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Macedo-Silva C, Miranda-Gonçalves V, Tavares NT, Barros-Silva D, Lencart J, Lobo J, Oliveira Â, Correia MP, Altucci L, Jerónimo C. Epigenetic regulation of TP53 is involved in prostate cancer radioresistance and DNA damage response signaling. Signal Transduct Target Ther 2023; 8:395. [PMID: 37840069 PMCID: PMC10577134 DOI: 10.1038/s41392-023-01639-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 08/23/2023] [Accepted: 09/06/2023] [Indexed: 10/17/2023] Open
Abstract
External beam radiotherapy (RT) is a leading first-line therapy for prostate cancer (PCa), and, in recent years, significant advances have been accomplished. However, RT resistance can arise and result in long-term recurrence or disease progression in the worst-case scenario. Thus, making crucial the discovery of new targets for PCa radiosensitization. Herein, we generated a radioresistant PCa cell line, and found p53 to be highly expressed in radioresistant PCa cells, as well as in PCa patients with recurrent/disease progression submitted to RT. Mechanism dissection revealed that RT could promote p53 expression via epigenetic modulation. Specifically, a decrease of H3K27me3 occupancy at TP53 gene promoter, due to increased KDM6B activity, was observed in radioresistant PCa cells. Furthermore, p53 is essential for efficient DNA damage signaling response and cell recovery upon stress induction by prolonged fractionated irradiation. Remarkably, KDM6B inhibition by GSK-J4 significantly decreased p53 expression, consequently attenuating the radioresistant phenotype of PCa cells and hampering in vivo 3D tumor formation. Overall, this work contributes to improve the understanding of p53 as a mediator of signaling transduction in DNA damage repair, as well as the impact of epigenetic targeting for PCa radiosensitization.
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Grants
- CJ’s Research is funded by Research Center of Portuguese Institute of Porto (BF.CBEG CI-IPOP-27-2016) and EpiParty PI 159-CI-IPOP-152-2021).
- CM-S holds a fellowship grant from UniCampania, Naples, Italy (2019-UNA2CLE-0170010).
- VM-G was funded by P.CCC: Centro Compreensivo de Cancro do Porto” – NORTE-01-0145-FEDER-072678, supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF).
- NTT was funded by P.CCC: Centro Compreensivo de Cancro do Porto” – NORTE-01-0145-FEDER-072678, supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF).
- DB-S holds a fellowship grant from FCT—Fundação para a Ciência e Tecnologia (SFRH/BD/136007/2018).
- MPC was funded by FCT—Fundação para a Ciência e Tecnologia (CEECINST/00091/2018).
- LA’s research is funded by Epi-MS under the VALERE 2019 Program; V:ALERE 2020—“CIRCE”; Campania Regional Government Technology Platform 2038 Lotta alle Patologie Oncologiche iCURE-B21C17000030007; Campania Regional Government FASE2: IDEAL; MIUR, Proof of Concept POC01_00043; POR Campania FSE 2014-2020 ASSE III; PON RI 2014/2020 “Dottorati Innovativi con caratterizzazione ndustrial”; Horizon EU: CAN-SERV BBMRI; EPI-MET MISE 2022; Bando giovani ricercatori D.R. n.834 del 30/09/2022 Università Vanvitelli project: Miranda; National Plan for NRRP Complementary Investments – Law Decree May 6, 2021, n. 59, converted and modified as to Law n. 101/2021Research initiatives for technologies and innovative trajectories in the health and care sectors: project ANTHEM (AdvaNced Technologies for Human-centrEd Medicine).
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Affiliation(s)
- Catarina Macedo-Silva
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/ CI-IPOP@ RISE (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
| | - Vera Miranda-Gonçalves
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/ CI-IPOP@ RISE (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
- Department of Pathology and Molecular Immunology, ICBAS-School of Medicine & Biomedical Sciences, University of Porto, R. Jorge de Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - Nuno Tiago Tavares
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/ CI-IPOP@ RISE (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Daniela Barros-Silva
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/ CI-IPOP@ RISE (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Joana Lencart
- Medical Physics, Radiobiology and Radiation Protection Group-Research Center of IPO Porto (CI-IPOP)/CI-IPOP@ RISE (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
- Department of Medical Physics, Portuguese Oncology Institute of Porto, 4200-072, Porto, Portugal
| | - João Lobo
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/ CI-IPOP@ RISE (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
- Department of Pathology and Molecular Immunology, ICBAS-School of Medicine & Biomedical Sciences, University of Porto, R. Jorge de Viterbo Ferreira 228, 4050-313, Porto, Portugal
- Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Ângelo Oliveira
- Department of Radiation Oncology, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Margareta P Correia
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/ CI-IPOP@ RISE (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
- Department of Pathology and Molecular Immunology, ICBAS-School of Medicine & Biomedical Sciences, University of Porto, R. Jorge de Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
- BIOGEM, Molecular Biology and Genetics Research Institute, 83100, Avellino, Italy
- IEOS, Institute of Endocrinology and Oncology, 80100, Naples, Italy
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/ CI-IPOP@ RISE (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal.
- Department of Pathology and Molecular Immunology, ICBAS-School of Medicine & Biomedical Sciences, University of Porto, R. Jorge de Viterbo Ferreira 228, 4050-313, Porto, Portugal.
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2
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Sequeira JP, Barros-Silva D, Ferreira-Torre P, Salta S, Braga I, Carvalho J, Freitas R, Henrique R, Jerónimo C. OncoUroMiR: Circulating miRNAs for Detection and Discrimination of the Main Urological Cancers Using a ddPCR-Based Approach. Int J Mol Sci 2023; 24:13890. [PMID: 37762193 PMCID: PMC10531069 DOI: 10.3390/ijms241813890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
The three most common genitourinary malignancies (prostate/kidney/bladder cancers) constitute a substantial proportion of all cancer cases, mainly in the elderly population. Early detection is key to maximizing the patients' survival, but the lack of highly accurate biomarkers that might be used through non-/minimally invasive methods has impaired progress in this domain. Herein, we sought to develop a minimally invasive test to detect and discriminate among those urological cancers based on miRNAs assessment through ddPCR. Plasma samples from 268 patients with renal cell (RCC; n = 119), bladder (BlCa; n = 73), and prostate (PCa; n = 76) carcinomas (UroCancer group), and 74 healthy donors were selected. Hsa-miR-126-3p, hsa-miR-141-3p, hsa-miR-153-5p, hsa-miR-155-5p, hsa-miR-182-5p, hsa-miR-205-5p, and hsa-miR-375-3p levels were assessed. UroCancer cases displayed significantly different circulating hsa-miR-182-5p/hsa-miR-375-3p levels compared to healthy donors. Importantly, the hsa-miR-155-5p/hsa-miR-375-3p panel detected RCC with a high specificity (80.54%) and accuracy (66.04%). Furthermore, the hsa-miR-126-3p/hsa-miR-375-3p panel identified BlCa with a 94.87% specificity and 76.45% NPV whereas higher hsa-miR-126-3p levels were found in PCa patients. We concluded that plasma-derived miRNAs can identify and discriminate among the main genitourinary cancers, with high analytical performance. Although validation in a larger cohort is mandatory, these findings demonstrate that circulating miRNA assessment by ddPCR might provide a new approach for early detection and risk stratification of the most common urological cancers.
