Cancer Biology& Epigenetics Group

Group Leader at IPO Porto since 2008

Invited Associate Professor with Full Professor’s Habilitation at Biomedical Sciences Institute(ICBAS) of University of Porto

Director of the Master Course in Oncology at Biomedical Sciences Institute(ICBAS) of University of Porto

(2001-2004) Post-doctoral researcher at IPO Porto and School of Medicine of Johns Hopkins University, Baltimore, USA

(2011) Aggregation in Pathology & Molecular Genetics at University of Porto

(2001) PhD in Biomedical Sciences at University of Porto

ORCID ID: 0000-0003-4186-5345

Group description and objectives

The long-term core goal of the Cancer Biology and Epigenetics Group (CBEG) is to portray the epigenetic mechanisms involved in the genesis of urological cancers. Recently, we have been tackling the contribution of deregulated non-coding RNAs expression and its interaction with other epigenetic mechanisms that may induce/promote malignant transformation.

Specifically, within the framework of Precision Medicine, we have four major lines of investigation ongoing:

(1) Using body fluids - liquid biopsies (plasma or serum) and urine - for detecting cell-free tumor-specific epigenetic biomarkers (methylated DNA or noncoding RNA) we aim at developing new cancer biomarkers for screening/ detection and to assist in patient’s clinical management. We have identified several putative markers in tissues of the four major human malignancies [those of breast (BrCa), prostate (PCa), colorectal (CRC) and lung (LCa)] as well in other urological cancers [bladder (BlCa), kidney (KCa) and testicular germ-cell tumors (TGCT)] that are already being tested in body fluids (Costa-Pinheiro, Epigenomics 2015, Costa AL, Epigenomics 2017).

(2) Due to the heterogeneous biology of PCa, only a limited proportion of tumors are deemed to be clinically significant. Because non-coding protein genes / non-coding RNA aberrations, particularly, long non-coding RNAs have been recently implicated in PCa carcinogenesis (Ramalho-Carvalho, CRM, 2017) we plan to focus our research to better understand their role in molecular pathways associated with PCa aggressiveness, AR and PTEN signaling pathways. Moreover, since long noncoding RNA (lncRNA) are target by also target by internal chemical modifications, such as N6-methyladenosine (m6A), that may impact in various cellular processes, through post-transcriptional regulation of gene expression (Fu, NRG 2014 & Roundtree, cell 2017) we will attempt to discover their role in PCa onset. Thus, it is likely then that unravelling the biological functions of ncRNAs in PCa will provide new insights into their functions, mechanisms of action, and potential usefulness as tools for PCa management.

(3) Despite nephrectomy is performed with curative intent, approximately 30% of patients with localized clear cell Renal Cell Carcinoma (ccRCC), develop metastases and perish due to this malignancy. Herein, we intend to discover Long non-coding RNAs (LnCRNAs) that might regulate Von Hippel-Lindau Pathway and its implication in metastization.

(4) Furthermore, in the same context of Precision Medicine, we are investigating the potential of epigenetic modulators (e.g., DNA methyltransferase and histone deacetylases inhibitors) for cancer therapy, through manipulation of cell lines, characterizing their biological effects and antineoplastic capabilities. Owing to the relevance that Immuno-oncology has demonstrated in recent years, we are also investigating the epigenetic modulation of expression of biomolecules involved in immune checkpoint regulation, aiming at the improvement of immunotherapeutic strategies by combination with epi-drugs.

LAB Keywords

Cancer Epigenetics & Epitranscriptomics, Precision medicine, Epi-markers, Epi-drugs

PROJECTS WITH EXTERNAL FUNDING

HyTherCaP- Hydralazine: Testing an off-label effect in Castration-Resistant Prostate Cancer FCT- POCI-01-0145-FEDER-29030, Budget: 196.448,85€ (2018-2020).

