Ipatimup

RESEARCHDIAGNOSTICSTRANSLATIONOUTREACH

José Carlos Machado

Name: José Carlos Machado

E-mail: josem@ipatimup.pt

Extension:

225570700

José Carlos Machado

Member of

Director of Ipatimup Diagnostics

Molecular Genetics Specialist of Ipatimup Diagnostics

Temporary of Intercellular Communication and Cancer

Short CV

José C. Machado (JCM) is Full Professor in the Faculty of Medicine of Porto, vice-president of the Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), and Coordinator of the Cancer Program at i3S. He studied Biology at the University of Porto and developed his PhD in the Universities of Tubingen, Germany and Porto, Portugal. The scientific goal that drives JCM's research group is to understand the biological significance of communication among cells of the tumor microenvironment, and determine how it influences cancer onset, progression, and clinical response. JCM has been awarded research projects by the Portuguese Foundation for Science and Technology (FCT), by the Portuguese Agency for Innovation (ADI), by the Portuguese Ministry of Health, by Worldwide Cancer Research and by the European Union. JCM is also the head of R&D at the molecular genetics laboratory of the IPATIMUP Diagnostics Unit. This is one of the reference laboratories in Portugal for the detection of cancer biomarkers, genetic diagnosis of hereditary cancer syndromes and pathology. As of November 2021, JCM co-authors 181 publications, with 12383 total citations, and with an h-index of 46 (Scopus Author ID 7102792651).

Supervisor of

Ana Vilarinho, Fellow
Research Fellowship (MSc)

Bárbara Adem, PhD Fellowship
PHD Grant

Bauke Ylstra, Temporary
Visiting Researcher

Carlos Resende, Research Technician
Research Technician

Carolina Peixoto, Research Trainee
Temporary

Cátia Pereira, Research Technician

Cecília Durães, Temporary
Visiting Researcher

Gonçalo Vale, Research Technician
Team Member

Helena Ferreira, PhD Fellowship
PHD Grant

João Feijão, Research Trainee
Temporary

Pedro Leite, Research Technician
Team Member

José Costa, Temporary
Visiting Researcher

José Guimarães, Fellow
Research Fellowship (MSc)

Lorena Pereira, Master Student (thesis)
MSc student

Luana Pereira, MSc student
Temporary

Márcia Baixia, Research Technician

Maria Quental, Research Technician

Marta Ferreira, Team Member
Young Research Technician

Nuno Bastos, PhD Fellowship
PHD Grant

Patrícia Domingues, Research Technician
Team Member

Raquel Silva, Young Research Technician

Regina Pinto, Lab Technician

Rui Silva, Quality manager

Rui Simões, Assistant Researcher

Sónia Melo, Principal Researcher
Researcher

Tânia Pereira, Administrative Assistant

Yoran Prycker, Research Trainee
Temporary

PI (running)

Influence of an optimized combined dietary and exercise intervention on cytokine profile and NK cell infiltration of the tumor: an exploratory pilot study

PI (closed)

Influence of an optimized combined dietary and exercise intervention on cytokine profile and NK cell infiltration of the tumor: an exploratory pilot study

GenomePT .: National Laboratory for Genome Sequencing and Analysis

TRICAN .: O papel dos Tregs na resposta imune ao cancro

Tiras de teste para rastreio de iomarcadores de tromboembolismo venoso em oncologia.

Detection of tumor biomarkers using circulating tumor cell-free nucleid acids/exosomes as a source for biomarkers of intra-tumor heterogenetity.

Horizontal transmission of mutation-driven therapy resistance.

The role of T lymphocyke differentiation in IBD - Associated colorectal carcinoma

The yin and yang of somatic mutations in cancer immunosurveillance

Detecção de mutações somáticas no plasma de doentes com cancro do pulmão”

Chemotherapy effect on Kinetics of regulatory T cells in Acute Myeloid Leukemia and high risk Myelodysplastic Syndromes

Consolidação de redes de equipamento de uso comum: contributo do Ipatimup para I3S

MuSA-Deteção de mutações e alterações epigenéticas em ADN tumoral circulante em sangue

Biomarcadores para avaliação de efectividade terapêutica no carcinoma colorectal

Helicobacter pylori diversity in pathogenesis, antibiotic resistance, and evasion from natural and vaccine-induced immune responses (HELDIVPAT)

Identification of genetic markers for prediction of the clinical course and development of complications in Portuguese Crohn's Disease patients.

