotype data defined by 17 Y-chromosome STRs. Forensic Sci Int:
Genetics. 4:e83-86.
• Gomes V, Sánchez-Diz P, Amorim A, Carracedo A, Gusmão L (2010) Digging deeper into East
African human Y chromosome lineages. Hum Genet 127:603-613.
• Gusmão A, Valente C, Gomes V, Alves C, Amorim A, Prata MJ, Gusmão L (2010) A Genetic
Historical Sketch of European Gypsies: The Perspective From Autosomal Markers. Am J Phys
Anthropol. 141:507-514.
• Gusmão L, Alves C (2010) Marcadores dos cromossomas sexuais em identificação. In
Genética Forense. Perspectivas da Identificação Genética. Edições Universidade Fernando
Pessoa. Porto, Portugal. ISBN 978-989-643-050-4.
• Lebreiro A, Martins E, Almeida J, Pimenta S, Bernardes JM, Machado JC, Abreu-Lima C. Value
of Molecular Diagnosis in a Family With Marfan Syndrome and an Atypical Vascular
Phenotype. Rev Esp Cardiol 2010 [Epub ahead of print].
• Longatto-Filho A, Lopes JM, Schmitt FC. Angiogenesis and breast cancer. J Oncol DOI:
10.1155/2010/576384, 2010.
• Longatto-Filho A, Schmitt FC. Cytology education in the 21st Century: living in the past or
crossing the Rubicon? Acta Cytol 54: 654-656, 2010.
• Lopes N, Sousa B, Martins D, Gomes M, Vieira D, Veronese L, Milanezi F, Paredes J, Costa JL,
Schmitt F. Alterations in Vitamin D signalling and metabolic pathways in breast cancer
progression: a study of VDR, CYP27B1 nad CYP24A1 expression in benign and malignant
breast lesions. BMC Cancer 10:483, 2010.
• Morling N, Schneider PM, Mayr W, Gusmao L, Prinz M (2010) Authentication of forensic DNA
samples. Forensic Sci Int: Genetics In Press.
• Nogueiro I, Manco L, Gomes V, Amorim A, Gusmão L (2010) Phylogeographic analysis of
paternal lineages in NE Portuguese Jewish communities. Am J Phys Anthropol 141(3): 373381.
• Pinheiro C, Albergaria A, Paredes J, Sousa B, Dufloth R, Vieira D, Schmitt F, Baltazar F.
Monocarboxylate transporter 1 is up-regulated in basal-like breast carcinoma.
Histopathology 56: 860-867, 2010.
• Pinheiro C, Reis RM, Ricardo S, Longatto-Filho A, Schmitt F, Baltazar F. Expression of
monocarboxylate transporters 1, 2, and 4 in human tumours and their association wutgh
CD147 nad CD44. Journal of Biomed Biotechnol DOI:10.1155/2010/427694, 2010.
• Pinto N, Gusmão L, Amorim A (2010) Likelihood ratios in kinship analysis: Contrasting kinship
classes, not genealogies. Forensic Sci Int: Genetics 4:218–219.
• Prieto L, Zimmermann B, Goios A, Rodriguez-Monge A, Paneto GG, Alves C, Alonso A,
Fridman C, Cardoso S, Lima G, Anjos MJ, Whittle M, Montesino M, Cicarelli RMB, Rocha AM,
_________________________________________________________________________________________________________________________________
65
•
•
•
•
•
Albarrán C, Pancorbo M, Pinheiro MF, Carvalho M, Sumita DR, Parson W (2010) The GHEP–
EMPOP collaboration on mtDNA population data—A new resource for forensic casework,
Forensic Sci. Int. Genet., doi:10.1016/j.fsigen.2010.10.013.
Rakha E, Reis-Filho JS, Baehner F, Dabbs D, Decker T, Eusebi V, Fox S, Ichihara S, Jácquemier
J, Lakhani S, Palacios J, Schnitt S, Schmitt FC, Tan P, Tse G, Badve S, Ellis I. Breast cancer
prognostic classification in the molecular era: the role of histological grade. Breast Cancer
Res 12: 207, 2010.
Sousa B, Paredes J, Milanezi F, Lopes N, Martins D, Dufloth R, Vieira D, Albergaria A,
Veronese L, Carneiro V, Carvalho S, Costa JL, Zeferino L, Schmitt F. P-Cadherin, vimentin and
CK14 for identification of basal-like phenotype in breast carcinomas: an
immunohistochemical study. Histol Histopathol 25: 963-974, 2010.
Syrjanen K, Di Bonito L, Gonçalves L, Murjal L, Santamaria M, Mahovlic V, Karakitsos P, Onal
B, Schmitt FC. Cervical cancer screening in Mediterranean countries: implications for the
future. Cytopathology DOI:10.1111/j.1365-2303.2010.00795.x, 2010.
Van Asch B, Alves C, Santos L, Pinheiro R, Pereira F, Gusmão L, Amorim A (2010) Genetic
profiles and sex identification of found-dead wolves determined by the use of an 11-loci PCR
multiplex. Forensic Sci Int Genet 4(2):68-72.
Van Asch B, Pinheiro R, Pereira R, Alves C, Pereira V, Pereira F, Gusmão L, Amorim A (2010) A
framework for the development of STR genotyping in domestic animal species:
characterisation and population study of twelve canine X-chromosome loci. Electrophoresis
31(2):303-8.
_________________________________________________________________________________________________________________________________
66
Internal Services
Technical Supervision
Improvement of equipment and rooms
- The HITACHI HPLC chromatograph after maintenance became operational;
- Two old vacuum pumps, after maintenance, became operational;
- Damaged front panels of Pre-PCR cameras were substituted for new ones;
- A second glass door was placed in the “biosafety level II room”;
- The “dark room” was completely remodeled;
- The “radioactive room” was remodeled in order to fulfill the radiologic plan requirements;
- The “gel and cell counter room” was remodeled: both “Chemidoc” and “Geldoc” image acquisition
systems were re-installed in a common new table.
- The IPATIMUP DIAGNOSTICOS warehouse space was increased (an extra shelf was placed) in order
to create space for the forensic genetics (paternity) material;
- The total warehouse space was redistributed between groups: it was attributed warehouse space to
the Genetic Diversity and Populations Genetics Groups;
- Establishment of a room for quarantine and primary cultures, non-existent
Other Activities
- Implementation of the “Preventive Maintenance Service” for micropipettes quarterly;
- Inventory of all scientific devices in the GPLI Database;
- Implementation of the procedure for weighing different kinds of wastes before they are collected
by the “SOMOS” company;
- Implementation Rules on the use of various facilities (Chemidoc XRS+, Geldoc, Cell Counter, Liquid
Nitrogen containers) and Rooms (“biosafety level II room”, “cell culture 1 and 2 rooms”, “dark
room”);
- Participation in the elaboration of the contents to put in the webpage of the IPATIMUP Cell Lines
Bank and in the operating rules of this internal service;
- Implementation of the logbook registry in equipment used by several groups.
Acquisitions of equipment
DEVICES ACQUIRED
Stereomicroscope Olympus
Incubator INP Memmert
Cell Counter BECKMAN-COULTER Z2 Series
QIAxcel QIAGEN
Densitometer GS-800
Fridge 4°C, Gram (2 units)
Mini-Fridge 4°C, KUNZ
Freezer -20°C, Gram (3 units)
Freezer -20°C, Liebherr
Incubator Aqualytic (+2 to 40°C)
Incubator Termaks (420L)
CO2 Incubator Heraeus
Inverted Microscope Nikon
Hypercassetes 18x24, GE Healthcare
1 Filter set 63HE mRFP, Zeiss
_________________________________________________________________________________________________________________________________
67
Centrifuge Rotor + Adaptors, Hettich
Digital Roller Mixer, Stuart
Orbital Shaker DOS-20L
Orbital Shaker KS 260
Liquid Nitrogen containers Taylor-Warthon
Warthon (25L) (2 units)
Magnetic Stirrer HeiMix S (4 units)
pH Electrode
Humidifier System, Pecon
PREVENTIVE MAINTENANCE CONTRACTS ESTABLISHED
Genetic Analyser 3130-16
16 Preventive Annual Contract
Flow Cytometer EPICS XL 4 Preventive Annual Contract
CO2 Incubators Preventive Annual Contract
(11 units)
Biosafety Cabinets Preventive Annual Contract (for 13 units)
Centrifuge Beckman J-25
25 Avanti Preventive Annual Contract
SG Water Purification System Preventive Annual Contract
Service Contract (under the license radioimmunoassay obtainment)
Equipments with Preventive Contract:
1 Microtome Shandon Finesse 325
2 Memmert UNE-200 Incubators
1 Cold Plate KUNZ CP4
1 Histologic Bath KUNZ Hir
1 Centrifuge Cytospin 3 SHANDON
Sequencing Service
The sequencing service of IPATIMUP been active since 2006. Last year (2010) there was a significant
increase in the use of the service.
Listed below are graphs illustrative of the use of the service in the years 2009 and 2010. No statistic
data available from years 2006--2008.
_________________________________________________________________________________________________________________________________
_________________________________________________________________________________________________________
68
Proteomics Unit of IPATIMUP – Highlights 2010
The Proteomic Unit of IPATIMUP continued its activity in the year 2010 with the analysis of hundreds
of samples from intramural and extramural research groups.
The groups requesting analysis were from IPATIMUP, IBMC, INEB, ICBAS and FCUP from the
University of Porto. In addition analyses were also requested by research groups from the
Universidade do Minho and from Universidade Técnica de Lisboa.
The type of analysis performed included Molecular Mass determination, Protein identification by
Peptide Mass Fingerprint, and Protein identification and characterization by PMF followed by de
novo peptide sequencing by MS/MS.