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Affiliation(s)
- José Pedro Sequeira
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (J.P.S.); (D.B.-S.); (P.F.-T.); (S.S.); (I.B.); (J.C.); (R.F.); (R.H.)
- Doctoral Programme in Biomedical Sciences, ICBAS-School of Medicine & Biomedical Sciences, University of Porto, Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Daniela Barros-Silva
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (J.P.S.); (D.B.-S.); (P.F.-T.); (S.S.); (I.B.); (J.C.); (R.F.); (R.H.)
| | - Patrícia Ferreira-Torre
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (J.P.S.); (D.B.-S.); (P.F.-T.); (S.S.); (I.B.); (J.C.); (R.F.); (R.H.)
| | - Sofia Salta
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (J.P.S.); (D.B.-S.); (P.F.-T.); (S.S.); (I.B.); (J.C.); (R.F.); (R.H.)
- Doctoral Programme in Molecular Pathology and Genetics, ICBAS-School of Medicine & Biomedical Sciences, University of Porto, Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Isaac Braga
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (J.P.S.); (D.B.-S.); (P.F.-T.); (S.S.); (I.B.); (J.C.); (R.F.); (R.H.)
- Department of Urology & Urology Clinics, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Doctoral Programme in Medical Sciences, ICBAS-School of Medicine & Biomedical Sciences, University of Porto, Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - João Carvalho
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (J.P.S.); (D.B.-S.); (P.F.-T.); (S.S.); (I.B.); (J.C.); (R.F.); (R.H.)
- Department of Urology & Urology Clinics, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Doctoral Programme in Medical Sciences, ICBAS-School of Medicine & Biomedical Sciences, University of Porto, Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Rui Freitas
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (J.P.S.); (D.B.-S.); (P.F.-T.); (S.S.); (I.B.); (J.C.); (R.F.); (R.H.)
- Department of Urology & Urology Clinics, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Doctoral Programme in Medical Sciences, ICBAS-School of Medicine & Biomedical Sciences, University of Porto, Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Rui Henrique
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (J.P.S.); (D.B.-S.); (P.F.-T.); (S.S.); (I.B.); (J.C.); (R.F.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, ICBAS–School of Medicine and Biomedical Sciences, University of Porto, Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (J.P.S.); (D.B.-S.); (P.F.-T.); (S.S.); (I.B.); (J.C.); (R.F.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, ICBAS–School of Medicine and Biomedical Sciences, University of Porto, Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
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Barros-Silva D, Tsui J, Jerónimo C, Jenster G, Martens-Uzunova ES. Site-specific analysis of ribosomal 2'O-methylation by quantitative reverse transcription PCR under low deoxynucleotide triphosphate concentrations. Biotechniques 2023. [PMID: 37272338 DOI: 10.2144/btn-2022-0122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023] Open
Abstract
Ribose 2'O-methylation (Nm, ribomethylation) is the most abundant RNA modification present in rRNA. It has been shown that alterations in ribosomal 2'O-methylation at individual Nm sites likely reflect regulated cellular processes. Although several analytical approaches for Nm detection and profiling have been developed, a simple and affordable method for the screening and measurement of individual Nm sites in large numbers of tissue samples is required to examine their potential for clinical translation. Here, we describe a new quantitative reverse transcription PCR-based method that can sensitively assess ribomethylation levels at specific rRNA sites at single-nucleotide resolution in low input amounts of total RNA.
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Affiliation(s)
- Daniela Barros-Silva
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Be-331, PO Box 2040, 3000 CA Rotterdam, The Netherlands
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Centre (Porto CCC), Rua Dr. António Bernardino de Almeida, Porto, 4200-072, Portugal
- Doctoral Programme in Molecular Pathology & Genetics, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, Porto, 4050-513, Portugal
| | - Johan Tsui
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Be-331, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Centre (Porto CCC), Rua Dr. António Bernardino de Almeida, Porto, 4200-072, Portugal
- Department of Pathology & Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, Porto, 4050-513, Portugal
| | - Guido Jenster
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Be-331, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Elena S Martens-Uzunova
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Be-331, PO Box 2040, 3000 CA Rotterdam, The Netherlands
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Lobo J, Tavares NT, Barros-Silva D, Rosinha A, Morais A, Jerónimo C, Rodrigues Â, Henrique R. MiR-371a-3p in cystic trophoblastic tumour of the testis: supporting a maturation phenomenon towards teratoma. Histopathology 2023. [PMID: 37099411 DOI: 10.1111/his.14929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/17/2023] [Accepted: 04/09/2023] [Indexed: 04/27/2023]
Affiliation(s)
- João Lobo
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), Porto, Portugal
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Porto, Portugal
| | - Nuno Tiago Tavares
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), Porto, Portugal
| | - Daniela Barros-Silva
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), Porto, Portugal
| | - Alina Rosinha
- Department of Medical Oncology, Portuguese Oncology Institute of Porto (IPOP), Porto, Portugal
| | - António Morais
- Department of Urology, Portuguese Oncology Institute of Porto (IPOP), Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Porto, Portugal
| | - Ângelo Rodrigues
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), Porto, Portugal
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Porto, Portugal
| | - Rui Henrique
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), Porto, Portugal
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Porto, Portugal
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Outeiro-Pinho G, Barros-Silva D, Moreira-Silva F, Lobo J, Carneiro I, Morais A, Martins EP, Gonçalves CS, Costa BM, Correia MP, Henrique R, Jerónimo C. Epigenetically-regulated miR-30a/c-5p directly target TWF1 and hamper ccRCC cell aggressiveness. Transl Res 2022; 249:110-127. [PMID: 35697274 DOI: 10.1016/j.trsl.2022.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 05/09/2022] [Accepted: 06/06/2022] [Indexed: 10/31/2022]
Abstract
Clear cell renal cell carcinoma (ccRCC) is highly prone to metastasize and displays an extremely low 5-year survival rate. Not only miRNAs (miRs) are key gene expression regulators but can also be epigenetically modified. Abnormal miR expression has been linked with epithelial-mesenchymal transition (EMT)-driven ccRCC progression. MiR-30a/c-5p were found downregulated in ccRCC and associated with aggressiveness. Herein, we sought to unravel miR-30a/c-5p mechanistic role in ccRCC. RNA sequencing and genome-wide methylome data of ccRCC and normal tissue samples from The Cancer Genome Atlas database were integrated to identify candidate miRs cytosine-phosphate-guanine (CpG) loci deregulated in ccRCC. TargetScan was searched to identify miR putative targets. MiR-30a/c-5p expression and promoter methylation was evaluated in vitro, by PCR. Western blot, functional and luciferase assays were performed after cell transfection with either pre-miR, antimiR, or siRNA against twinfilin-1 (TWF1). Immunohistochemistry (IHC) was performed in ccRCC tissues. We found miR-30c-5p downregulation and aberrant promoter methylation in ccRCC tissues. In vitro studies revealed concomitant miR-30a/c-5p downregulation and increased promoter methylation, as well as a significant re-expression following decitabine treatment. Functional assays demonstrated that both miRs significantly decreased cell aggressiveness and the protein levels of EMT-promoting players, while upregulating epithelial markers, namely Claudin-1 and ZO-1. Importantly, we confirmed TWF1 as a direct target of both miRs, and its potential involvement in epithelial-mesenchymal transition/mesenchymal-epithelial transition regulation. IHC analysis revealed higher TWF1 expression in primary tissues from patients that developed metastases, after surgical treatment. Our results implicate miR-30a/c-5p in ccRCC cells' aggressiveness attenuation by directly targeting TWF1 and hampering EMT.