Desenvolvimento de um novo método de detecção de mutações com relevância preditiva na resposta de doentes com carcinoma colo rectal ao tratamento com cetuximab

Characterization of a population with increased risk of Gastric Cancer: First Degree Relatives of Early Onset Gastric Carcinoma Patients

Acção dos ácidos gordos polinsaturados n-3 na modulação do processo da inflamação e tumorigénese

Identification of a susceptibility locus for gastric cancer in the IL1 gene cluster region

Identification of Genetic markers for prediction of the clinical course and development of complications in portuguese Crohn's Disease patients

Evaluation and Control of Neglected Mucosal Enteric Infections in Childhood

Acções Integradas Luso-Espanholas

Acções Integradas Luso-Francesas

The role of chronic infections in the development of cancer

Parasite and host genetic diversity in Helicobacter infections

Teste de susceptibilidade genética para determinação de risco de desenvolvimento de Doença de Crohn na população portuguesa”, ADI, Programa Ideia – Promotor GENETEST

First Author

1. Machado JC, Reis J, Fernandes M, Silva R, Cirnes L, Carneiro F, Costa JL

Tumor-specific neoantigens drive T-cell clonotype convergence European journal of cancer (Oxford, England : 1990) 92: S11-S11, 2018. [Meeting Abstract]

7.2 (*)

2. Machado JC, Reis J, Fernandes M, Silva R, Cirnes L, Chaudhary R, Carneiro F, Costa JL

Determining tumor mutation load using an NGS-based, target gene panel European journal of cancer (Oxford, England : 1990) 92: S4-S5, 2018. [Meeting Abstract]

7.2 (*)

3. Machado JC, Figueiredo C, Canedo P, Pharoah P, Carvalho R, Nabais S, Castro Alves C, Campos ML, Van Doorn LJ, Caldas C, Seruca R, Carneiro F, Sobrinho-Simões M

A proinflammatory genetic profile increases the risk for chronic atrophic gastritis and gastric carcinoma. Gastroenterology 125: 364-71, 2003. [Article]

PMID: 12891537.

393

12.7

4. Figueiredo C, Machado JC

Re: Helicobacter pylori and interleukin 1 genotyping: An opportunity to identify high-risk individuals for gastric carcinoma Journal of the National Cancer Institute 95: 760-761, 2003. [Letter]

13.8

5. Machado JC, Pharoah P, Sousa S, Carvalho R, Oliveira C, Figueiredo C, Amorim A, Seruca R, Caldas C, Carneiro F, Sobrinho-Simões M

Interleukin 1B and interleukin 1RN polymorphisms are associated with increased risk of gastric carcinoma. Gastroenterology 121: 823-9, 2001. [Article]

PMID: 11606496.

344

13.0

6. Machado JC, Oliveira C, Carvalho R, Soares P, Berx G, Caldas C, Seruca R, Carneiro F, Sobrinho-Simöes M

E-cadherin gene (CDH1) promoter methylation as the second hit in sporadic diffuse gastric carcinoma. Oncogene 20: 1525-8, 2001. [Article]

doi: 10.1038/sj.onc.1204234 PMID: 11313896.

215

6.7

7. Machado JC, Nogueira AM, Carneiro F, Reis CA, Sobrinho-Simões M

Gastric carcinoma exhibits distinct types of cell differentiation: an immunohistochemical study of trefoil peptides (TFF1 and TFF2) and mucins (MUC1, MUC2, MUC5AC, and MUC6). The Journal of pathology 190: 437-43, 2000. [Article]

doi: 10.1002/(SICI)1096-9896(200003)190:4<437::AID-PATH547>3.0.CO;2-1 PMID: 10699992.

126

4.1

8. Machado J, Carneiro F, Sobrinho-Simões M

E-cadherin mutations in gastric carcinoma. The Journal of pathology 191: 466-8, 2000. [Letter]

doi: 10.1002/1096-9896(200008)191:4<466::AID-PATH626>3.0.CO;2-Q PMID: 10918224.

4.1

9. Machado JC, Reis CA, Carneiro F, Sobrinho-Simões M

Primary signet-ring cell carcinomas of the lung. Human pathology 31: 272, 2000. [Letter]

PMID: 10685649.

2.9

10. Machado JC, Soares P, Carneiro F, Rocha A, Beck S, Blin N, Berx G, Sobrinho-Simões M

E-cadherin gene mutations provide a genetic basis for the phenotypic divergence of mixed gastric carcinomas. Laboratory investigation; a journal of technical methods and pathology 79: 459-65, 1999. [Article]

PMID: 10211998.