In 2010, the Proteomic Unit of IPATIMUP participated in national and european projects leading to
the publication of various articles in international scientific journals. The Proteomic Unit of
IPATIMUP applied in 2010 to be a full member of the RNEM (Rede Nacional de Espectrometria de
Massa).
Animal House
IPATIMUP’s Animal House Facility, located in the Medical Faculty of the University of Porto, is
working as a service to our scientific community since 2009. We understand that the quality of our
research models has a direct impact on what matters most to our research partners. With our core
program of Animal Welfare based essentially on the principles of the 3Rs (that is the replacement,
refinement and reduction of the use of animals in research). The 3Rs are important from a legal,
ethical and scientific point of view. At our institution all research using animals, is regulated by the
European and National Law that regulate the use of animals in research. The 3Rs are implicit in the
DIRECTIVE 2010/63/EU OF THE EUROPEAN PARLIAMENT AND OF THE COUNCIL of 22nd September
2010 on the protection of animals used for scientific purposes, and any researcher planning to use
animals in their research must first demonstrate why there is no alternative and that the number of
animals used and any suffering caused will be kept to a minimum.
A considerable number of experiments have been performed using immunodeficient nude mouse
originated from NIH type II athymic (nude) mice colony, lacking a thymus, what unable them to
produce T and B cells, as well as NK cells. At the animal facilities we have also some strains of
knockout C57BL6 mice that are been used by some of the researcher engaged in work concerning
the role that specific genes play in the process of carcinogenesis and cancer progression.
For the past year, in order to improve the quality of the service and animal wellbeing, an effort was
made concerning the certification of personnel as well as the facilities by the National Regulator
Entity (DGV – Direcção Geral de Veterinária).
Post-graduation Unit of IPATIMUP
The Pos-graduation Unit of IPATIMUP was created in 2010 for the coordination of the activities of
Post-graduation performed by members of IPATIMUP.
In 2010 IPATIMUP participated in various Doctoral Programs: such as the organization of the
modules of “Oncobiology” and “Applied Human Genetics” for the Graduate Program in Basic and
Applied Biology Areas - GABBA Program from the University of Porto.
In 2010, members of IPATIMUP also organized the Oncobiology course of the PhD programme on
Molecular Medical Oncology of the Medical Faculty of the University of Porto; and the Oncobiology
course of the program for advanced medical education of the Gulbenkian/Champalimaud
foundation.
_________________________________________________________________________________________________________________________________
69
In this year, IPATIMUP continued the traineeship programs of students from several Master
programs of various Faculties of the University of Porto. In addition, IPATIMUP continued receiving
many trainee students from EU countries, as well as from Latin America countries.
Administrative Office
The new model of internal management was implemented:
With the implementation of the new management software, in January 2010 was created a database,
adjusted to the administrative needs supporting the General Secretary, to the execution and control
of research projects, to the maintenance and conservation of equipment and to the organization of
Human Resources.
The new model of communication has increased the availability and accessibility to information and
as improved the feedback of administrative services and allowed the transparency to provide the
accounts reports.
The internal communication instruments were improved:
- The introduction of the Helpdesk, through ticketing, allowed that the request for technical
intervention become more quickly and effectively;
- the submission of requisitions to the suppliers became the responsibility of the Secretary and
approved in the information system;
- orders reception and staff registration is now validated in the information system.
Training
Participation in vocational training: management of human resources, administrative management
of accounting, applying the new contributive code and application to the SNC – Accounting
Standardization System.
Future Objectives
One of the objectives for 2011 will be the implementation of a digital document system integrated
with the accounting program.
The new document scanning process will improve the administrative and financial management of
the research projects.
Secretary activity
Records
Human Resources:
Personnel Entry
84
Updated
114
Ongoing Projects:
158
Project / Account Management: Active Accounts
Opening Projects
Management Requirements:
Correspondence:
Maintenance
Equipment / Infrastructure:
Volume
234
57
Submitted
Sent abroad
6070
3631
Outgoing Correspondence
10856
Entry of Official Correspondence
572
Tickets Opened
255
Tickets Closed
279
_________________________________________________________________________________________________________________________________
70
Accounting movements
Movements
Treasury:
Volume
Movements
Suppliers / Customers
3273
7075
Supplier Payments
Accounting
Document Processing Average Number of contractors / grantees
1215
No. of Independent
29
Accounting Total Movements 2010
76
11233
_________________________________________________________________________________________________________________________________
71
Recent PhDs
André Albergaria
Transcription Factors and Epigenetics in Breast Cancer: New Findings in CDH3/P-CadherinGene
Regulation
Life and Health Sciences Research Institute, School of Health Sciences of Minho University, July 2010
Bárbara Van Asch
On the origin of animals: individuals, populations and derived products
Faculty of Sciences, University of Porto, July 2010
Iva Gomes
X chromosome markers: Genetic characterizations, Population
applications.Tese de Doutoramento em Ciencias Forenses e Patoloxía.
University of Santiago de Compostela, October 2010
analysis
and
Forensic
Margarida Coelho
Studying the evolutionary history of single markers and the demographic history of African
populations: The evolution of lactase persistence; Genetic structure of Bantu-speaking populations;
and the microevolutionary impact of the Atlantic slave trade.
Faculty of Sciences, University of Porto, January 2010
Raquel Lima
Relevance of latent EBV infection in drug response of Burkitt lymphoma cells
Faculty of Pharmacy, University of Porto, December 2010
Rita Barros
Identification of signalling pathways involved in CDX2 regulation in metaplastic lesions.
Faculty of Medicine, University of Porto, December 2010
Sérgia Velho
The role of BRAF and KRAS activating mutations in deficient and proficient MMR
colorectal carcinomas
Faculty of Medicine, University of Porto, May 2010
Sílvia Carvalho
Signalling Pathways in Basal-Like Breast Carcinomas: A Clue for Pathogenesis and Therapeutic
Targets
Faculty of Medicine, University of Porto, November 2010
Sofia Quental
Expression and structural investigation of the mutational spectrum of portuguese maple syrup urine
disease patients
Faculty of Sciences, University of Porto, January 2010
Sónia Melo
Epigenetic, Genetic and Functional Analyses of microRNA-machinery in Human Cancer
Faculty of Medicine, University of Porto, April 2010
Ana Machado.
Helicobacter pylori infection as a factor of genetic instability in gastric cells
University of Roskilde, Denmark, March 2010
_________________________________________________________________________________________________________________________________
72
Research Projects
1.
A strategy for preventing H.pylori-associated gastric cancer based on materials with specific
receptors to the bacterin-form SAMS to Gly-R chitosan microspheses
2.
Alterações metabólicas e cancro: GRIM-19 um gene do metabolismo celular e um gene
supressor tumoral, que poderá ser um target terapêutico interssante
3.
Analysis of the function and mechanisms of action of a novel Wnt pathway member in
vertebrate tumourigenesis and development
4.
Approaching basal-like breast carcinomas to target therapy. A project combining the
reinforcement of logistic facilities with translational research
5.
Are genetic polymorphisms in inflammatory molecules risk factors for the development of
autoimmune thyroiditis? (This project implies the establishment of a tumour database)
6.
Bacterial protein azurin as a new candidate drug to trat poor-prognosis breast cancer
7.
Basal-like Breast Cancer: are mammary stem cells new targets for cancer therapy?
8.
Cancer risk and irradiation: an epidemiological and genetic study of a cohort irradiated for
Tinea Capitis
9.
CDX2 autoregulation in the reversibility/irreversibility of gastric intestinal metaplasia
10. Challenges in target-based therapy: Mechanisms of resistance to trastuzumab in her2overexpressing breast carcinomas
11. Characterization of the 17q21microdeletion-predisposing inversion polymorphism in the
Portuguese population
12. Co-Evolutionary Study of Nad Biochemical Networks
13. Colonization, inflammation and infection on Portuguese cystic fibrosis patients
14. Comparative analysis of DNA sequence evolution in nuclear and mitochondrial backgrounds
in inbreb mice
15. Computational disease prediction systems based on molecular markers
16. Description and analysis of genetic polymorphism in micro-ruminants
17. Desenvolvimento de um novo método de detecção de mutações com relevância preditiva
na resposta de doentes com carcinoma colo rectal ao tratamento com cetuximab
18. Desenvolvimento de um sistema de informação médica sobre Cancro Hereditário da Mama e
Colorectal
19. Determining the CCAAT/enhancer binding protein ß (C/EBPß) partnership profile in gastric
carcinogenesis
20. Development of siRNA-loaded nanoparticles to circumvent chemoresistance in cancer stem
cells
21. Development of tools for automatic comparison of biological sequences
22. 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
23. Dissection of the molecular role of O-GLcNAc in the multinucleation phenotype of the
neoplasic cells in Hodgkin´s lymphoma
24. Does P-cadherin expression interfere with E-cadherin function in invasive breast cancer
cells?