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Affiliation(s)
- Gonçalo Outeiro-Pinho
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, Porto, Portugal; Master in Molecular Medicine and Oncology, Faculty of Medicine-University of Porto (FMUP), Alameda Prof. Hernâni Monteiro, Porto, Portugal
| | - Daniela Barros-Silva
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, Porto, Portugal
| | - Filipa Moreira-Silva
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, Porto, Portugal
| | - João Lobo
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, Porto, Portugal; Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Isa Carneiro
- Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - António Morais
- Department of Urology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, Porto, Portugal
| | - Eduarda P Martins
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Céline S Gonçalves
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Bruno M Costa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Margareta P Correia
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, Porto, Portugal; Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences - University of Porto (ICBAS-UP), Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, Porto, Portugal; Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal; Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences - University of Porto (ICBAS-UP), Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, Porto, Portugal; Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences - University of Porto (ICBAS-UP), Porto, Portugal.
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Outeiro-Pinho G, Barros-Silva D, Aznar E, Sousa AI, Vieira-Coimbra M, Oliveira J, Gonçalves CS, Costa BM, Junker K, Henrique R, Jerónimo C. Correction: MicroRNA-30a-5pme: a novel diagnostic and prognostic biomarker for clear cell renal cell carcinoma in tissue and urine samples. J Exp Clin Cancer Res 2022; 41:247. [PMID: 35965325 PMCID: PMC9377117 DOI: 10.1186/s13046-022-02450-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Abstract
Ribosomes are essential nanomachines responsible for all protein production in cells. Ribosome biogenesis and function are energy costly processes, they are tightly regulated to match cellular needs. In cancer, major pathways that control ribosome biogenesis and function are often deregulated to ensure cell survival and to accommodate the continuous proliferation of tumour cells. Ribosomal RNAs (rRNAs) are abundantly modified with 2'-O-methylation (Nm, ribomethylation) being one of the most common modifications. In eukaryotic ribosomes, ribomethylation is performed by the methyltransferase Fibrillarin guided by box C/D small nucleolar RNAs (snoRNAs). Accumulating evidences indicate that snoRNA expression and ribosome methylation profiles are altered in cancer. Here we review our current knowledge on differential snoRNA expression and rRNA 2ʹ-O methylation in the context of human malignancies, and discuss the consequences and opportunities for cancer diagnostics, prognostics, and therapeutics.
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Affiliation(s)
- Daniela Barros-Silva
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands.,Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal
| | - Jonathan Klavert
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Guido Jenster
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (Icbas-up), Porto, Portugal
| | - Denis L J Lafontaine
- Rna Molecular Biology, Fonds De La Recherche Scientifique (F.r.s./fnrs), Université Libre De Bruxelles (Ulb), BioPark Campus, Gosselies, Belgium
| | - Elena S Martens-Uzunova
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
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8
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Barros-Silva D, Sacchetti A, Van Royen M, Van Kooij A, Soetermeer H, Jenster G, Jerónimo C, Martens-Uzunova E. Depletion of ribosomal 2’-O-methylation at 28S-Gm4593 mediated by snoRNA SNORD78 reduces the aggressive phenotype of prostate cancer. EUR UROL SUPPL 2021. [DOI: 10.1016/s2666-1683(21)01192-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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9
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Miranda-Gonçalves V, Lobo J, Guimarães-Teixeira C, Barros-Silva D, Guimarães R, Cantante M, Braga I, Maurício J, Oing C, Honecker F, Nettersheim D, Looijenga LHJ, Henrique R, Jerónimo C. The component of the m 6A writer complex VIRMA is implicated in aggressive tumor phenotype, DNA damage response and cisplatin resistance in germ cell tumors. J Exp Clin Cancer Res 2021; 40:268. [PMID: 34446080 PMCID: PMC8390281 DOI: 10.1186/s13046-021-02072-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/11/2021] [Indexed: 12/22/2022]
Abstract
Background Germ cell tumors (GCTs) are developmental cancers, tightly linked to embryogenesis and germ cell development. The recent and expanding field of RNA modifications is being increasingly implicated in such molecular events, as well as in tumor progression and resistance to therapy, but still rarely explored in GCTs. In this work, and as a follow-up of our recent study on this topic in TGCT tissue samples, we aim to investigate the role of N6-methyladenosine (m6A), the most abundant of such modifications in mRNA, in in vitro and in vivo models representative of such tumors. Methods Four cell lines representative of GCTs (three testicular and one mediastinal), including an isogenic cisplatin resistant subline, were used. CRISPR/Cas9-mediated knockdown of VIRMA was established and the chorioallantoic membrane assay was used to study its phenotypic effect in vivo. Results We demonstrated the differential expression of the various m6A writers, readers and erasers in GCT cell lines representative of the major classes of these tumors, seminomas and non-seminomas, and we evidenced changes occurring upon differentiation with all-trans retinoic acid treatment. We showed differential expression also among cells sensitive and resistant to cisplatin treatment, implicating these players in acquisition of cisplatin resistant phenotype. Knockdown of VIRMA led to disruption of the remaining methyltransferase complex and decrease in m6A abundance, as well as overall reduced tumor aggressiveness (with decreased cell viability, tumor cell proliferation, migration, and invasion) and increased sensitivity to cisplatin treatment, both in vitro and confirmed in vivo. Enhanced response to cisplatin after VIRMA knockdown was related to significant increase in DNA damage (with higher γH2AX and GADD45B levels) and downregulation of XLF and MRE11. Conclusions VIRMA has an oncogenic role in GCTs confirming our previous tissue-based study and is further involved in response to cisplatin by interfering with DNA repair. These data contribute to our better understanding of the emergence of cisplatin resistance in GCTs and support recent attempts to therapeutically target elements of the m6A writer complex. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-02072-9.