134

11. Machado JC, Carneiro F, Ribeiro P, Blin N, Sobrinho-Simões M

pS2 protein expression in gastric carcinoma. An immunohistochemical and immunoradiometric study. European journal of cancer (Oxford, England : 1990) 32A: 1585-90, 1996. [Article]

PMID: 8911122.

12. Machado JC, Carneiro F, Blin N, Sobrinho-Simões M

Pattern of pS2 protein expression in premalignant and malignant lesions of gastric mucosa. European journal of cancer prevention : the official journal of the European Cancer Prevention Organisation (ECP) 5: 169-79, 1996. [Article]

PMID: 8818606.

13. Machado JC, Carneiro F, Gärtner F, Ribeiro P, Sobrinho-Simões M

Female sex hormone receptors are not involved in gastric carcinogenesis. A biochemical and immunohistochemical study. European journal of cancer prevention : the official journal of the European Cancer Prevention Organisation (ECP) 3 Suppl 2: 31-7, 1994. [Proceedings Paper]

PMID: 7735043.

Senior Author

1. R Teixeira M, Oliveira J, Borralho P, O Fernandes MG, Almodovar T, Fernandes I, Macedo D, Ferreira A, Barroso A, Teixeira E, Machado JC

Portuguese Consensus Recommendations for Next-Generation Sequencing of Lung Cancer, Rare Tumors, and Cancers of Unknown Primary Origin in Clinical Practice. Acta medica portuguesa 35: 677-690, 2022. [Article]

doi: 10.20344/amp.17680 PMID: 35816050.

1.7 (*)

2. Freitas JA, Gullo I, Garcia D, Miranda S, Spaans L, Pinho L, Reis J, Sousa F, Baptista M, Resende C, Leitão D, Durães C, Costa JL, Carneiro F, Machado JC

The Adaptive Immune Landscape of the Colorectal Adenoma-Carcinoma Sequence. International journal of molecular sciences 22: ., 2021. [Article]

doi: 10.3390/ijms22189791 PMID: 34575971.

5.9 (*)

3. Garcia D, Spaans L, Miranda S, Gonçalves G, Reis J, Costa JL, Durães C, Carneiro F, Machado JC

The Influence of the Genetic and Immunologic Context in the Development of Colorectal Adenoma: A Case Series Report. Acta medica portuguesa 33: 297-304, 2020. [Article]

doi: 10.20344/amp.12462 PMID: 32416752.

0.6 (*)

4. Baixia M, Sousa S, Pina MJ, Silva RM, Cirnes L, Canedo P, Castedo S, Machado JC

The bigger the better? Evaluation of the value of large multi-gene panels in Portuguese cardiomyopathy genetic testing Medicine 99: -, 2020. [Meeting Abstract]

1.6 (*)

5. Resende C, Gomes CP, Machado JC

Review: Gastric cancer: Basic aspects. Helicobacter 25 Suppl 1: e12739, 2020. [Article; Proceedings Paper]

doi: 10.1111/hel.12739 PMID: 32918356.

4.0 (*)

6. Camargo MC, Figueiredo C, Machado JC

Review: Gastric malignancies: Basic aspects. Helicobacter 24 Suppl 1: e12642, 2019. [Review]

doi: 10.1111/hel.12642 PMID: 31486241.

4.0

7. Garcia D, Gullo I, Spaans L, Miranda S, Reis J, Costa JL, Carneiro F, Machado JC

The influence of the genetic and immunologic context in the development of colorectal adenoma Virchows Archiv 475: S200-S200, 2019. [Meeting Abstract]

2.9

8. Malfertheiner P, Megraud F, O'Morain CA, Gisbert JP, Kuipers EJ, Axon AT, Bazzoli F, Gasbarrini A, Atherton J, Graham DY, Hunt R, Moayyedi P, Rokkas T, Rugge M, Selgrad M, Suerbaum S, Sugano K, El-Omar EM, European Helicobacter and Microbiota Study Group and Consensus panel EM

Management of Helicobacter pylori infection-the Maastricht V/Florence Consensus Report. Gut 66: 6-30, 2017. [Article]

doi: 10.1136/gutjnl-2016-312288 PMID: 27707777.

1522

17.0

9. Figueiredo C, Camargo MC, Leite M, Fuentes-Pananá EM, Rabkin CS, Machado JC

Pathogenesis of Gastric Cancer: Genetics and Molecular Classification. Current topics in microbiology and immunology 400: 277-304, 2017. [Review; Book Chapter]

doi: 10.1007/978-3-319-50520-6_12 PMID: 28124158.