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73
25. Early detection of cancer using serum biomarkers based on aberrant post-translational
modifications of O-glycoproteins, O-PTM-Biomarkers
26. Ethnicity and genetics in Sub-Saharan Africa
27. Evaluation and Control of Neglected Mucosal Enteric Infections in Childhood
28. Exploring the role of E-cadherin trafficking deregulation in epithelial cancer progression
29. Exploring the role of E-Cadherin-HER interaction in the search of molecular biomarkers for
the clinical management of gastric cancer patient
30. Galectins as modulators of tumor progression:Establishement of anti-cancer action of
bioactive fragments from pectin by inhibiting galectin - 3
31. Genetic analysis of 15STR loci in the population of the Acre province, Northern Brazil
32. Genetic and chronological characterization of the European settlement by modern humans
in the Upper Palaeolithic
33. Genetic of populations of jewis origin
34. Glycosylation alterations in cancer - characterization by proximity ligation (PLA) Assays and
by production of glycopeptide specific monoclonal antibodies
35. HeliSysBio - Molecular Systems Biology Helicobacter pylori
36. Identificação de factores prognósticos e de selecção terapêutica em carcinomas
diferenciados da tireoide
37. Identificação de vias de sinalização mediadas pelo oncogene MUC1 em linhas celulares de
carcinoma gástrico e em células gástricas imortalizadas
38. Identification of Genetic markers for prediction of the clinical course and development of
complications in portuguese Chron's Disease patients
39. Identification of SNP backgrounds of the Androgen Receptor gene: an attempt to
understand AR diversity and the mechanisms of instability underlying CAG and GGC coding
repeats
40. In Vitro characterization of cancer stem cell features mediated by P-cadherin expression in
cancer cell lines and primary carcinomas of the breast
41. Integrated Micro-Nano-OPTO Fluidic systems for high-content diagnosis and studies of rare
cancer cells
42. Interacção entre Helicobacter pylori e as junções intercelulares de aclusão
43. Interaction of HER receptors (EGFR and HER2) and E-Cadherin. Search of molecular
biomarkers for clinical management of gastric cancer patients
44. Is the mTOR pathway relevant in the initiation/progression and/or a putative therapeutic
target in melanomas?
45. Large inversion polymorphisms in the human genome
46. Looking for evidences of human adaptation in the proteolysis universe: the case-study of
serine protease inhibitors
47. Males lineages in South Amerindian populations
48. miRNAs como alvos moleculares em leucemia humana
49. MLK3, um novo gene mutado em cancro colorectal com instabilidade de microssatélites
50. Molecular and nanotecchnology-based approaches to improve the antitumor activity of
small molecules
51. Molecular diagnosis of OTC deficiency: too many unsolved cases
_________________________________________________________________________________________________________________________________
74
52. mTOR expression in breast carcinomas and the ability of everolimus (RAD 001) to modulate
its expression
53. Mutated suppressor tRNAs as a therapeutic tool for cancer associated syndromes: HDGC as
a model
54. New E-cadherin RNAs: the dark side of a tumour suppressor gene
55. Non-coding DNA structural information in phylogeny, evolution and disease
56. 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
57. O Nemátode-Da-Madeira-Do-Pinheiro (NMP), Bursaphelenchus Xyliophilus
58. Pharmacogenetics
59. PIK the Fraternity
60. Portuguese Wild Mushrooms: Chemical characterization and functional study of
antiproliferative and proapoptotic properties in cancer cell lines
61. Prevention and early diagnosis of cancer
62. Primary hyperparathyroidism - from geneside to bedside
63. Regulation of P-cadherin Expression in Breast Cancer
64. Research launching in Aspergillus fumigatus genetics
65. S1H-RAS expression and activity regulation;implications in tumorigenesis
66. Search for genomic structural variants in azoopermia:a study in the Portuguese population
67. SOX2 and CDX2 negative cross-regulation in the establishement of intestinal metaplasia of
the stomach
68. SOX2 and CDX2 negative cross-regulation in the establishment of intestinal metaplasia of the
stomach
69. Study of mTOR pathway in human cancer
70. Study of SDH alterations in GIST
71. Study of the role played by TGF-B dual effect in the progression of papillary thyroid
carcinoma
72. The causes and consequences of mitochondrial DNA deletions in animals cells
73. The involvement of CDH1 in CG angiogenesis
74. The involvement of microRNAs in gastric cancer
75. The role of protein quality control in cancer
76. The Role of Protein Quality Control in the regulation of E-cadherin and its relevance in
cancer
77. Transcriptional and post-transcriptional mechanisms of LRP1B inactivation in sporadic and
familial non-medullary thyroid cancer
78. Unraveling the genetics of neuroendocrine tumors by high throughput methods
79. Unveiling GRIM-19 functional roles in cancer metabolism
80. Vitamin D, a candidate for new therapy of basal-like breast carcinomas
81. X chromosone and autosomal indel markers in kinship analysis
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75
Other Projects
1.
Banco de Tumores - Amostras Congeladas
2.
Cancer Mobile
3.
Congresso Europeu de Patologia em Lisboa
4.
Criação de um Banco de DNA e RNA acoplado ao Banco de Tecidos e Tumores do H. S. João
5.
Do IT - Desenvolvimento e Operacionalização da Investigação de Translação
6.
Fellowship para apoio ao Internato de Anatomia Patológica no Hospital de S. João
7.
Formação Avançada em Microscopia
8.
Formação Pessoal
9.
Laboratório Aberto
10. Modelos de Sistemas de Gestão do Risco na Investigação em Ciências da Vida e da Saúde
11. Pilot Project
12. Prestação de Serviços para desenvolvimento da aplicação informática para gestão da base
de dados da futura Rede Nacional de Banco de Tumores
13. Projecto de Desenvolvimento e Implementação de um modelo de ensino inclusivo da Ciência
numa população de alunos cegos ou com baixa visão
14. Seminar
_________________________________________________________________________________________________________________________________
76
Scientific Papers
1.
Behar DM, Yunusbayev B, Metspalu M, Metspalu E, Rosset S, Parik J, Rootsi S, Chaubey G,
Kutuev I, Yudkovsky G, Khusnutdinova EK, Balanovsky O, Semino O, Pereira L, Comas D,
Gurwitz D, Bonne-Tamir B, Parfitt T, Hammer MF, Skorecki K, Villems R The genome-wide
structure of the Jewish people. Nature 466: 238-42, 2010 [Article] IF=34,48
2.
Rei M, Freitas R, Sousa A, Caffrey T, Hollingsworth MA, Santos-Silva F Characterization of
MUC1 signaling pathways in pancreatic cancer stem cells. Gastroenterology 138, 2010 []
IF=12,899
3.
Machado AM, Figueiredo C, Seruca R, Rasmussen LJ Helicobacter pylori infection generates
genetic instability in gastric cells. Biochimica et Biophysica acta-Reviews on Cancer 1806: 5865, 2010 [Review] IF=11,685
4.
Cerny V, Mulligan CJ, Fernandes V, Silva NM, Alshamali F, Non A, Harich N, Cherni L, El Gaaied
AB, Al-Meeri A, Pereira L Internal diversification of mitochondrial haplogroup R0a reveals
post-Last Glacial Maximum demographic expansions in South Arabia. Molecular biology and
evolution , 2010 [Epub ahead of print] IF=9,872
5.
Svrcek M, Buhard O, Colas C, Coulet F, Dumont S, Massaoudi I, Lamri A, Hamelin R, Cosnes J,
Oliveira C, Seruca R, Gaub MP, Legrain M, Collura A, Lascols O, Tiret E, Fléjou JF, Duval A
Methylation tolerance due to an O6-methylguanine DNA methyltransferase (MGMT) field
defect in the colonic mucosa: an initiating step in the development of mismatch repairdeficient colorectal cancers. Gut 59: 1516-26, 2010 [Article] IF=9,357
6.
Pinheiro H, Bordeira-Carriço R, Seixas S, Carvalho J, Senz J, Oliveira P, Inácio P, Gusmão L,
Rocha J, Huntsman D, Seruca R, Oliveira C Allele-specific CDH1 downregulation and
hereditary diffuse gastric cancer. Human molecular genetics 19: 943-52, 2010 [Article]
IF=7,386
7.
Velho S, Oliveira C, Paredes J, Sousa S, Leite M, Matos P, Milanezi F, Ribeiro AS, Mendes N,
Licastro D, Karhu A, Oliveira MJ, Ligtenberg M, Hamelin R, Carneiro F, Lindblom A, Peltomaki
P, Castedo S, Schwartz S, Jordan P, Aaltonen LA, Hofstra RM, Suriano G, Stupka E, Fialho
AM, Seruca R Mixed lineage kinase 3 gene mutations in mismatch repair deficient
gastrointestinal tumours. Human molecular genetics 19: 697-706, 2010 [Article] IF=7,386
8.
Albergaria A, Ribeiro AS, Pinho S, Milanezi F, Carneiro V, Sousa B, Sousa S, Oliveira C,
Machado JC, Seruca R, Paredes J, Schmitt F ICI 182,780 induces P-cadherin overexpression in
breast cancer cells through chromatin remodelling at the promoter level: a role for
C/EBPbeta in CDH3 gene activation. Human molecular genetics 19: 2554-66, 2010 [Article]
IF=7,386
9.