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Affiliation(s)
- Vera Miranda-Gonçalves
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal.,Department of Pathology and Molecular Immunology, ICBAS - School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513, Porto, Portugal
| | - João Lobo
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal.,Department of Pathology and Molecular Immunology, ICBAS - School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal.,Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584, CS, Utrecht, The Netherlands
| | - Catarina Guimarães-Teixeira
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Daniela Barros-Silva
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Rita Guimarães
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Mariana Cantante
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Isaac Braga
- Department of Urology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Joaquina Maurício
- Department of Medical Oncology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Christoph Oing
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section of Pneumology, Mildred Scheel Cancer Career Center HaTriCs4, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Friedemann Honecker
- Tumour and Breast Center ZeTuP St. Gallen, Rorschacher Strasse 150, 9006, St. Gallen, Switzerland
| | - Daniel Nettersheim
- Department of Urology, Urological Research Lab, Translational UroOncology, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
| | - Leendert H J Looijenga
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584, CS, Utrecht, The Netherlands
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal. .,Department of Pathology and Molecular Immunology, ICBAS - School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513, Porto, Portugal. .,Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal.
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal. .,Department of Pathology and Molecular Immunology, ICBAS - School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513, Porto, Portugal.
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Outeiro-Pinho G, Barros-Silva D, Correia MP, Henrique R, Jerónimo C. Renal Cell Tumors: Uncovering the Biomarker Potential of ncRNAs. Cancers (Basel) 2020; 12:cancers12082214. [PMID: 32784737 PMCID: PMC7465320 DOI: 10.3390/cancers12082214] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/30/2020] [Accepted: 08/05/2020] [Indexed: 12/24/2022] Open
Abstract
Renal cell tumors (RCT) remain as one of the most common and lethal urological tumors worldwide. Discrimination between (1) benign and malignant disease, (2) indolent and aggressive tumors, and (3) patient responsiveness to a specific therapy is of major clinical importance, allowing for a more efficient patient management. Nonetheless, currently available tools provide limited information and novel strategies are needed. Over the years, a putative role of non-coding RNAs (ncRNAs) as disease biomarkers has gained relevance and is now one of the most prolific fields in biological sciences. Herein, we extensively sought the most significant reports on ncRNAs as potential RCTs' diagnostic, prognostic, predictive, and monitoring biomarkers. We could conclude that ncRNAs, either alone or in combination with currently used clinical and pathological parameters, might represent key elements to improve patient management, potentiating the implementation of precision medicine. Nevertheless, most ncRNA biomarkers require large-scale validation studies, prior to clinical implementation.
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Affiliation(s)
- Gonçalo Outeiro-Pinho
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (G.O.-P.); (D.B.-S.); (M.P.C.); (R.H.)
| | - Daniela Barros-Silva
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (G.O.-P.); (D.B.-S.); (M.P.C.); (R.H.)
| | - Margareta P. Correia
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (G.O.-P.); (D.B.-S.); (M.P.C.); (R.H.)
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (G.O.-P.); (D.B.-S.); (M.P.C.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira n. 228, 4050-313 Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (G.O.-P.); (D.B.-S.); (M.P.C.); (R.H.)
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira n. 228, 4050-313 Porto, Portugal
- Correspondence: ; Tel.: +351-225084000; Fax: +351-225084199
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11
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Lima AR, Pinto J, Barros-Silva D, Jerónimo C, Henrique R, Bastos MDL, Carvalho M, Guedes Pinho P. New findings on urinary prostate cancer metabolome through combined GC-MS and 1H NMR analytical platforms. Metabolomics 2020; 16:70. [PMID: 32495062 DOI: 10.1007/s11306-020-01691-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 05/28/2020] [Indexed: 02/08/2023]
Abstract
INTRODUCTION The inherent sensitivity of metabolomics allows the detection of subtle alterations in biological pathways, making it a powerful tool to study biomarkers and the mechanisms that underlie cancer. OBJECTIVES The purpose of this work was to characterize the urinary metabolic profile of prostate cancer (PCa) patients and cancer-free controls to obtain a holistic coverage of PCa metabolome. METHODS Two groups of samples, a training set (n = 41 PCa and n = 42 controls) and an external validation set (n = 18 PCa and n = 18 controls) were analyzed using a dual analytical platform, namely gas chromatography-mass spectrometry (GC-MS) and proton nuclear magnetic resonance spectroscopy (1H NMR). RESULTS The multivariate analysis models revealed a good discrimination between cases and controls with an AUC higher than 0.8, a sensitivity ranging from 67 to 89%, a specificity ranging from 74 to 89% and an accuracy from 73 to 86%, considering the training and external validation sets. A total of 28 metabolites (15 from GC-MS and 13 from 1H NMR) accounted for the separation. These discriminant metabolites are involved in 14 biochemical pathways, indicating that PCa is highly linked to dysregulation of metabolic pathways associated with amino acids and energetic metabolism. CONCLUSION These findings confirmed the complementary information provided by GC-MS and 1H NMR, enabling a more comprehensive picture of the altered metabolites, underlying pathways and deepening the understanding of PCa development and progression.
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Affiliation(s)
- Ana Rita Lima
- UCIBIO/REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal.
| | - Joana Pinto
- UCIBIO/REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Daniela Barros-Silva
- Cancer Biology & Epigenetics Group, Research Center (CI-IPOP) Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group, Research Center (CI-IPOP) Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
- Department of Pathology and Molecular Immunology-Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Rui Henrique
- Cancer Biology & Epigenetics Group, Research Center (CI-IPOP) Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
- Department of Pathology and Molecular Immunology-Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Maria de Lourdes Bastos
- UCIBIO/REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Márcia Carvalho
- UCIBIO/REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal.
- UFP Energy, Environment and Health Research Unit (FP-ENAS), University Fernando Pessoa, Porto, Portugal.
| | - Paula Guedes Pinho
- UCIBIO/REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal.