Prostate cancer (PCa) is one of the most commonly diagnosed malignancies worldwide and a leading cause of cancer-related deaths among men. In Portugal, it is the most incident cancer and the 3rd cause of death (1, 2). Although most of PCa are clinically indolent, a variable proportion of patients develop castration-resistant PCa (CRPC), an aggressive and lethal form of disease, associated with metastatic dissemination (3). Currently, most therapeutic strategies for CRPC are not curative and largely ineffective, only marginally increasing in survival (4). Therefore, novel therapeutics strategies, ideally based on PCa biology, are urgently needed. Androgen receptor (AR) plays a central role in PCa development and progression. Androgen deprivation therapy is the standard initial care for metastatic PCa (5). Most resistance mechanisms to ADT are related with AR overexpression or mutations, amplification, alternative splice variants, and epigenetic alterations (6, 7). However, 20-30% of CRPC are characterized by a wide loss of AR expression (8, 9) which is not related to either mutations or deletions (10, 11). Promoter hypermethylation is one of the main mechanisms for AR loss of expression (12, 13). Recently, we demonstrated that hydralazine, a non-nucleoside inhibitor of DNA methyltransferases (DNMTi), attenuates malignant phenotype of PCa cells (14). Remarkably, CRPC cell line harboring AR promoter methylation, DU145, achieved the best drug response. Hydralazine restored AR expression and re-sensitized these cells to conventional androgen deprivation therapy, showing promise as innovative therapy for PCa. The major aims of this project are to confirm Hydralazine’s mechanism of action in CRPC and define which subgroup of CRPC patients will benefit from this therapy. To achieve these goals, this project is based on the vast experience of a multidisciplinary team with knowhow in epigenetic editing, 2D and 3D in vitro cell culture, molecular biology, nanotechnology and pathology. The activities that will be carried out include a) AR in vitro methylation, in collaboration with an expert in this methodology; b) Assembly of 3D Prostate Cancer by CICECO members to test hydralazine effects in more complex cancer models; c) Test Hydralazine delivery in nanoliposomes, developed by NanoSTAR, to reduce drug concentration d) Identification of biomarkers predictive of response to hydralazine and subsequent validation in a cohort of PCa patients. This activity as well as all pharmacological and phenotypic assays.

Publications:

Marques-Magalhães Â, Graça I, Henrique R, Jerónimo C. Targeting DNA Methyltranferases in Urological Tumors. Front Pharmacol 13;9:366, 2018.

EpiMarkGermCell-“DEVELOPMENT OF NOVEL PROGNOSTIC AND PREDICTIVE EPIGENETIC BIOMARKERS FOR MALIGNANT TESTICULAR GERM CELL TUMORS”- FCT- POCI-01-0145-FEDER-29043, Budget: 239.923,86€ (2018-2020).

This project aims to contribute to the improvement of care provided to patients with malignant testicular germ cell tumors (TGCT) and is a result of the recognition of IPO Porto (in partnership with Oporto Hospital Center) as a Reference Center for diagnosis and treatment of Testicular cancer. In the North Region, according with the most recent data from RORENO (2011), the standardized incidence rate for testicular cancer is 4.3/100,000 (about 75 cases/year), being the most frequent cancer in young men (15- 44 years) [1]. Similar values are observed worldwide, with the number of new cases expected to exceed 65,000 by 2030 [2]. Despite the excellent prognosis, about 15-20% of the patients with disseminated tumor develop recurrence, presenting poor prognosis. Some tumors are resistant to cisplatin therapy, and neither the underlying mechanisms are fully understood nor predictive biomarkers exist to identify tumors which are likely to endure cisplatin-resistance. Finally, the sensitivity of serum markers in use is less than 60%, limiting patient monitoring and early identification of relapse. The PI and Co-PI research team has been dedicated for more than a decade to characterizing the epigenome of tumor cells by establishing the DNA methylation profile, post-translational histone modifications, and altered miRNA expression patterns, identifying functional alterations involved in the loss of epigenetic homeostasis. This knowledge was translated into the development of epigenetic biomarkers aimed at the early detection, diagnosis, prognosis and prediction of response to therapy in urological tumors, favoring its use in clinical samples obtained by non-invasive or minimally invasive methods such as liquid biopsies, including plasma and urinary sediments. Thus, panels of epigenetic markers for prostate (APC promoter methylation for prognostic stratification [3] and promoter methylation of genes encoding miR-34b/c, miR-129-2 and miR-193b for early prostate cancer detection in urine [4]), bladder (promoter methylation of GDF15, TMEFF2 and VIM for accurate detection in urine [5]) and kidney (expression levels of miR-141 and miR-200b for specific detection of major histological types and prognostication [6]) cancer. Thus, we intend to develop a set of novel epigenetic biomarkers for TGCT, which can be analyzed in liquid biopsies, allowing for improved evaluation of prognosis and prediction of resistance to chemotherapy, aiding in monitoring during and after treatment. In addition to the experience accumulated in CEBG, we have the collaboration of Prof. Leendert Looijenga (Erasmus University, Rotterdam), renowned researcher in this field, as a scientific consultant, permitting the use of state-of-the-art equipment for the discovery of new biomarkers (aberrant DNA methylation, chromatin remodeling enzymes and differential expression of microRNAs).