Ribeiro AS, Albergaria A, Sousa B, Correia AL, Bracke M, Seruca R, Schmitt FC, Paredes J
Extracellular cleavage and shedding of P-cadherin: a mechanism underlying the invasive
behaviour of breast cancer cells. Oncogene 29: 392-402, 2010 [Article] IF=7,135
10. Prazeres H, Torres J, Rodrigues F, Pinto M, Pastoriza MC, Gomes D, Cameselle-Teijeiro J,
Vidal A, Martins TC, Sobrinho-Simões M, Soares P Chromosomal, epigenetic and microRNAmediated inactivation of LRP1B, a modulator of the extracellular environment of thyroid
cancer cells. Oncogene , 2010 [Epub ahead of print] IF=7,135
11. Santos NP, Ribeiro-Rodrigues EM, Ribeiro-Dos-Santos AK, Pereira R, Gusmão L, Amorim A,
Guerreiro JF, Zago MA, Matte C, Hutz MH, Santos SE Assessing individual interethnic
admixture and population substructure using a 48-insertion-deletion (INSEL) ancestryinformative marker (AIM) panel. Human mutation 31: 184-90, 2010 [Article] IF=6,887
12. Pereira F, Carneiro J, Matthiesen R, van Asch B, Pinto N, Gusmão L, Amorim A Identification
of species by multiplex analysis of variable-length sequences. Nucleic acids research 38:
e203, 2010 [] IF=6,878
13. Buckland G, Agudo A, Luján L, Jakszyn P, Bueno-de-Mesquita HB, Palli D, Boeing H, Carneiro
F, Krogh V, Sacerdote C, Tumino R, Panico S, Nesi G, Manjer J, Regnér S, Johansson I,
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77
Stenling R, Sanchez MJ, Dorronsoro M, Barricarte A, Navarro C, Quirós JR, Allen NE, Key TJ,
Bingham S, Kaaks R, Overvad K, Jensen M, Olsen A, Tjønneland A, Peeters PH, Numans ME,
Ocké MC, Clavel-Chapelon F, Morois S, Boutron-Ruault MC, Trichopoulou A, Lagiou P,
Trichopoulos D, Lund E, Couto E, Boffeta P, Jenab M, Riboli E, Romaguera D, Mouw T,
González CA Adherence to a Mediterranean diet and risk of gastric adenocarcinoma within
the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort study. The
American journal of clinical nutrition 91: 381-90, 2010 [Article] IF=6,74
14. Fitzgerald RC, Hardwick R, Huntsman D, Carneiro F, Guilford P, Blair V, Chung DC, Norton J,
Ragunath K, Van Krieken JH, Dwerryhouse S, Caldas C, Hereditary diffuse gastric cancer:
updated consensus guidelines for clinical management and directions for future research.
Journal of medical genetics 47: 436-44, 2010 [Article] IF=5,751
15. Duell EJ, Travier N, Lujan-Barroso L, Boutron-Ruault MC, Clavel-Chapelon F, Palli D, Krogh V,
Mattiello A, Tumino R, Sacerdote C, Rodriguez L, Sanchez-Cantalejo E, Navarro C, Barricarte
A, Dorronsoro M, Khaw KT, Wareham N, Allen NE, Tsilidis KK, Bueno-de-Mesquita HB,
Jeurnink SM, Numans ME, Peeters PH, Lagiou P, Valanou E, Trichopoulou A, Kaaks R,
Lukanova-McGregor A, Bergman MM, Boeing H, Manjer J, Lindkvist B, Stenling R, Hallmans
G, Dahm CC, Overvad K, Olsen A, Tjonneland A, Bakken K, Lund E, Jenab M, McCormack V,
Rinaldi S, Michaud D, Mouw T, Nesi G, Carneiro F, Riboli E, González CA Menstrual and
reproductive factors, exogenous hormone use, and gastric cancer risk in a cohort of women
from the European prospective investigation into cancer and nutrition. American journal of
epidemiology 172: 1384-93, 2010 [Article] IF=5,589
16. Rakha EA, Reis-Filho JS, Baehner F, Dabbs DJ, Decker T, Eusebi V, Fox SB, Ichihara S,
Jacquemier J, Lakhani SR, Palacios J, Richardson AL, Schnitt SJ, Schmitt FC, Tan PH, Tse GM,
Badve S, Ellis IO Breast cancer prognostic classification in the molecular era: the role of
histological grade. Breast cancer research : BCR 12: 207, 2010 [Review] IF=5,326
17. Amorim A, Silva RM FKS2 Mutations Associated with Decreased Echinocandin Susceptibility
of Candida glabrata following Anidulafungin Therapy Antimicrobial agents and
chemotherapy 000, 2010 [] IF=4,802
18. Leite M, Corso G, Sousa S, Milanezi F, Afonso LP, Henrique R, Soares JM, Castedo S, Carneiro
F, Roviello F, Oliveira C, Seruca R MSI phenotype and MMR alterations in familial and
sporadic gastric cancer. International journal of cancer. Journal international du cancer ,
2010 [Epub ahead of print] IF=4,722
19. Peixoto A, Santos C, Pinheiro M, Pinto P, Soares MJ, Rocha P, Gusmão L, Amorim A, van der
Hout A, Gerdes AM, Thomassen M, Kruse TA, Cruger D, Sunde L, Bignon YJ, Uhrhammer N,
Cornil L, Rouleau E, Lidereau R, Yannoukakos D, Pertesi M, Narod S, Royer R, Costa MM,
Lazaro C, Feliubadaló L, Graña B, Blanco I, de la Hoya M, Caldés T, Maillet P, Benais-Pont G,
Pardo B, Laitman Y, Friedman E, Velasco EA, Durán M, Miramar MD, Valle AR, Calvo MT, Vega
A, Blanco A, Diez O, Gutiérrez-Enríquez S, Balmaña J, Ramon Y Cajal T, Alonso C, Baiget M,
Foulkes W, Tischkowitz M, Kyle R, Sabbaghian N, Ashton-Prolla P, Ewald IP, Rajkumar T,
Mota-Vieira L, Giannini G, Gulino A, Achatz MI, Carraro DM, de Paillerets BB, Remenieras A,
Benson C, Casadei S, King MC, Teugels E, Teixeira MR International distribution and age
estimation of the Portuguese BRCA2 c.156_157insAlu founder mutation. Breast cancer
research and treatment , 2010 [Epub ahead of print] IF=4,696
20. Pópulo H, Soares P, Faustino A, Rocha AS, Azevedo F, Lopes JM. mTOR pathway activation is
associated with worse prognosis characteristics in cutaneous melanoma. Pigmented Cell
and Melanoma Research 2010 Oct 28. doi: 10.1111/j.1755-148X.2010.00796.x. [Epub ahead of
print]. IF=4,63
21. Regalo G, Resende C, Wen X, Gomes B, Durães C, Seruca R, Carneiro F, Machado JC C/EBP
alpha expression is associated with homeostasis of the gastric epithelium and with gastric
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78
carcinogenesis. Laboratory investigation; a journal of technical methods and pathology 90:
1132-9, 2010 [Article] IF=4,602
22. da Cunha CB, Oliveira C, Wen X, Gomes B, Sousa S, Suriano G, Grellier M, Huntsman DG,
Carneiro F, Granja PL, Seruca R De novo expression of CD44 variants in sporadic and
hereditary gastric cancer. Laboratory investigation; a journal of technical methods and
pathology 90: 1604-14, 2010 [Article] IF=4,602
23. Machado P, Pereira R, Rocha AM, Manco L, Fernandes N, Miranda J, Ribeiro L, do Rosário
VE, Amorim A, Gusmão L, Arez AP Malaria: looking for selection signatures in the human
PKLR gene region. British journal of haematology 149: 775-84, 2010 [Article] IF=4,597
24. Gomes V, Sánchez-Diz P, Amorim A, Carracedo A, Gusmão L Digging deeper into East African
human Y chromosome lineages. Human genetics 127: 603-13, 2010 [Article] IF=4,523
25. Velho S, Corso G, Oliveíra C, Seruca R KRAS signaling pathway alterations in microsatellite
unstable gastrointestinal cancers. Advances in cancer research 109: 123-43, 2010 [] IF=4,456
26. Conze T, Carvalho AS, Landegren U, Almeida R, Reis CA, David L, Söderberg O MUC2 mucin is
a major carrier of the cancer-associated sialyl-Tn antigen in intestinal metaplasia and gastric
carcinomas. Glycobiology 20: 199-206, 2010 [Article] IF=4,446
27. de Oliveira JT, de Matos AJ, Gomes J, Vilanova M, Hespanhol V, Manninen A, Rutteman G,
Chammas R, Gärtner F, Bernardes ES Coordinated expression of galectin-3 and galectin-3binding sites in malignant mammary tumors: implications for tumor metastasis.