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12
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Outeiro-Pinho G, Barros-Silva D, Aznar E, Sousa AI, Vieira-Coimbra M, Oliveira J, Gonçalves CS, Costa BM, Junker K, Henrique R, Jerónimo C. MicroRNA-30a-5p me: a novel diagnostic and prognostic biomarker for clear cell renal cell carcinoma in tissue and urine samples. J Exp Clin Cancer Res 2020; 39:98. [PMID: 32487203 PMCID: PMC7323611 DOI: 10.1186/s13046-020-01600-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/19/2020] [Indexed: 12/13/2022]
Abstract
Background The rising incidence of renal cell carcinomas (RCC) constitutes a significant challenge owing to risk of overtreatment. Because aberrant microRNA (miR) promoter methylation contributes to cancer development, we investigated whether altered miR-30a-5p expression associates with DNA promoter methylation and evaluated the usefulness as clear cell RCC (ccRCC) diagnostic and prognostic markers. Methods Genome-wide methylome and RNA sequencing data from a set of ccRCC and normal tissue samples from The Cancer Genome Atlas (TCGA) database were integrated to identify candidate CpG loci involved in cancer onset. MiR-30a-5p expression and promoter methylation were quantitatively assessed by PCR in a tissue set (Cohort #1) and urine sets (Cohorts #2 and 3) from IPOPorto and Homburg University Hospital. Non-parametric tests were used for comparing continuous variables. MiR-30a-5p promoter methylation (miR-30a-5pme) performance as diagnostic (receiver operator characteristics [ROC] - validity estimates) and prognostic [metastasis-free (MFS) and disease-specific survival (DSS)] biomarker was further validated in urine samples from ccRCC patients by Kaplan Meier curves (with log rank) and both univariable and multivariable analysis. Results Two significant hypermethylated CpG loci in TCGA ccRCC samples, correlating with miR-30a-5p transcriptional downregulation, were disclosed. MiR-30a-5pme in ccRCC tissues was confirmed in an independent patient’s cohort of IPOPorto and associated with shorter time to relapse. In urine samples, miR-30a-5pme levels identified cancer both in testing and validation cohorts, with 83% sensitivity/53% specificity and 63% sensitivity/67% specificity, respectively. Moreover, higher miR-30a-5pme levels independently predicted metastatic dissemination and survival. Conclusion To the best of our knowledge, this is the first study validating the diagnostic and prognostic potential of miR-30a-5pme for ccRCC in urine samples, providing new insights for its clinical usefulness as non-invasive cancer biomarker.
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Affiliation(s)
- Gonçalo Outeiro-Pinho
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal.,Master in Molecular Medicine and Oncology, Faculty of Medicine-University of Porto (FMUP), Porto, Portugal
| | - Daniela Barros-Silva
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Elena Aznar
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal.,Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat de València, CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Camino de Vera s/n, 46022, Valencia, Spain
| | - Ana-Isabel Sousa
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Márcia Vieira-Coimbra
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Jorge Oliveira
- Department of Urology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Céline S Gonçalves
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Bruno M Costa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Kerstin Junker
- Department of Urology and Pediatric Urology, Saarland University, Homburg, Saar, Germany
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira n.° 228, 4050-313, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal. .,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira n.° 228, 4050-313, Porto, Portugal.
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Guerreiro IM, Barros-Silva D, Lopes P, Cunha AL, Lobo J, Antunes L, Rodrigues A, Soares MAS, Henrique R, Jerónimo C. RAD51Bme as predictive biomarker for PD-1 blockade response in non-small cell lung cancer. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.e15235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e15235 Background: Lung cancer (LC) cells frequently express high levels of programmed death-ligand 1 (PD-L1). Although these levels grossly correlate with likelihood of response to specific checkpoint inhibitors, prediction of response is rather imperfect and, thus, more accurate predictive biomarkers are mandatory. We examined the methylation profile of RAD51B, a DNA-repair gene, as candidate predictive biomarker for efficacy of anti-PD-1 therapy in patients with non-small cell lung cancer (NSCLC), correlating with patients’ outcome. Methods: PD-L1 immunoexpression and RAD51Bme levels were analysed in samples of NSCLC obtained from patients not treated with anti-PD-1 blockade (testing cohort) and patients treated with anti-PD-1 (validation cohort). Results: Of a total of 127 patients assessed, 58.3% depicted positivity for PD-L1 (PD-L1+). RAD51Bme levels significantly associated with PD-L1 immunoexpression. Patients with clinical benefit from immunotherapy disclosed higher RAD51Bme levels (p = 0.04) and significantly higher median progression free survival (PFS) (p = 0.02). PD-L1+ was also associated with longer overall survival (p = 0.03). Conclusions: We demonstrated that RAD51Bme levels might be combined with validated predictive biomarker PD-L1 immunostaining to select patients who will most likely experience clinical benefit from PD-1 blockade. The predictive value of RAD51Bme should be confirmed in prospective studies.
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Affiliation(s)
| | | | - Paula Lopes
- Department of Pathology, Portuguese Institute of Oncology of Porto, Porto, Portugal
| | - Ana Luísa Cunha
- Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - João Lobo
- Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Luís Antunes
- Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Ana Rodrigues
- Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | | | - Rui Henrique
- Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Carmen Jerónimo
- Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
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Guerreiro IM, Barros-Silva D, Lopes P, Cantante M, Cunha AL, Lobo J, Antunes L, Rodrigues A, Soares M, Henrique R, Jerónimo C. RAD51Bme Levels as a Potential Predictive Biomarker for PD-1 Blockade Response in Non-Small Cell Lung Cancer. J Clin Med 2020; 9:jcm9041000. [PMID: 32252414 PMCID: PMC7230458 DOI: 10.3390/jcm9041000] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 12/11/2022] Open
Abstract
Lung cancer (LC) cells frequently express high levels of programmed death-ligand 1 (PD-L1). Although these levels grossly correlate with the likelihood of response to specific checkpoint inhibitors, the response prediction is rather imperfect, and more accurate predictive biomarkers are mandatory. We examined the methylation profile of RAD51B (RAD51Bme) as a candidate predictive biomarker for anti-PD-1 therapy efficacy in non-small cell lung cancer (NSCLC), correlating with patients’ outcome. PD-L1 immunoexpression and RAD51Bme levels were analysed in NSCLC samples obtained from patients not treated with anti-PD-1 (Untreated Cohort (#1)) and patients treated with PD-1 blockade (Treated Cohort (#2)). Of a total of 127 patients assessed, 58.3% depicted PD-L1 positivity (PD-L1+). RAD51Bme levels were significantly associated with PD-L1 immunoexpression. Patients with PD-1 blockade clinical benefit disclosed higher RAD51Bme levels (p = 0.0390) and significantly lower risk of disease progression (HR 0.37; 95% CI: 0.15–0.88; p = 0.025). Combining RAD51Bme+ with PD-L1+ improved the sensitivity of the test to predict immunotherapy response. PD-L1+ was also associated with lower risk of death (HR 0.35; 95% CI: 0.15–0.81; p = 0.014). Thus, RAD51Bme levels might be combined with validated predictive biomarker PD-L1 immunostaining to select patients who will most likely experience clinical benefit from PD-1 blockade. The predictive value of RAD51Bme should be confirmed in prospective studies.
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Affiliation(s)
- Inês Maria Guerreiro
- Department of Medical Oncology, Portuguese Oncology Institute of Porto (IPO-Porto), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (A.R.); (M.S.)