5.8

10. Azevedo J, Pista A, Lisboa C, Santo I, Azevedo L, Cunha MJ, HERCOLES Study Group MJ

Epidemiology of human papillomavirus on anogenital warts in Portugal - The HERCOLES study. Journal of the European Academy of Dermatology and Venereology : JEADV 31: 1342-1348, 2017. [Article]

doi: 10.1111/jdv.14311 PMID: 28485812.

4.3

11. Figueiredo C, Camargo MC, Leite M, Fuentes-Pananá EM, Rabkin CS, Machado JC

Erratum to: Pathogenesis of Gastric Cancer: Genetics and Molecular Classification. Current topics in microbiology and immunology 400: E1, 2017. [Correction; Book Chapter]

doi: 10.1007/978-3-319-50520-6_15 PMID: 28608027.

5.8

12. Resende C, Regalo G, Durães C, Pinto MT, Wen X, Figueiredo C, Carneiro F, Machado JC

Interleukin-1B signalling leads to increased survival of gastric carcinoma cells through a CREB-C/EBPß-associated mechanism. Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association 19: 74-84, 2016. []

doi: 10.1007/s10120-014-0448-x PMID: 25740226.

5.5

13. Figueiredo C, Costa S, Karameris A, Machado JC

Pathogenesis of Gastric Cancer. Helicobacter 20 Suppl 1: 30-5, 2015. [Article]

doi: 10.1111/hel.12254 PMID: 26372822.

3.9

14. Correia M, Casal S, Vinagre J, Seruca R, Figueiredo C, Touati E, Machado JC

Helicobacter pylori's cholesterol uptake impacts resistance to docosahexaenoic acid. International journal of medical microbiology : IJMM 304: 314-20, 2014. [Article]

doi: 10.1016/j.ijmm.2013.11.018 PMID: 24447914.

3.6

15. Figueiredo C, Garcia-Gonzalez MA, Machado JC

Molecular pathogenesis of gastric cancer. Helicobacter 18 Suppl 1: 28-33, 2013. [Review]

doi: 10.1111/hel.12083 PMID: 24011242.

3.0

16. Costa JL, Sousa S, Justino A, Kay T, Fernandes S, Cirnes L, Schmitt F, Machado JC

Nonoptical massive parallel DNA sequencing of BRCA1 and BRCA2 genes in a diagnostic setting. Human mutation 34: 629-35, 2013. [Article]

doi: 10.1002/humu.22272 PMID: 23315985.

5.1

17. Malfertheiner P, Megraud F, O'Morain CA, Atherton J, Axon AT, Bazzoli F, Gensini GF, Gisbert JP, Graham DY, Rokkas T, El-Omar EM, Kuipers EJ, European Helicobacter Study Group European Helicobacter Study Group

Management of Helicobacter pylori infection--the Maastricht IV/ Florence Consensus Report. Gut 61: 646-64, 2012. [Review]

doi: 10.1136/gutjnl-2012-302084 PMID: 22491499.

1580

10.7

18. Ferreira AC, Suriano G, Mendes N, Gomes B, Wen X, Carneiro F, Seruca R, Machado JC

E-cadherin impairment increases cell survival through Notch-dependent upregulation of Bcl-2. Human molecular genetics 21: 334-43, 2012. [Article]

doi: 10.1093/hmg/ddr469 PMID: 21989054.

7.7

19. Botelho MC, Oliveira PA, Lopes C, Correia da Costa JM, Machado JC

Urothelial dysplasia and inflammation induced by Schistosoma haematobium total antigen instillation in mice normal urothelium. Urologic oncology 29: 809-14, 2011. [Article]

doi: 10.1016/j.urolonc.2009.09.017 PMID: 19945304.

3.2

20. Resende C, Ristimäki A, Machado JC

Genetic and epigenetic alteration in gastric carcinogenesis. Helicobacter 15 Suppl 1: 34-9, 2010. [Review]

doi: 10.1111/j.1523-5378.2010.00782.x PMID: 21054651.

3.1

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 carcinogenesis. Laboratory investigation; a journal of technical methods and pathology 90: 1132-9, 2010. [Article]

doi: 10.1038/labinvest.2010.79 PMID: 20386538.

4.4

22. Botelho M, Oliveira P, Gomes J, Gartner F, Lopes C, da Costa JM, Machado JC

Tumourigenic effect of Schistosoma haematobium total antigen in mammalian cells. International journal of experimental pathology 90: 448-53, 2009. [Article]

doi: 10.1111/j.1365-2613.2009.00650.x PMID: 19659903.