Glycobiology 20: 1341-52, 2010 [Article] IF=4,446
28. Rodríguez-Suárez E, Gubb E, Alzueta IF, Falcón-Pérez JM, Amorim A, Elortza F, Matthiesen R
Virtual expert mass spectrometrist: iTRAQ tool for database-dependent search, quantitation
and result storage. Proteomics 10: 1545-56, 2010 [Article] IF=4,426
29. Badve S, Dabbs DJ, Schnitt SJ, Baehner FL, Decker T, Eusebi V, Fox SB, Ichihara S,
Jacquemier J, Lakhani SR, Palacios J, Rakha EA, Richardson AL, Schmitt FC, Tan PH, Tse GM,
Weigelt B, Ellis IO, Reis-Filho JS Basal-like and triple-negative breast cancers: a critical review
with an emphasis on the implications for pathologists and oncologists. Modern pathology :
an official journal of the United States and Canadian Academy of Pathology, Inc , 2010 [Epub
ahead of print] IF=4,406
30. Peleteiro B, Lopes C, Figueiredo C, Lunet N Salt intake and gastric cancer risk according to
Helicobacter pylori infection, smoking, tumour site and histological type. British journal of
cancer , 2010 [Epub ahead of print] IF=4,346
31. Eussen SJ, Vollset SE, Hustad S, Midttun Ø, Meyer K, Fredriksen A, Ueland PM, Jenab M,
Slimani N, Ferrari P, Agudo A, Sala N, Capellá G, Del Giudice G, Palli D, Boeing H, Weikert C,
Bueno-de-Mesquita HB, Büchner FL, Carneiro F, Berrino F, Vineis P, Tumino R, Panico S,
Berglund G, Manjer J, Stenling R, Hallmans G, Martínez C, Arrizola L, Barricarte A, Navarro C,
Rodriguez L, Bingham S, Linseisen J, Kaaks R, Overvad K, Tjønneland A, Peeters PH, Numans
ME, Clavel-Chapelon F, Boutron-Ruault MC, Morois S, Trichopoulou A, Lund E, Plebani M,
Riboli E, González CA Vitamins B2 and B6 and genetic polymorphisms related to one-carbon
metabolism as risk factors for gastric adenocarcinoma in the European prospective
investigation into cancer and nutrition. Cancer epidemiology, biomarkers & prevention : a
publication of the American Association for Cancer Research, cosponsored by the American
Society of Preventive Oncology 19: 28-38, 2010 [Article] IF=4,31
32. Peleteiro B, Lunet N, Carrilho C, Durães C, Machado JC, La Vecchia C, Barros H Association
between cytokine gene polymorphisms and gastric precancerous lesions: systematic review
and meta-analysis. Cancer epidemiology, biomarkers & prevention : a publication of the
American Association for Cancer Research, cosponsored by the American Society of
Preventive Oncology 19: 762-76, 2010 [Article] IF=4,31
33. Pereira L, Silva NM, Franco-Duarte R, Fernandes V, Pereira JB, Costa MD, Martins H, Soares
P, Behar DM, Richards MB, Macaulay V Population expansion in the North African late
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79
Pleistocene signalled by mitochondrial DNA haplogroup U6. BMC evolutionary biology 10:
390, 2010 [] IF=4,294
34. Quental R, Azevedo L, Matthiesen R, Amorim A Comparative analyses of the Conserved
Oligomeric Golgi (COG) complex in vertebrates. BMC evolutionary biology 10: 212, 2010
[Article] IF=4,294
35. Harich N, Costa MD, Fernandes V, Kandil M, Pereira JB, Silva NM, Pereira L The trans-Saharan
slave trade - clues from interpolation analyses and high-resolution characterization of
mitochondrial DNA lineages. BMC evolutionary biology 10: 138, 2010 [Article] IF=4,294
36. Lado-Abeal J, Celestino R, Bravo SB, Garcia-Rendueles ME, de la Calzada J, Castro I, Castro P,
Espadinha C, Palos F, Soares P, Alvarez CV, Sobrinho-Simões M, Cameselle-Teijeiro J
Identification of a paired box gene 8-peroxisome proliferator-activated receptor gamma
(PAX8-PPARgamma) rearrangement mosaicism in a patient with an autonomous functioning
follicular thyroid carcinoma bearing an activating mutation in the TSH receptor. Endocrinerelated cancer 17: 599-610, 2010 [Article] IF=4,282
37. Boaventura P, Bastos J, Pereira D, Soares P, Teixeira-Gomes JM Alopecia in women
submitted to childhood X-ray epilation for tinea capitis treatment. The British journal of
dermatology 163: 643-4, 2010 [Letter] IF=4,26
38. Carvalho AS, Harduin-Lepers A, Magalhães A, Machado E, Mendes N, Costa LT, Matthiesen
R, Almeida R, Costa J, Reis CA Differential expression of alpha-2,3-sialyltransferases and
alpha-1,3/4-fucosyltransferases regulates the levels of sialyl Lewis a and sialyl Lewis x in
gastrointestinal carcinoma cells. The international journal of biochemistry & cell biology 42:
80-9, 2010 [Article] IF=4,178
39. Corso G, Pedrazzani C, Pinheiro H, Fernandes E, Marrelli D, Rinnovati A, Pascale V, Seruca R,
Oliveira C, Roviello F E-cadherin genetic screening and clinico-pathologic characteristics of
early onset gastric cancer. European journal of cancer (Oxford, England : 1990) , 2010 [Epub
40. Corso G, Velho S, Paredes J, Pedrazzani C, Martins D, Milanezi F, Pascale V, Vindigni C,
Pinheiro H, Leite M, Marrelli D, Sousa S, Carneiro F, Oliveira C, Roviello F, Seruca R Oncogenic
mutations in gastric cancer with microsatellite instability. European journal of cancer
(Oxford, England : 1990) , 2010 [Epub ahead of print] IF=4,121
41. Seca H, Almeida GM, Guimarães JE, Vasconcelos MH miR signatures and the role of miRs in
acute myeloid leukaemia. European journal of cancer (Oxford, England : 1990) 46: 1520-1527,
2010 [Review] IF=4,121
42. Pall M, Azziz R, Beires J, Pignatelli D The phenotype of hirsute women: a comparison of
polycystic ovary syndrome and 21-hydroxylase-deficient nonclassic adrenal hyperplasia.
Fertility and sterility 94: 684-9, 2010 [Article] IF=3,97
43. Suarez-Kurtz G, Amorim A, Damasceno A, Hutz MH, de Moraes MO, Ojopi EB, Pena SD, Perini
JA, Prata MJ, Ribeiro-dos-Santos A, Romano-Silva MA VKORC1 polymorphisms in Brazilians:
comparison with the Portuguese and Portuguese-speaking Africans and pharmacogenetic
implications. Pharmacogenomics 11: 1257-67, 2010 [Article] IF=3,893
44. Alvarenga CA, Vinagre J, Paravidino PI, Alvarenga MA, Billish A, Castilho LN, Prando A,
Soares P, Lopes JM Paraganglioma of vesicle seminal and chromophobe renal cell
carcinoma: a rare sporadic or hereditary association? Histopathology 243, 2010 [] IF=3,855
45. Saieg MA, Cury AN, Oliveira AK, Nascimento AO, Melo M, Soares P, Sobrinho-Simões M
Study of the histological profile of papillary thyroid carcinoma associated to hashimoto
thyroiditis Histopathology 192, 2010 [] IF=3,855
46. Pinheiro C, Albergaria A, Paredes J, Sousa B, Dufloth R, Vieira D, Schmitt F, Baltazar F
Monocarboxylate transporter 1 is up-regulated in basal-like breast carcinoma.
Histopathology 56: 860-7, 2010 [Article] IF=3,855
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80
47. Pinto N, Silva PV, Amorim A General derivation of the sets of pedigrees with the same
kinship coefficients. Human heredity 70: 194-204, 2010 [Article] IF=3,806
48. Lopes AM, Burgoyne PS, Ojarikre A, Bauer J, Sargent CA, Amorim A, Affara NA
Transcriptional changes in response to X chromosome dosage in the mouse: implications for
X inactivation and the molecular basis of Turner Syndrome. BMC genomics 11: 82, 2010
[Article] IF=3,759
49. Magalhães A, Ismail MN, Reis CA Sweet receptors mediate the adhesion of the gastric
pathogen Helicobacter pylori: glycoproteomic strategies. Expert review of proteomics 7:
307-10, 2010 [Editorial Material] IF=3,57
50. Pereira L, Cerný V, Cerezo M, Silva NM, Hájek M, Vasíková A, Kujanová M, Brdicka R, Salas A
Linking the sub-Saharan and West Eurasian gene pools: maternal and paternal heritage of
the Tuareg nomads from the African Sahel. European journal of human genetics : EJHG 18:
915-23, 2010 [Article] IF=3,564
51. Zanetti E, Barozzi P, Brown EE, Bosco R, Vallerini D, Riva G, Quadrelli C, Potenza L, Forghieri
F, Montagnani G, D'Amico R, Del Giovane C, Duraes C, Whitby D, Machado JC, Schulz TF,
Torelli G, Luppi M Common vascular endothelial growth factor variants and risk for
posttransplant Kaposi sarcoma. Transplantation 90: 337-8, 2010 [Letter] IF=3,498
52. Madeira PP, Reis CA, Rodrigues AE, Mikheeva LM, Zaslavsky BY Solvent properties
governing solute partitioning in polymer/polymer aqueous two-phase systems: nonionic
compounds. The journal of physical chemistry. B 114: 457-62, 2010 [Article] IF=3,471
53. Barros R, Camilo V, Pereira B, Freund JN, David L, Almeida R Pathophysiology of intestinal
metaplasia of the stomach: emphasis on CDX2 regulation. Biochemical Society transactions
38: 358-63, 2010 [Proceedings Paper] IF=3,378
54. Queiroz MJ, Calhelha RC, Vale-Silva LA, Pinto E, Lima RT, Vasconcelos MH Efficient synthesis
of 6-(hetero)arylthieno[3,2-b]pyridines by Suzuki-Miyaura coupling. Evaluation of growth
inhibition on human tumor cell lines, SARs and effects on the cell cycle. European journal of
medicinal chemistry 45: 5628-34, 2010 [Article] IF=3,269
55. Peleteiro B, Lunet N, Barros R, La Vecchia C, Barros H Factors contributing to the
underestimation of Helicobacter pylori-associated gastric cancer risk in a high-prevalence
population. Cancer causes & control : CCC 21: 1257-64, 2010 [Article] IF=3,199
56. Huerta JM, Navarro C, Chirlaque MD, Tormo MJ, Steindorf K, Buckland G, Carneiro F,
Johnsen NF, Overvad K, Stegger J, Tjønneland A, Boutron-Ruault MC, Clavel-Chapelon F,
Morois S, Boeing H, Kaaks R, Rohrmann S, Vigl M, Lagiou P, Trichopoulos D, Trichopoulou A,
Bas Bueno-de-Mesquita H, Monninkhof EM, Numans ME, Peeters PH, Mattiello A, Pala V,
Palli D, Tumino R, Vineis P, Agudo A, Ardanaz E, Arriola L, Molina-Montes E, Rodríguez L,
Lindkvist B, Manjer J, Stenling R, Lund E, Crowe FL, Key TJ, Khaw KT, Wareham NJ, Jenab M,
Norat T, Romaguera D, Riboli E, González CA Prospective study of physical activity and risk
of primary adenocarcinomas of the oesophagus and stomach in the EPIC (European
Prospective Investigation into Cancer and nutrition) cohort. Cancer causes & control : CCC
21: 657-69, 2010 [Article] IF=3,199
57. Vellón L, Royo F, Matthiesen R, Torres-Fuenzalida J, Lorenti A, Parada LA Functional
blockade of a5ß1 integrin induces scattering and genomic landscape remodeling of hepatic