- Correspondence: (I.M.G.); (C.J.); Tel.: +351-225-084-000 (I.M.G.); Fax: +351-225-084-001 (I.M.G.)
| | - Daniela Barros-Silva
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (D.B.-S.); (P.L.); (M.C.); (A.L.C.); (J.L.); (R.H.)
| | - Paula Lopes
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (D.B.-S.); (P.L.); (M.C.); (A.L.C.); (J.L.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Mariana Cantante
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (D.B.-S.); (P.L.); (M.C.); (A.L.C.); (J.L.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Ana Luísa Cunha
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (D.B.-S.); (P.L.); (M.C.); (A.L.C.); (J.L.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - João Lobo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (D.B.-S.); (P.L.); (M.C.); (A.L.C.); (J.L.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge de Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Luís Antunes
- Cancer Epidemiology Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal;
| | - Ana Rodrigues
- Department of Medical Oncology, Portuguese Oncology Institute of Porto (IPO-Porto), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (A.R.); (M.S.)
| | - Marta Soares
- Department of Medical Oncology, Portuguese Oncology Institute of Porto (IPO-Porto), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (A.R.); (M.S.)
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (D.B.-S.); (P.L.); (M.C.); (A.L.C.); (J.L.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge de Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (D.B.-S.); (P.L.); (M.C.); (A.L.C.); (J.L.); (R.H.)
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge de Viterbo Ferreira, 228, 4050-313 Porto, Portugal
- Correspondence: (I.M.G.); (C.J.); Tel.: +351-225-084-000 (I.M.G.); Fax: +351-225-084-001 (I.M.G.)
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Lima AR, Pinto J, Azevedo AI, Barros-Silva D, Jerónimo C, Henrique R, de Lourdes Bastos M, Guedes de Pinho P, Carvalho M. Identification of a biomarker panel for improvement of prostate cancer diagnosis by volatile metabolic profiling of urine. Br J Cancer 2019; 121:857-868. [PMID: 31588123 PMCID: PMC6889512 DOI: 10.1038/s41416-019-0585-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/21/2019] [Accepted: 09/04/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The lack of sensitive and specific biomarkers for the early detection of prostate cancer (PCa) is a major hurdle to improve patient management. METHODS A metabolomics approach based on GC-MS was used to investigate the performance of volatile organic compounds (VOCs) in general and, more specifically, volatile carbonyl compounds (VCCs) present in urine as potential markers for PCa detection. RESULTS Results showed that PCa patients (n = 40) can be differentiated from cancer-free subjects (n = 42) based on their urinary volatile profile in both VOCs and VCCs models, unveiling significant differences in the levels of several metabolites. The models constructed were further validated using an external validation set (n = 18 PCa and n = 18 controls) to evaluate sensitivity, specificity and accuracy of the urinary volatile profile to discriminate PCa from controls. The VOCs model disclosed 78% sensitivity, 94% specificity and 86% accuracy, whereas the VCCs model achieved the same sensitivity, a specificity of 100% and an accuracy of 89%. Our findings unveil a panel of 6 volatile compounds significantly altered in PCa patients' urine samples that was able to identify PCa, with a sensitivity of 89%, specificity of 83%, and accuracy of 86%. CONCLUSIONS It is disclosed a biomarker panel with potential to be used as a non-invasive diagnostic tool for PCa.
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Affiliation(s)
- Ana Rita Lima
- UCIBIO/REQUIMTE, Department of Biological Sciences, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, Porto, Portugal.
| | - Joana Pinto
- UCIBIO/REQUIMTE, Department of Biological Sciences, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Ana Isabel Azevedo
- UCIBIO/REQUIMTE, Department of Biological Sciences, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Daniela Barros-Silva
- Cancer Biology & Epigenetics Group, Research Center (CI-IPOP) Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group, Research Center (CI-IPOP) Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
- Department of Pathology and Molecular Immunology-Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Rui Henrique
- Cancer Biology & Epigenetics Group, Research Center (CI-IPOP) Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
- Department of Pathology and Molecular Immunology-Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Maria de Lourdes Bastos
- UCIBIO/REQUIMTE, Department of Biological Sciences, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Paula Guedes de Pinho
- UCIBIO/REQUIMTE, Department of Biological Sciences, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, Porto, Portugal.
| | - Márcia Carvalho
- UCIBIO/REQUIMTE, Department of Biological Sciences, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, Porto, Portugal.
- UFP Energy, Environment and Health Research Unit (FP-ENAS), University Fernando Pessoa, Porto, Portugal.
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Bidarra D, Constâncio V, Barros-Silva D, Ramalho-Carvalho J, Moreira-Barbosa C, Antunes L, Maurício J, Oliveira J, Henrique R, Jerónimo C. Circulating MicroRNAs as Biomarkers for Prostate Cancer Detection and Metastasis Development Prediction. Front Oncol 2019; 9:900. [PMID: 31572685 PMCID: PMC6749029 DOI: 10.3389/fonc.2019.00900] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 08/30/2019] [Indexed: 12/24/2022] Open
Abstract
Prostate Cancer (PCa) overdiagnosis and overtreatment, as a consequence of the limited specificity of current detection and prognostication methods, remains a major challenge in clinical practice. Therefore, development and validation of new molecular biomarkers amenable of detecting clinically significant disease is crucial. MicroRNAs (miRNA) deregulation is common in cancer, constituting potential non-invasive biomarkers for PCa detection and prognostication. Herein, we evaluated the screening and prognostic biomarker potential of two onco-microRNAs (miR-182-5p and miR-375-3p) in liquid biopsies (plasma) of PCa patients with clinically localized disease undergoing curative-intent treatment. A first cohort of 98 PCa and 15 normal prostates were used to assess PCa-specificity of miR-182-5p in tissues. A cohort composed of PCa 252 patients and 52 asymptomatic controls allowed for assessment of diagnostic and prognostic value in plasmas. After RNA extraction from tissue and plasma samples, cDNA synthesis specific for miRNAs was performed followed by measurement of miR-182-5p and miR-375-3p relative expression by RT-qPCR, using U6 snRNA gene as reference. MiR-182-5p was significantly overexpressed in PCa tissues (p < 0.0001) and in plasma of PCa patients (p = 0.0020), compared to respective controls. Moreover, miR-182-5p expression identified PCa with AUC = 0.81 (95% CI: 0.725–0.892, p = 0.0001) in tissue and with 77% specificity and 99% NPV (AUC = 0.64, 95% CI: 0.561–0.709, p = 0.0021) in plasma. Both circulating miR-182-5p and miR-375-3p levels associated with more advanced pathologic stage and the former was significantly higher in patients that developed metastasis (p = 0.0145). Indeed, at the time of diagnosis, circulating miR-375-3p levels predicted which patients would develop metastasis, with almost 50% sensitivity, 76% specificity, and a NPV of 89% (AUC = 0.62, 95% CI: 0.529–0.713, p = 0.0149). We conclude that these two circulating miRNAs might be clinical useful as non-invasive biomarkers for detection and prediction of metastasis development at the diagnosis together with clinical variables used in routine practice.