1.9

23. Ferreira AC, Suriano G, Seruca R, Machado JC

Notch Inhibition Overturns the Apoptosis Resistance Conferred by E-cadherin Deficiency Helicobacter 14: 379-380, 2009. [Meeting Abstract]

2.9

24. Correia MM, Michel V, Oliveira MJ, Ferreira R, Figueiredo C, Seruca R, Touati E, Machado JC

Omega 3 Docosahexaenoic Acid Inhibits H-pylori Gastric Colonization in C57BL/6 Mice Helicobacter 14: 332-333, 2009. [Meeting Abstract]

2.9

25. Canedo P, Corso G, Pereira F, Lunet N, Suriano G, Figueiredo C, Pedrazzani C, Moreira H, Barros H, Carneiro F, Seruca R, Roviello F, Machado JC

The interferon gamma receptor 1 (IFNGR1) -56C/T gene polymorphism is associated with increased risk of early gastric carcinoma. Gut 57: 1504-8, 2008. [Article]

doi: 10.1136/gut.2007.143578 PMID: 18593809.

9.8

26. Canedo P, Castanheira-Vale AJ, Lunet N, Pereira F, Figueiredo C, Gioia-Patricola L, Canzian F, Moreira H, Suriano G, Barros H, Carneiro F, Seruca R, Machado JC

The interleukin-8-251*T/*A polymorphism is not associated with risk for gastric carcinoma development in a Portuguese population. European journal of cancer prevention : the official journal of the European Cancer Prevention Organisation (ECP) 17: 28-32, 2008. [Article]

doi: 10.1097/CEJ.0b013e32809b4d0f PMID: 18090907.

1.9

27. Canedo P, Durães C, Pereira F, Regalo G, Lunet N, Barros H, Carneiro F, Seruca R, Rocha J, Machado JC

Tumor necrosis factor alpha extended haplotypes and risk of gastric carcinoma. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 17: 2416-20, 2008. [Article]

doi: 10.1158/1055-9965.EPI-08-0413 PMID: 18768512.

4.8

28. Resende C, Regalo G, Durães C, Carneiro F, Machado JC

Genetic changes of CEBPA in cancer: mutations or polymorphisms? Journal of clinical oncology : official journal of the American Society of Clinical Oncology 25: 2493-4; author reply 2494-5, 2007. [Letter]

doi: 10.1200/JCO.2007.10.7227 PMID: 17557966.

15.5

29. Canedo P, Figueiredo C, Machado JC

After Helicobacter pylori, genetic susceptibility to gastric carcinoma revisited. Helicobacter 12 Suppl 2: 45-9, 2007. [Article; Proceedings Paper]

doi: 10.1111/j.1523-5378.2007.00564.x PMID: 17991176.

2.4

30. Canedo P, Machado JC

Genetic susceptibility to gastric carcinoma. Acta Endoscopica 37: 239-47, 2007. [Article]

31. Regalo G, Canedo P, Suriano G, Resende C, Campos ML, Oliveira MJ, Figueiredo C, Rodrigues-Pereira P, Blin N, Seruca R, Carneiro F, Machado JC

C/EBPbeta is over-expressed in gastric carcinogenesis and is associated with COX-2 expression. The Journal of pathology 210: 398-404, 2006. [Article]

doi: 10.1002/path.2063 PMID: 16981245.

5.8

32. Regalo G, Wright NA, Machado JC

Trefoil factors: from ulceration to neoplasia. Cellular and molecular life sciences : CMLS 62: 2910-5, 2005. [Review]

doi: 10.1007/s00018-005-5478-4 PMID: 16374578.

4.6

33. Figueiredo C, Machado JC

Re: Helicobacter pylori and interleukin 1 genotyping: An opportunity to identify high-risk individuals for gastric carcinoma Journal of the National Cancer Institute 95: 760-761, 2003. [Letter]

13.8

34. Carvalho R, Kayademir T, Soares P, Canedo P, Sousa S, Oliveira C, Leistenschneider P, Seruca R, Gött P, Blin N, Carneiro F, Machado JC

Loss of heterozygosity and promoter methylation, but not mutation, may underlie loss of TFF1 in gastric carcinoma. Laboratory investigation; a journal of technical methods and pathology 82: 1319-26, 2002. [Article]

PMID: 12379766.

4.0

@ 2014 Ipatimup Institute of Molecular Pathology and Immunology of the University of Porto