Publications:

1. Lobo J, Barros-Silva D, Henrique R, Jerónimo C. The Emerging Role of Epitranscriptomics in Cancer: Focus on Urological Tumors. Genes 9(11). pii: E552, 2018.

2. Lobo J, Henrique R, Jerónimo C.The Role of DNA/Histone Modifying Enzymes and Chromatin Remodeling Complexes in Testicular Germ Cell Tumors. Cancers (Basel) 11(1). pii: E6., 2018.

3. Lobo J, Costa AL, Vilela-Salgueiro B, Rodrigues Â, Guimarães R, Cantante M, Lopes P, Antunes L, Jerónimo C, Henrique R. Testicular germ cell tumors: revisiting a series in light of the new WHO classification and AJCC staging systems, focusing on challenges for pathologists. Hum Pathol. pii: S0046-8177 (18) 30283-1, 2018.

4. Costa AL, Moreira-Barbosa C, Lobo J, Vilela-Salgueiro B, Cantante M, Guimarães R, Lopes P, Braga I, Oliveira J, Antunes L, Henrique R, Jerónimo C. DNA methylation profiling as a tool for testicular germ cell tumors subtyping. Epigenomics. 2018. doi: 10.2217/epi-2018-0034

PROJECTS WITH INTERNAL FUNDING

MethylBiom4Can– CI-IPOP-74-2016, Budget: 152.850,09€ (2016-2019).

MCTKidCan– CI-IPOP-92-2018, Budget: 35,000€ (2018-2019).

Selected Publications

1. Graça I, et al. Anti-neoplastic properties of hydralazine in prostate cancer. Oncotarget. 5(15): 5950-64, 2014. (IF: 6.359)

2. Bartosch C, et al. Pathologic Findings in Prophylactic and Nonprophylactic Hysterectomy Specimens of Patients With Lynch Syndrome. Am J Surg Pathol 40(9):1177-91, 2016. (IF: 5.363)

3. Ramalho-Carvalho J et al. Epigenetic disruption of miR-130a promotes prostate cancer by targeting SEC23B and DEPDC1. Cancer Lett 385:150-159, 2017. (IF: 6.375)

4. Padrao, NA, et al. MicroRNA promoter methylation: a new tool for accurate detection of urothelial carcinoma. Br J Cancer;116(5):634-9, 2017. (IF: 6.176)

5. Torres-Ferreira J, et al. MiR-193b promoter methylation accurately detects prostate cancer in urine sediments and miR-34b/c or miR-129-2 promoter methylation define subsets of clinically aggressive tumors. Mol Cancer16(1):26, 2017. (IF: 6.204)

6. Ramalho-Carvalho J, et al. Downregulation of miR-130b~301b cluster is mediated by aberrant promoter methylation and impairs cellular senescence in prostate cancer. J Hematol Oncol 10(1):43, 2017. (IF: 7.333)