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Affiliation(s)
- David Bidarra
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Master in Oncology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Porto, Portugal
| | - Vera Constâncio
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Master in Oncology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Porto, Portugal
| | - Daniela Barros-Silva
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - João Ramalho-Carvalho
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Catarina Moreira-Barbosa
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Luís Antunes
- Department of Epidemiology, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Joaquina Maurício
- Urology Clinic, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Jorge Oliveira
- Urology Clinic, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Porto, Portugal
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17
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Vieira-Silva TS, Monteiro-Reis S, Barros-Silva D, Ramalho-Carvalho J, Graça I, Carneiro I, Martins AT, Oliveira J, Antunes L, Hurtado-Bagès S, Buschbeck M, Henrique R, Jerónimo C. Histone variant MacroH2A1 is downregulated in prostate cancer and influences malignant cell phenotype. Cancer Cell Int 2019; 19:112. [PMID: 31164793 PMCID: PMC6489299 DOI: 10.1186/s12935-019-0835-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 04/23/2019] [Indexed: 12/11/2022] Open
Abstract
Background Prostate cancer (PCa), a major cause of cancer-related morbidity and mortality worldwide and mostly asymptomatic at earliest stages, is characterized by disruption of genetic and epigenetic balance. A better understanding of how those mechanisms orchestrate disease might improve diagnostic and prognostic tools, allowing for improvements in treatment efficacy. Replacement of canonical histones, an epigenetic mechanism, is highly conserved among species and altered expression of histones variants (e.g., MacroH2A1) has been associated with tumorigenesis. H2AFY gene encodes two isoforms of H2A histone variant MacroH2A1: MacroH2A1.1 and MacroH2A1.2. Specifically, MacroH2A1.1 isoform inhibits cell proliferation and promotes cellular differentiation. Because the contribution of this histone variant to carcinogenesis has been reported in several cancer types, but not for PCa, we aimed to investigate the contribution of MacroH2A1 for prostate carcinogenesis. Methods MacroH2A1, MacroH2A1.1 and MacroH2A1.2 isoforms and the corresponding splicing regulators transcript levels were evaluated by RT-qPCR, in a tissue cohort composed by PCa, prostatic intraepithelial neoplasia (PIN) and normal prostate cases. Knockdown for MacroH2A1 and MacroH2A1.1 was performed through lentiviral transduction in DU145 cells, and MacroH2A1.1 overexpression was achieved in LNCaP cells by plasmid transfection, followed by functional assays. Biological and/or experimental replicates were performed when necessary, and specific statistical tests were applied to perform data analysis. Results MacroH2A1.1 transcript levels were downregulated in PIN and primary PCa compared to normal prostate tissues. The same was found for QKI, a MacroH2A1.1’s splicing regulator. Moreover, lower MacroH2A1.1 and QKI expression levels associated with less differentiated tumors (Gleason score ≥ 7). Interestingly, MacroH2A1.1, but more impressively DDX17 (AUC = 0.93; p < 0.0001) and QKI (AUC = 0.94; p < 0.0001), accurately discriminated cancerous from noncancerous prostate tissues. Furthermore, in PCa cell lines, total MacroH2A1 knockdown augmented malignant features, whereas MacroH2A1.1 overexpression impressively attenuated the malignant phenotype. Conclusions Overall, our data, derived from primary PCa tissues and cell lines, anticipate a tumor suppressive role for MacroH2A1, particularly for the MacroH2A1.1 isoform, in prostate carcinogenesis. Electronic supplementary material The online version of this article (10.1186/s12935-019-0835-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tânia Soraia Vieira-Silva
- Cancer Biology & Epigenetics Group, Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Research Center-LAB 3, F Bdg., 1st Floor, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Sara Monteiro-Reis
- Cancer Biology & Epigenetics Group, Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Research Center-LAB 3, F Bdg., 1st Floor, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Daniela Barros-Silva
- Cancer Biology & Epigenetics Group, Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Research Center-LAB 3, F Bdg., 1st Floor, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - João Ramalho-Carvalho
- Cancer Biology & Epigenetics Group, Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Research Center-LAB 3, F Bdg., 1st Floor, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Inês Graça
- Cancer Biology & Epigenetics Group, Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Research Center-LAB 3, F Bdg., 1st Floor, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Isa Carneiro
- Cancer Biology & Epigenetics Group, Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Research Center-LAB 3, F Bdg., 1st Floor, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Ana Teresa Martins
- Cancer Biology & Epigenetics Group, Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Research Center-LAB 3, F Bdg., 1st Floor, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Jorge Oliveira
- Department of Urology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Luis Antunes
- Department of Epidemiology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Sarah Hurtado-Bagès
- 5Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Germans Trias i Pujol, Campus Can Ruti, 08916 Badalona, Spain.,Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Barcelona, Spain
| | - Marcus Buschbeck
- 5Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Germans Trias i Pujol, Campus Can Ruti, 08916 Badalona, Spain.,Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Barcelona, Spain
| | - Rui Henrique
- Cancer Biology & Epigenetics Group, Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Research Center-LAB 3, F Bdg., 1st Floor, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.,7Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group, Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Research Center-LAB 3, F Bdg., 1st Floor, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.,7Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
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18
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Constâncio V, Barros-Silva D, Jerónimo C, Henrique R. Known epigenetic biomarkers for prostate cancer detection and management: exploring the potential of blood-based liquid biopsies. Expert Rev Mol Diagn 2019; 19:367-375. [PMID: 30961397 DOI: 10.1080/14737159.2019.1604224] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Although prostate cancer (PCa) stands as an important cause of cancer-related deaths, a sizeable proportion of diagnosed cases are clinically insignificant. Hence, novel and more specific biomarkers to identify clinically significant PCa are needed. Liquid biopsies offer the potential to accurately identify cancer markers, including PCa. Epigenetic biomarkers such as cell-free DNA and circulating RNAs have emerged as minimally invasive cancer markers. Areas covered: Herein, we provide an overview of epigenetic biomarkers current state based on a comprehensive review of the relevant literature in blood-based liquid biopsies and challenges/limitations of this new and growing field of cancer biomarkers. Expert opinion: The epigenetic-based biomarkers characteristics make them attractive to the clinics and their minimally invasive assessment are a promising opportunity for PCa detection/management. The main limitations are the lack of robust validation studies and integrated approaches. Future studies would benefit from a change in focus to a 'selected PCa detection'.