progenitor cells. BMC cell biology 11: 81, 2010 [Article] IF=3,157
58. Vasconcelos M. Helena, Vaz J A., Barros L, Martins A, Santos-Buelga C, Ferreira I C.F.R.
Chemical composition of wild edible mushrooms and antioxidant properties of their water
soluble polysaccharidic and ethanolic fractions Food Chemistry 126: 610-616, 2010 []
IF=3,146
59. van Asch B, Pinheiro R, Pereira R, Alves C, Pereira V, Pereira F, Gusmão L, Amorim A A
framework for the development of STR genotyping in domestic animal species:
characterization and population study of 12 canine X-chromosome loci. Electrophoresis 31:
303-8, 2010 [Article] IF=3,077
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81
60. Kianmanesh R, Ruszniewski P, Rindi G, Kwekkeboom D, Pape UF, Kulke M, Sevilla Garcia I,
Scoazec JY, Nilsson O, Fazio N, Lesurtel M, Chen YJ, Eriksson B, Cioppi F, O'Toole D,
Collaborators, including Lopes JM . ENETS consensus guidelines for the management of
peritoneal carcinomatosis from neuroendocrine tumors. Neuroendocrinology 91: 333-40,
2010 [] IF=3,074
61. Kos-Kudla B, O'Toole D, Falconi M, Gross D, Klöppel G, Sundin A, Ramage J, Oberg K,
Wiedenmann B, Komminoth P, Van Custem E, Mallath M, Papotti M, Caplin M, Collaborators,
including Lopes JM . ENETS consensus guidelines for the management of bone and lung
metastases from neuroendocrine tumors. Neuroendocrinology 91: 341-50, 2010 [] IF=3,074
62. Pavel M, Grossman A, Arnold R, Perren A, Kaltsas G, Steinmuller T, de Herder W, Nikou G,
Plockinger U, Lopes JM, Sasano H, Buscombe J, Lind P, O'Toole D, Oberg K. ENETS
consensus guidelines for the management of brain, cardiac and ovarian metastases from
neuroendocrine tumors. Neuroendocrinology. 2010; 91: 326-33[] IF=3,074
63. O'Toole D, Rindi G, Plöckinger U, Wiedenmann B, Collaborators, including Lopes JM ENETS
consensus guidelines for the management of patients with rare metastases from digestive
neuroendocrine
tumors:
rationale
and
working
framework.
Introduction.
Neuroendocrinology 91: 324-5, 2010 [] IF=3,074
64. Amorim A, Guedes-Vaz L, Araujo R Susceptibility to five antifungals of Aspergillus fumigatus
strains isolated from chronically colonised cystic fibrosis patients receiving azole therapy.
International journal of antimicrobial agents 35: 396-9, 2010 [Article] IF=3,032
65. Alves J, Machado P, Silva J, Gonçalves N, Ribeiro L, Faustino P, do Rosário VE, Manco L,
Gusmão L, Amorim A, Arez AP Analysis of malaria associated genetic traits in Cabo Verde, a
melting pot of European and sub Saharan settlers. Blood cells, molecules & diseases 44: 628, 2010 [Article] IF=2,901
66. Quental S, Vilarinho L, Martins E, Teles EL, Rodrigues E, Diogo L, Garcia P, Eusébio F, Gaspar
A, Sequeira S, Amorim A, Prata MJ Incidence of maple syrup urine disease in Portugal.
Molecular genetics and metabolism 100: 385-7, 2010 [Article] IF=2,897
67. Lopes AM, Miguel RN, Sargent CA, Ellis PJ, Amorim A, Affara NA The human RPS4 paralogue
on Yq11.223 encodes a structurally conserved ribosomal protein and is preferentially
expressed during spermatogenesis. BMC molecular biology 11: 33, 2010 [Article] IF=2,81
68. Toscanini U, Salas A, García-Magariños M, Gusmão L, Raimondi E Population stratification in
Argentina strongly influences likelihood ratio estimates in paternity testing as revealed by a
simulation-based approach. International journal of legal medicine 124: 63-9, 2010 [Article]
IF=2,793
69. Martins JA, Costa JC, Paneto GG, Figueiredo RF, Gusmão L, Sánchez-Diz P, Carracedo A,
Cicarelli RM Genetic profile characterization of 10 X-STRs in four populations of the
southeastern region of Brazil. International journal of legal medicine 124: 427-32, 2010
[Article] IF=2,793
70. Pereira L, Alshamali F, Andreassen R, Ballard R, Chantratita W, Cho NS, Coudray C, Dugoujon
JM, Espinoza M, González-Andrade F, Hadi S, Immel UD, Marian C, Gonzalez-Martin A,
Mertens G, Parson W, Perone C, Prieto L, Takeshita H, Rangel Villalobos H, Zeng Z,
Zhivotovsky L, Camacho R, Fonseca NA PopAffiliator: online calculator for individual
affiliation to a major population group based on 17 autosomal short tandem repeat
genotype profile. International journal of legal medicine , 2010 [Epub ahead of print]
IF=2,793
71. Lopes N, Sousa B, Martins D, Gomes M, Vieira D, Veronese LA, Milanezi F, Paredes J, Costa
JL, Schmitt F Alterations in Vitamin D signalling and metabolic pathways in breast cancer
progression: a study of VDR, CYP27B1 and CYP24A1 expression in benign and malignant
breast lesions Vitamin D pathways unbalanced in breast lesions. BMC cancer 10: 483, 2010
[Article] IF=2,736
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82
72. Oropouche virus experimental infection in the golden hamster (Mesocrisetus auratus). Virus
research , 2010 [Epub ahead of print] IF=2,563
73. Vilarinho L, Tafulo S, Sibilio M, Kok F, Fontana F, Diogo L, Venâncio M, Ferreira M, Nogueira
C, Valongo C, Parenti G, Amorim A, Azevedo L Identification of novel L2HGDH gene
mutations and update of the pathological spectrum. Journal of human genetics 55: 55-8,
2010 [Article] IF=2,547
74. Vergara CI, Acevedo N, Jiménez S, Martínez B, Mercado D, Gusmão L, Barnes KC, Caraballo L
A Six-SNP haplotype of ADAM33 is associated with asthma in a population of Cartagena,
Colombia. International archives of allergy and immunology 152: 32-40, 2010 [Article]
IF=2,542
75. Acevedo N, Vergara C, Gusmão L, Jiménez S, Martínez B, Mercado D, Caraballo L The C-509T
promoter polymorphism of the transforming growth factor beta-1 gene is associated with
levels of total and specific IgE in a Colombian population. International archives of allergy
and immunology 151: 237-46, 2010 [Article] IF=2,542
76. van Asch B, Alves C, Santos L, Pinheiro R, Pereira F, Gusmão L, Amorim A Genetic profiles
and sex identification of found-dead wolves determined by the use of an 11-loci PCR
multiplex. Forensic science international. Genetics 4: 68-72, 2010 [Article] IF=2,421
77. Pinto N, Gusmão L, Amorim A Likelihood ratios in kinship analysis: contrasting kinship
classes, not genealogies. Forensic science international. Genetics 4: 218-9, 2010 [Letter]
IF=2,421
78. Amorim A A comment on "The hare and the tortoise: One small step for four SNPs, one
giant leap for SNP-kind" Forensic science international. Genetics , 2010 [Epub ahead of
print] IF=2,421
79. Gomes V, Alves C, Amorim A, Carracedo A, Sánchez-Diz P, Gusmão L Nilotes from Karamoja,
Uganda: haplotype data defined by 17 Y-chromosome STRs. Forensic science international.
Genetics 4: e83-6, 2010 [Article] IF=2,421
80. Prieto L, Zimmermann B, Goios A, Rodriguez-Monge A, Paneto GG, Alves C, Alonso A,
Fridman C, Cardoso S, Lima G, Anjos MJ, Whittle MR, Montesino M, Cicarelli RM, Rocha AM,
Albarrán C, de Pancorbo MM, Pinheiro MF, Carvalho M, Sumita DR, Parson W The GHEPEMPOP collaboration on mtDNA population data-A new resource for forensic casework.
Forensic science international. Genetics , 2010 [Epub ahead of print] IF=2,421
81. Carvalho M, Brito P, Bento AM, Gomes V, Antunes H, Costa HA, Lopes V, Serra A, Balsa F,
Andrade L, Anjos MJ, Corte-Real F, Gusmão L Paternal and maternal lineages in GuineaBissau population. Forensic science international. Genetics , 2010 [Epub ahead of print]
IF=2,421
82. Ferreira da Silva IH, Barbosa AG, Azevedo DA, Sánchez-Diz P, Gusmão L, Tavares CC,
Carvalho EF, Ferreira da Silva LA An X-chromosome pentaplex in two linkage groups:
haplotype data in Alagoas and Rio de Janeiro populations from Brazil. Forensic science
international. Genetics 4: e95-100, 2010 [Article] IF=2,421
83. de Assis Poiares L, de Sá Osorio P, Spanhol FA, Coltre SC, Rodenbusch R, Gusmão L, Largura
A, Sandrini F, da Silva CM Allele frequencies of 15 STRs in a representative sample of the
Brazilian population. Forensic science international. Genetics 4: e61-3, 2010 [Article] IF=2,421
84. Pereira V, Tomas C, Amorim A, Morling N, Gusmão L, Prata MJ Study of 25 X-chromosome
SNPs in the Portuguese. Forensic science international. Genetics , 2010 [Epub ahead of
print] IF=2,421
85. Andreassen R, Pereira L, Dupuy BM, Mevaag B Icelandic population data for the STR loci in
the AMPFlSTR SGM Plus system and the PowerPlex Y-system. Forensic science international.