7. Barros-Silva D, et al. MicroRNA-27a-5p regulation by promoter methylation and MYC signaling in prostate carcinogenesis. Cell Death Dis 9(2):167, 2018. (IF: 5.638)

8. Vilela-Salgueiro B, et al. Germ cell tumour subtypes display differential expression of microRNA371a-3p. Philos Trans R Soc Lond B Biol Sci. 373, 2018.(IF: 5.666)

9. Moreira-Barbosa C, et al. Comparing diagnostic and prognostic performance of two-gene promoter methylation panels in tissue biopsies and urines of prostate cancer patients. Clin Epigenetics. 10(1):132. 2018. (IF: 6.091)

10. Salta S, Nunes SP et al. A DNA Methylation-Based Test for Breast Cancer Detection in Circulating Cell-Free DNA. J Clin Med. 7;7(11). pii: E420, 2018 (IF: 5.583)

Research Team

Senior Researcher

· Rui Henrique, MD, PhD

ORCID ID: 0000-0003-3171-4666

Director of the Department of Pathology

Director of the Tumor Bank of the Department Pathology

Invited Full Professor at ICBAS-UP

Email: henrique@ipoporto.min-saude.pt / rmhenrique@icbas.up.pt

Junior Researchers

· Carla Bartosch, MD, PhD

ORCID ID: 0000-0003-0646-7667

Pathologist at IPO Porto

Email: carlabartosch@yahoo.com

· Vânia Camilo, PhD

ORCID ID: 0000-0002-4661-8186

Email: vania.gomes.camilo@ipoporto.min-saude.pt

· Vera Miranda-Gonçalves, PhD

ORCID ID: 0000-0002-4231-5532

Email: vera.miranda.goncalves@ipoporto.min-saude.pt

PhD Students

· Daniela Barros-Silva, MSc; Email: daniela.silva@ipoportomin-saude.pt

· João Lobo, MD; Email: jpedro.lobo@ipoporto.min-saude.pt

· Juliana Felgueiras, MSc (Co-supervision); Email: julianacfelgueiras@ua.pt

· Mário Fontes e Sousa, MD; Email: mario_fontes_sousa@hotmail.com

· Nuno Coimbra, MD; Email: nuno.coimbra@ipoporto.min-saude.pt

· Rita Canário, MD (Co-supervision); Email: rita.canario@ipatimup.pt

· Sara Monteiro-Reis, MSc; Email: sara.raquel.reis@ipoporto.min-saude.pt

· Sofia Salta, MSc; Email: sofia.salta@ipoporto.min-saude.pt

Research Assistants

· Ana Lameirinhas, MSc; Email: analameirinhas@gmail.com

· Catarina Macedo-Silva, MSc; Email: catarina.silva3005@gmail.com

· Sandra P. Nunes, MSc; Email: sandra22nunes@gmail.com

Research trainees

Carina Carvalho-Maia, MSc; Email: carina.carvalho.maia@ipoporto.min-saude.pt

MSc Students

Catarina Guimarães-Teixeira; Cláudia Martins-Lima; Helena Estevão-Pereira, Gonçalo Outeiro-Pinho; Mariana Brütt; Rita Guimarães; Rita Silva-Oliveira; Vera Constâncio

Other Collaborators

Ana Luísa Cunha, MD; Paula Lopes, BSc; Ana S. Pires-Luis, MD, PhD; Ana Teresa Martins, MSc; Ângelo Rodrigues, MD; Davide Gigliano, MD; Diana Montezuma, MD; Fernanda Silva, BSc; Filipa Quintela-Vieira, PhD; Francisco Duarte Menezes, MD; Inês Graça, PhD; Isa Carneiro, MSc; Joana Matos Loureiro, MD; Jorge Torres-Ferreira, MSc; Mª Conceição Martins, BSC; Mariana Cantante, BSc; Mónica Domingos Farinha, MD; Paula Monteiro, MD; Paula Dias, BSc; Renata Vieira, BSc; Sara Petronilho, MD; Sofia Paulino, MSc; Sónia Carvalho, MD; Verónica Ferreira, BSc.

Selected Publications (Last 10 years)

1. Costa VL, Henrique R, Danielsen SA, Duarte-Pereira S, Eknaes M, Skotheim RI, Rodrigues A, Magalhães JS, Oliveira J, Lothe RA, Teixeira MR, Jeronimo C*, Lind GE*.Three epigenetic biomarkers, GDF15, TMEFF2 and VIM, accurately predict bladder cancer from DNA-based analyses of urine samples. Clin Cancer Res 16(23):5842-51, 2010 (*Joint senior authors). (IF: 7.338)

2. Sousa EJ, Graça I, Baptista T, Vieira FQ, Palmeira C, Henrique R, Jerónimo C. Enoxacin inhibits growth of prostate cancer cells and effectively restores microRNA processing. Epigenetics 8(5):548-58, 2013. (IF: 5.108)

3. Monteiro-Reis S, Leça L, Almeida M, Antunes L, Monteiro P, Dias PC, Morais A, Oliveira J, Henrique R, Jerónimo C. Accurate detection of upper tract urothelial carcinoma in tissue and urine by means of quantitative GDF15, TMEFF2 and VIM promoter methylation. Eur J Cancer 50(1):226-33, 2014. (IF: 5.417)

4. Graça I, Sousa EJ, Costa-Pinheiro P, Vieira FQ, Torres-Ferreira J, Martins MG, Henrique R, Jerónimo C. Anti-neoplastic properties of hydralazine in prostate cancer. Oncotarget. 5(15): 5950-64, 2014. (IF: 6.359)

5. Junqueira-Neto S, Vieira FQ, Montezuma D, Costa NR, Antunes L, Baptista T, Oliveira AI, Graça I, Rodrigues A, Magalhães JS, Oliveira J, Henrique R, Jerónimo C. Phenotypic impact of deregulated expression of class I histone deacetylases in urothelial cell carcinoma of the bladder. Mol Carcinog. 54(7):523-31, 2015. (IF: 4.722)

6. Bartosch C, Pires-Luís AS, Meireles C, Baptista M, Gouveia A, Pinto C, Shannon KM, Jerónimo C, Teixeira MR, Lopes JM, Oliva E. Pathologic Findings in Prophylactic and Nonprophylactic Hysterectomy Specimens of Patients With Lynch Syndrome. Am J Surg Pathol 40(9):1177-91, 2016. (IF: 5.363)

7. Ramalho-Carvalho J, Martins JB, Cekaite L, Sveen A, Torres-Ferreira J, Graça I, Costa-Pinheiro P, Eilertsen IA, Antunes L, Oliveira J, Lothe RA, Henrique R, Jerónimo C. Epigenetic disruption of miR-130a promotes prostate cancer by targeting SEC23B and DEPDC1. Cancer Lett 385:150-159, 2017. (IF: 6.375)

8. Padrao, NA, Monteiro-Reis, S, Torres-Ferreira, J, Antunes, L, Leca, L, Montezuma, D, Ramalho-Carvalho, J, Dias, PC, Monteiro, P, Oliveira, J, Henrique, R and Jeronimo, C. MicroRNA promoter methylation: a new tool for accurate detection of urothelial carcinoma. Br J Cancer 2017;116(5):634-9. (IF: 6.176)

9. Torres-Ferreira J, Ramalho-Carvalho J, Gomez A, Menezes FD, Freitas R, Oliveira J, Antunes L, Bento MJ, Esteller M, Henrique R, Jerónimo C. MiR-193b promoter methylation accurately detects prostate cancer in urine sediments and miR-34b/c or miR-129-2 promoter methylation define subsets of clinically aggressive tumors. Mol Cancer 16(1):26, 2017. (IF: 6.204)

10. Barros-Silva D, Costa-Pinheiro P, Duarte H, Sousa EJ, Evangelista AF, Graça I, Carneiro I, Martins AT, Oliveira J, Carvalho AL, Marques MM, Henrique R, Jerónimo C. MicroRNA-27a-5p regulation by promoter methylation and MYC signaling in prostate carcinogenesis. Cell Death Dis 9(2):167, 2018. (IF: 5.965)

Internationalization

Networks

PI was MC substitute member of Action TD0905 (CMST) - Epigenetics: Bench to Bedside and presently she is MC member and Chair of Working group WG2 of COST Action CM1406 (CMST) - Epigenetic Chemical Biology (EPICHEM) and MC member of COST Action European Epitranscriptomics Network- CA16120-EPITRAN.