Genetics 4: e101-3, 2010 [Article] IF=2,421
86. Sousa B, Paredes J, Milanezi F, Lopes N, Martins D, Dufloth R, Vieira D, Albergaria A,
Veronese L, Carneiro V, Carvalho S, Costa JL, Zeferino L, Schmitt F P-cadherin, vimentin and
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83
CK14 for identification of basal-like phenotype in breast carcinomas: an
immunohistochemical study. Histology and histopathology 25: 963-74, 2010 [Article]
IF=2,404
87. Palmeira A, Paiva A, Sousa E, Seca H, Almeida GM, Lima RT, Fernandes MX, Pinto M,
Vasconcelos MH Insights into the in vitro antitumor mechanism of action of a new
pyranoxanthone. Chemical biology & drug design 76: 43-58, 2010 [Article] IF=2,375
88. Nogueiro I, Manco L, Gomes V, Amorim A, Gusmão L Phylogeographic analysis of paternal
lineages in NE Portuguese Jewish communities. American journal of physical anthropology
141: 373-81, 2010 [Article] IF=2,353
89. Gusmão A, Valente C, Gomes V, Alves C, Amorim A, Prata MJ, Gusmão L A genetic historical
sketch of European Gypsies: The perspective from autosomal markers. American journal of
physical anthropology 141: 507-14, 2010 [Article] IF=2,353
90. Reis CA, Osorio H, Silva L, Gomes C, David L Alterations in glycosylation as biomarkers for
cancer detection. Journal of clinical pathology 63: 322-9, 2010 [Review] IF=2,333
91. da Costa A, Oliveira JT, Gärtner F, Kohn B, Gruber AD, Klopfleisch R Potential markers for
detection of circulating canine mammary tumor cells in the peripheral blood. Veterinary
journal (London, England : 1997) , 2010 [Epub ahead of print] IF=2,323
92. Immunohistochemical analysis of urokinase plasminogen activator and its prognostic value
in canine mammary tumours. Veterinary journal (London, England : 1997) , 2010 [Epub
93. Quental R, Moleirinho A, Azevedo L, Amorim A Evolutionary history and functional
diversification of phosphomannomutase genes. Journal of molecular evolution 71: 119-27,
2010 [Article] IF=2,323
94. Gama A, Alves A, Schmitt F Expression and prognostic significance of CK19 in canine
malignant mammary tumours. Veterinary journal (London, England : 1997) 184: 45-51, 2010
[Article] IF=2,323
95. Bonin S, Hlubek F, Benhattar J, Denkert C, Dietel M, Fernandez PL, Höfler G, Kothmaier H,
Kruslin B, Mazzanti CM, Perren A, Popper H, Scarpa A, Soares P, Stanta G, Groenen PJ.
Multicentre validation study of nucleic acids extraction from FFPE tissues. Virchows
Arch.457:309-17, 2010 [Article] IF=2,305
96. Carvalho S, Milanezi F, Costa JL, Amendoeira I, Schmitt F PIKing the right isoform: the
emergent role of the p110beta subunit in breast cancer. Virchows Archiv : an international
journal of pathology 456: 235-43, 2010 [Article] IF=2,305
97. Sobrinho-Simoes M: How to separate follicular adenoma from follicular carcinoma and
follicular variant PTC? Virchows Archiv 457:128, 2010 IF=2,305
98. Araujo R, Amorim A, Gusmão L Genetic diversity of Aspergillus fumigatus in indoor hospital
environments. Medical mycology : official publication of the International Society for Human
and Animal Mycology 48: 832-8, 2010 [Article] IF=2,133
99. Pereira V, Gomes V, Amorim A, Gusmão L, João Prata M Genetic characterization of
uniparental lineages in populations from Southwest Iberia with past malaria endemicity.
American journal of human biology : the official journal of the Human Biology Council 22:
588-95, 2010 [Article] IF=2,121
100. Silva F, Pereira R, Gusmão L, Santos C, Amorim A, Prata MJ, Bettencourt C, Lourenço P, Lima
M Genetic profiling of the Azores Islands (Portugal): data from 10 X-chromosome STRs.
American journal of human biology : the official journal of the Human Biology Council 22: 2213, 2010 [Article] IF=2,121
101. Vasconcelos M. Helena, Vaz Josiana A., Barros L, Martins A, Sá Morais J, Ferreira I C.F.R.
Phenolic profile of seventeen Portuguese wild mushrooms LWT - Food Science and
Technology I: 0, 2010 [Article] IF=2,114
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84
102. Vaz JA, Heleno SA, Martins A, Almeida GM, Vasconcelos MH, Ferreira IC Wild mushrooms
Clitocybe alexandri and Lepista inversa: in vitro antioxidant activity and growth inhibition of
human tumour cell lines. Food and chemical toxicology : an international journal published
for the British Industrial Biological Research Association 48: 2881-4, 2010 [Article] IF=2,114
103. Barros R, Peleteiro B, Almeida R, Figueiredo C, Barros H, David L, Lunet N Relevance of high
virulence Helicobacter pylori strains and futility of CDX2 expression for predicting intestinal
metaplasia after eradication of infection. Scandinavian journal of gastroenterology 45: 82834, 2010 [Article] IF=2,084
104. Pópulo H, Soares P, Rocha AS, Silva P, Lopes JM Evaluation of the mTOR pathway in ocular
(uvea and conjunctiva) melanoma. Melanoma research 20: 107-17, 2010 [Article] IF=2,061
105. Ferreira JA, Azevedo NF, Vieira MJ, Figueiredo C, Goodfellow BJ, Monteiro MA, Coimbra MA
Identification of cell-surface mannans in a virulent Helicobacter pylori strain. Carbohydrate
research 345: 830-8, 2010 [Article] IF=2,025
106. Pintalhao M, Dias-Neto M, Peleteiro B, Lopes C, Figueiredo C, David L, Lunet N Salt intake
and type of intestinal metaplasia in helicobacter pylori-infected portuguese men. Nutrition
and cancer 62: 1153-60, 2010 [Article] IF=1,974
107. Pinheiro C, Reis RM, Ricardo S, Longatto-Filho A, Schmitt F, Baltazar F Expression of
monocarboxylate transporters 1, 2, and 4 in human tumours and their association with
CD147 and CD44. Journal of biomedicine & biotechnology 2010: 427694, 2010 [Article]
IF=1,75
108. Silva LM, Carvalho AS, Guillon P, Seixas S, Azevedo M, Almeida R, Ruvoën-Clouet N, Reis CA,
Le Pendu J, Rocha J, David L Infection-associated FUT2 (Fucosyltransferase 2) genetic
variation and impact on functionality assessed by in vivo studies. Glycoconjugate journal 27:
61-8, 2010 [Article] IF=1,743
109. Santos AA, Oliveira JT, Lopes CC, Amorim IF, Vicente CM, Gärtner FR, Matos AJ
Immunohistochemical expression of vascular endothelial growth factor in canine mammary
tumours. Journal of comparative pathology 143: 268-75, 2010 [] IF=1,725
110. Overexpression of Vimentin in Canine Prostatic Carcinoma. Journal of comparative
pathology , 2010 [Epub ahead of print] IF=1,725
111. Pereira PD, Lopes CC, Matos AJ, Cortez PP, Gärtner F, Medeiros R, Lopes C Caveolin-1 in
diagnosis and prognosis of canine mammary tumours: comparison of evaluation systems.
Journal of comparative pathology 143: 87-93, 2010 [Article] IF=1,725
112. Costa BM, Caeiro C, Guimaraes I, Martinho O, Jaraquemada T, Augusto I, Castro L, Osorio L,
Linhares P, Honavar M, Resende M, Braga F, Silva A, Pardal F, Amorim J, Nabico R, Almeida
R, Alegria C, Pires M, Pinheiro C, Carvalho E, Lopes JM, Costa P, Damasceno M, Reis RM.
Prognostic value of MGMT promoter methylation in glioblastoma patients treated with
temozolomide-based chemoradiation: a Portuguese multicentre study. Oncol Rep 23: 16551662, 2010 [Article] IF=1,59
113. Gil da Costa RM, Rema A, Pires MA, Gärtner F Two canine Merkel cell tumours:
immunoexpression of c-KIT, E-cadherin, beta-catenin and S100 protein. Veterinary
dermatology 21: 198-201, 2010 [Article] IF=1,543
114. Portela A, Vasconcelos M, Branco R, Gartner F, Faria M, Cavalheiro J An in vitro and in vivo
investigation of the biological behavior of a ferrimagnetic cement for highly focalized
thermotherapy. Journal of materials science. Materials in medicine 21: 2413-23, 2010
[Proceedings Paper] IF=1,471
115. Gil da Costa RM, Oliveira JP, Saraiva AL, Seixas F, Faria F, Gärtner F, Pires MA, Lopes C
Immunohistochemical Characterization of 13 Canine Renal Cell Carcinomas. Veterinary
pathology , 2010 [Epub ahead of print] IF=1,367
116. Syrjänen K, Di Bonito L, Gonçalves L, Murjal L, Santamaria M, Mahovlic V, Karakitsos P, Onal
B, Schmitt FC Cervical cancer screening in Mediterranean countries: implications for the
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85
future. Cytopathology : official journal of the British Society for Clinical Cytology 21: 359-367,
2010 [Review] IF=1,349
117. Vilarinho S, Guimarães NM, Ferreira RM, Gomes B, Wen X, Vieira MJ, Carneiro F, Godinho T,
Figueiredo C Helicobacter pylori colonization of the adenotonsillar tissue: fact or fiction?