Editorial Board positions

Carmen Jerónimo

2014- Associate Editor of BMC Cancer

2015-Associate Editor of Clinical Epigenetics

2016-International Editorial Board Member of Tumori Journal

Rui Henrique

2011-Associate Editor of Frontiers in Genetics, Section of Epigenomics and Epigenetics

2014-Associate Editor of BMC Clinical Pathology, Section of Histopathology

2016-International Editorial Board Member of Tumori Journal

Collaborations

National

Bruno Costa, ICVS/3Bs, University of Minho

Fernando Jorge Monteiro & Susana Sousa; INEB, I3S

João F Mano, CICECO - Aveiro Institute of Materials of the University of Aveiro

Luisa Helguero & Margarida Fardilha, IBiMED, University of Aveiro

Paula Guedes and Márcia Carvalho (Biological Chemistry research, REQUIMTE)

Renata Freitas, IBMC, I3S

International

Dr. Aamir Ahmed, Centre for Stem Cells & Regenerative Medicine, King’s College London, UK

Prof. Antonio Lopez-Beltran, Department of Pathology, Cordoba University Medical School, Spain

Dr. Florence Le Calvez-Kelm, IARC, Lyon, France

Dr. G**o Lind, Radium Hospital, Oslo, Norway

Prof. Leendert H. J. Looijenga, Laboratory for Experimental Patho-Oncology, Department of Pathology, Erasmus University,Rotterdam, The Netherlands

Prof. Manel Esteller, IDIBELL Barcelona, Spain

Prof. Márcia M. Marques, Barretos Cancer Hospital, S. Paulo, Brazil

Dr. Paola Arimondo, Institute Pasteur, Paris, France

Prof. Ragnhild Lothe, Radium Hospital, Oslo, Norway

Dr. Wilbert Zwart, NKI, Amsterdam, Netherlands

Former Members

PhD Students

(2010) Vera L. Costa

(2017) João Ramalho-Carvalho

Research Assistants

(2012) Ana Isabel Oliveira

MSc Students

(2009) Filipa Loureiro Paiva; Joana Savva-Bordalo; Sara P. M. Duarte-Pereira

(2010) Mafalda Almeida; Patrícia Patrício

(2012) António J. Polónia; Elsa J. Sousa; João Barbosa-Martins; Susana Junqueira-Neto; Tiago Baptista;

(2013) Fátima Liliana Monteiro; Pedro Costa-Pinheiro; Rui Silva-Santos

(2014) Diogo Almeida-Rios; Henrique Duarte; Márcia Vieira-Coimbra

(2016) Eva Pereira-Silva; Fábio Ferreira; Francisca Diniz; Maria João Ferreira; Micaela Freitas; T. Soraia Vieira-Silva

(2017) Ana Laura Costa; Ângela Marques-Magalhães; Catarina Moreira-Barbosa; David Bidarra; João Gama; Maria Amorim; Rafael Amorim

(2018) Bárbara Vilela-Salgueiro; Ana Luísa Pinto

Patents

2012 – Methods and biomarkers for detection of bladder cancer (US 20130210011/ EP 2630261 A1/ WO 2012052844 A1)

Useful links

IPO Porto http://www.ipoporto.pt/

Associação Portuguesa de Investigação em Cancro (ASPIC) http://www.aspic.pt/pt-pt

European Association for Cancer Research (EACR) https://www.eacr.org/

European Epitranscriptomics Network (EPITRAN) https://epitran.eu/

Epigenetic Chemical Biology (EPICHEM) http://epichembio.eu/