International journal of pediatric otorhinolaryngology 74: 807-11, 2010 [Article] IF=1,148
118. Baptista CS, Bastos E, Santos S, Gut IG, Guedes-Pinto H, Gärtner F, Chaves R TWIST1 Gene:
First Insights in Felis catus. Current genomics 11: 212-20, 2010 [Article] IF=1,077
119. Teixeira D, Vargens D, Príncipe A, Oliveira E, Amorim A, Prata MJ, Suarez-Kurtz G High
prevalence of the GSTM3*A/B polymorphism in sub-Sarahan African populations. Brazilian
journal of medical and biological research = Revista brasileira de pesquisas médicas e
biológicas / Sociedade Brasileira de Biofísica ... [et al.] 43: 677-80, 2010 [Article] IF=1,075
120. Magalhães A, Reis CA Helicobacter pylori adhesion to gastric epithelial cells is mediated by
glycan receptors. Brazilian journal of medical and biological research = Revista brasileira de
pesquisas médicas e biológicas / Sociedade Brasileira de Biofísica ... [et al.] 43: 611-8, 2010
[Review] IF=1,075
121. Bartosch C, Exposito MI, Lopes JM Low-grade endometrial stromal sarcoma and
undifferentiated endometrial sarcoma: a comparative analysis emphasizing the importance
of distinguishing between these two groups. International journal of surgical pathology 18:
286-91, 2010 [Article] IF=0,912
122. Sobrinho-Simões M, Eloy C, Vinagre J, Soares P Molecular pathology of thyroid tumors:
diagnostic and prognostic relevance. International journal of surgical pathology 18: 209S212S, 2010 [Proceedings Paper] IF=0,912
123. Prazeres H, Torres J, Soares P, Sobrinho-Simões M The familial counterparts of follicular cell-derived thyroid tumors. International journal of surgical pathology 18: 233-42, 2010
[Review] IF=0,912
124. Carneiro F Molecular pathology tools in gastrointestinal pathology. International journal of
surgical pathology 18: 53S-55S, 2010 [Proceedings Paper] IF=0,912
125. Carneiro F, Oliveira C, Seruca R Pathology and genetics of familial gastric cancer.
International journal of surgical pathology 18: 33S-36S, 2010 [Proceedings Paper] IF=0,912
126. Sobrinho-Simões M, Magalhães J, Soares P Hot topics in papillary thyroid carcinoma.
International journal of surgical pathology 18: 190S-193S, 2010 [Proceedings Paper] IF=0,912
127. Filho AL, Schmitt FC Cytology education in the 21st century: living in the past or crossing the
Rubicon? Acta cytologica 54: 654-6, 2010 [Letter] IF=0,69
128. Carvalho M, Brito P, Lopes V, Andrade L, Anjos MJ, Real FC, Gusmão L Analysis of paternal
lineages in Brazilian and African populations Genetics and Molecular biology 422-427, 2010 []
IF=0
129. Almeida AP, Dethoup T, Singburaudom N, Lima R, Pinto M, Kijjoa A, Vasconcelos M. Helena
The in vitro anticancer activity of the crude extract of the sponge-associated fungus
Eurotium cristatum and its secondary metabolites Journal of Natural Pharmaceuticals 1: 2529, 2010 [] IF=0
130. Araújo R Endemism Versus Dispersion: Contribution of Microbial Genetics forForensic
Evidences The Open Forensic Science Jounal 3: 14-21, 2010 [] IF=0
131. Guimarães S, Lopes JM, Oliveira JB, Santos A Idiopathic infantile arterial calcification: a rare
cause of sudden unexpected death in childhood. Pathology research international 2010:
185314, 2010 [] IF=0
132. Soares P, Achilli A, Semino O, Davies W, Macaulay V, Bandelt HJ, Torroni A, Richards MB The
archaeogenetics of Europe. Current biology : CB 20: R174-83, 2010 [] IF=0
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133. Gubb E, Matthiesen R Introduction to omics. Methods in molecular biology (Clifton, N.J.)
593: 1-23, 2010 [] IF=0
134. Aransay AM, Matthiesen R, Regueiro MM SNP-PHAGE: high-throughput SNP discovery
pipeline. Methods in molecular biology (Clifton, N.J.) 593: 49-65, 2010 [] IF=0
135. Frades I, Matthiesen R Overview on techniques in cluster analysis. Methods in molecular
biology (Clifton, N.J.) 593: 81-107, 2010 [] IF=0
136. Matthiesen R, Carvalho AS Methods and algorithms for relative quantitative proteomics by
mass spectrometry. Methods in molecular biology (Clifton, N.J.) 593: 187-204, 2010 [] IF=0
137. Lasso G, Matthiesen R Computational methods for analysis of two-dimensional gels.
Methods in molecular biology (Clifton, N.J.) 593: 231-62, 2010 [] IF=0
138. Hackenberg M, Matthiesen R Algorithms and methods for correlating experimental results
with annotation databases. Methods in molecular biology (Clifton, N.J.) 593: 315-40, 2010 []
IF=0
139. Monterrosa JC, Morales JA, Yurrebaso I, Gusmão L, García O Population data for 12 Ychromosome STR loci in a sample from El Salvador. Legal medicine (Tokyo, Japan) 12: 46-51,
2010 [Article] IF=0
140. Vasconcelos MH, Palmeira A Pharmacophore-Based Screening as a Clue for the Discovery of
new P-Glycoprotein Inhibitors Advances in Bioinformatics 175-180, 2010 [] IF=0
141. Silva RM, Pereira F, Carneiro J, Amorim A Microevolution in a Natural Population of Daphnia
longispina Exposed to Acid Mine Drainage Interdisciplinary Studies on Environmental
Chemestry 213-218, 2010 [] IF=0
142. Pereira F Origin and spread of goat pastoralism Encyclopedia of Life Sciences 1, 2010 [] IF=0
143. Carneiro F, Milne AN, Offerhaus GJA Histopathology of familial and early onset gastric
cancer Diagnostic Histopathology 1, 2010 [] IF=0
144. Carneiro F, Rodrigues S, Pereira P, Magro F, Lopes S, Albuquerque A, Lopes J, Macedo G
Dysplasia surveillance in na ulcerative colitis patient: successful detection with narrow band
imaging and magnification Journal of Crohn's Colitis 54-56, 2010 [] IF=0
145. Bernardes N, Seruca R, Chakrabarty AM, Fialho AM Microbial-based therapy of cancer:
Current progress and future prospects. Bioengineered bugs 1: 178-190, 2010 [] IF=0
146. Bartosch C, Vieira J, Teixeira MR, Lopes JM Endometrial endometrioid adenocarcinoma
associated with primitive neuroectodermal tumour of the uterus: a poor prognostic subtype
of uterine tumours. Medical oncology (Northwood, London, England) , 2010 [Epub ahead of
print] IF=0
147. Longatto Filho A, Lopes JM, Schmitt FC Angiogenesis and breast cancer. Journal of oncology
2010: 576384, 2010 [] IF=0
148. Matthiesen R, Amorim A Proteomics facing the combinatorial problem. Methods in
molecular biology (Clifton, N.J.) 593: 175-86, 2010 [] IF=0
149. Destro-Bisol G, Jobling MA, Rocha J, Novembre J, Richards MB, Mulligan C, Batini C, Manni F
Molecular Anthropology in the genomic era. Journal of anthropological sciences = Rivista di
antropologia : JASS / Istituto italiano di antropologia 88: 93-112, 2010 [] IF=0
150. Rocha J Bantu-Khoisan interactions at the edge of the Bantu expansions: insights from
southern Angola. Journal of anthropological sciences = Rivista di antropologia : JASS /
Istituto italiano di antropologia 88: 5-8, 2010 [] IF=0
151. Carvalho S, Schmitt F Potential role of PI3K inhibitors in the treatment of breast cancer.
Future oncology (London, England) 6: 1251-63, 2010 [Review] IF=0
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152. Pópulo H, Vinagre J, Lopes JM, Soares P Analysis of GNAQ mutations, proliferation and
MAPK pathway activation in uveal melanomas. The British journal of ophthalmology , 2010
[Epub ahead of print] IF=0
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Members of IPATIMUP at Editorial Boards
•
Acta Cytologica (SCI PRINTERS & PUBL INC)
•
Advances in Anatomic Pathology (LIPPINCOTT WILLIAMS & WILKINS)
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Advances in Clinical and Experimental Medicine (AKADEMIA MEDYCZNA WE WROCŁAWIU)
•
Archives of Pathology and Laboratory Medicine (COLLEGE OF AMERICAN PATHOLOGISTS)
•
BMC Cancer (BIOMED CENTRAL LTD)
•
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)
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Forensic Science International: Genetics (ELSEVIER SCI IRELAND LTD)
•
Gut Pathogens (BIOMED CENTRAL)
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Helicobacter (BLACKWELL PUBLISHING LTD)
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Hereditary Cancer in Clinical Practice (UICC GLOBAL CANCER CONTROL)
•
Histopathology (BLACKWELL PUBLISHING LTD)
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Human Biology (WAYNE STATE UNIVERSITY PRESS)
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International Journal of Surgical Pathology (WESTMINSTER PUBL INC)
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Journal of Cellular and Molecular Medicine (CAROL DAVILA UNIV PRESS)
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Journal of Pathology (JON WILEY & SONS LTD)
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The Open Pathology Journal (BENTHAM OPEN)
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The Open Forensic Sciene Journal (BENTHAM OPEN)
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Pathology Research & Practice (URBAN & FISCHER VERLAG)
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Seminars in Diagnostic Pathology (W B SAUNDERS CO)
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Ultrastructural Pathology (TAYLOR & FRANCIS INC)
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Virchows Archiv (SPRINGER)
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