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Affiliation(s)
- Vera Constâncio
- a Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP) , Portuguese Oncology Institute of Porto (IPO Porto) , Porto , Portugal
| | - Daniela Barros-Silva
- a Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP) , Portuguese Oncology Institute of Porto (IPO Porto) , Porto , Portugal
| | - Carmen Jerónimo
- a Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP) , Portuguese Oncology Institute of Porto (IPO Porto) , Porto , Portugal.,b Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS) , University of Porto , Porto , Portugal
| | - Rui Henrique
- a Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP) , Portuguese Oncology Institute of Porto (IPO Porto) , Porto , Portugal.,b Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS) , University of Porto , Porto , Portugal.,c Department of Pathology , Portuguese Oncology Institute of Porto (IPO Porto) , Porto , Portugal
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Vilela-Salgueiro B, Barros-Silva D, Lobo J, Costa AL, Guimarães R, Cantante M, Lopes P, Braga I, Oliveira J, Henrique R, Jerónimo C. Germ cell tumour subtypes display differential expression of microRNA371a-3p. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0338. [PMID: 29685967 DOI: 10.1098/rstb.2017.0338] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2018] [Indexed: 12/15/2022] Open
Abstract
Testicular germ cell tumours (TGCTs) are a heterogeneous group of neoplasms, mostly affecting young men. Curability rates are high and adequate treatment relies on careful and accurate pathological and clinical assessment. Indeed, TGCTs' histopathological subtyping is critical for adequate therapeutic decision. Considering the limitation of currently available serum biomarkers, novel candidates have been proposed, most notably miR-371a-3p, which outperformed classical serum markers, but no detailed information concerning TGCT subtype was available. Thus, we carried out evaluation of miR-371a-3p expression levels among TGCT subtypes using a consecutive cohort of tissue samples. MiR-371a-3p discriminated TGCTs from control tissues with high sensitivity and specificity (AUC = 0.99). Furthermore, seminomas displayed higher miR-371a-3p expression levels compared to non-seminomatous TGCTs, which also showed significant differences among them. Nonetheless, prepubertal TGCTs depicted lower miR-371a-3p expression levels than postpubertal TGCTs. Globally, miR-371a-3p expression levels decreased in parallel with progressive cell differentiation. We concluded that miR-371a-3p is TGCTs-specific and it might be clinically useful for early detection and disease monitoring.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.
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Affiliation(s)
- Bárbara Vilela-Salgueiro
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal
| | - Daniela Barros-Silva
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal.,Master in Oncology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira n.° 228, 4050-313, Porto, Portugal
| | - João Lobo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira n.° 228, 4050-313, Porto, Portugal
| | - Ana Laura Costa
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal.,Master in Oncology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira n.° 228, 4050-313, Porto, Portugal
| | - Rita Guimarães
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal
| | - Mariana Cantante
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal
| | - Paula Lopes
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal
| | - Isaac Braga
- Department of Urology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal
| | - Jorge Oliveira
- Department of Urology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira n.° 228, 4050-313, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de almeida, 4200-072, Porto, Portugal .,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira n.° 228, 4050-313, Porto, Portugal
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Guerreiro I, Barros-Silva D, Lopes P, Cunha A, Lobo J, Rodrigues A, Soares M, Antunes L, Henrique R, Jerónimo C. Correlative analysis of gene expression changes and PD-L1 immunoexpression in non-small cell lung cancer. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy493.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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21
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Moreira-Barbosa C, Barros-Silva D, Costa-Pinheiro P, Torres-Ferreira J, Constâncio V, Freitas R, Oliveira J, Antunes L, Henrique R, Jerónimo C. Comparing diagnostic and prognostic performance of two-gene promoter methylation panels in tissue biopsies and urines of prostate cancer patients. Clin Epigenetics 2018; 10:132. [PMID: 30373654 PMCID: PMC6206889 DOI: 10.1186/s13148-018-0564-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 10/10/2018] [Indexed: 12/15/2022] Open
Abstract
Background Prostate cancer (PCa) is one of the most common cancers among men worldwide. Current screening methods for PCa display limited sensitivity and specificity, not stratifying for disease aggressiveness. Hence, development and validation of new molecular markers is needed. Aberrant gene promoter methylation is common in PCa and has shown promise as clinical biomarker. Herein, we assessed and compared the diagnostic and prognostic performance of two-gene panel promoter methylation in the same sample sets. Methods Promoter methylation of panel #1 (singleplex-miR-34b/c and miR-193b) and panel #2 (multiplex-APC, GSTP1, and RARβ2) was evaluated using MethyLight methodology in two different cohorts [prostate biopsy (#1) and urine sediment (#2)]. Biomarkers’ diagnostic (validity estimates) and prognostic (disease-specific survival, disease-free survival, and progression-free survival) performance was assessed. Results Promoter methylation levels of both panels showed the highest levels in PCa samples in both cohorts. In tissue samples, methylation panel #1 and panel #2 detected PCa with AUC of 0.9775 and 1.0, respectively, whereas in urine samples, panel #2 demonstrated superior performance although a combination of miR-34b/c, miR-193b, APC, and RARβ2 disclosed the best results (AUC = 0.9817). Furthermore, higher mir-34b/c and panel #2 methylation independently predicted for shorter DSS. Furthermore, time-dependent ROC curves showed that both miR-34b/c and GSTP1 methylation levels identify with impressive performance patients that relapse up to 15 years after diagnosis (AUC = 0.751 and AUC = 0.765, respectively). Conclusions We concluded that quantitative gene panel promoter methylation might be a clinically useful tool for PCa non-invasive detection and risk stratification for disease aggressiveness in both tissue biopsies and urines. Electronic supplementary material The online version of this article (10.1186/s13148-018-0564-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Catarina Moreira-Barbosa
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Daniela Barros-Silva
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Pedro Costa-Pinheiro
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Jorge Torres-Ferreira
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Vera Constâncio
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Rui Freitas
- Department of Urology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Jorge Oliveira
- Department of Urology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Luís Antunes
- Department of Epidemiology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal. .,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal. .,Cancer Biology and Epigenetics Group - Research Center (LAB3), Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino Almeida, 4200-072, Porto, Portugal.
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22
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Barros-Silva D, Marques CJ, Henrique R, Jerónimo C. Profiling DNA Methylation Based on Next-Generation Sequencing Approaches: New Insights and Clinical Applications. Genes (Basel) 2018; 9:genes9090429. [PMID: 30142958 PMCID: PMC6162482 DOI: 10.3390/genes9090429] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 07/28/2018] [Accepted: 08/20/2018] [Indexed: 12/19/2022] Open
Abstract
DNA methylation is an epigenetic modification that plays a pivotal role in regulating gene expression and, consequently, influences a wide variety of biological processes and diseases. The advances in next-generation sequencing technologies allow for genome-wide profiling of methyl marks both at a single-nucleotide and at a single-cell resolution. These profiling approaches vary in many aspects, such as DNA input, resolution, coverage, and bioinformatics analysis. Thus, the selection of the most feasible method according with the project’s purpose requires in-depth knowledge of those techniques. Currently, high-throughput sequencing techniques are intensively used in epigenomics profiling, which ultimately aims to find novel biomarkers for detection, diagnosis prognosis, and prediction of response to therapy, as well as to discover new targets for personalized treatments. Here, we present, in brief, a portrayal of next-generation sequencing methodologies’ evolution for profiling DNA methylation, highlighting its potential for translational medicine and presenting significant findings in several diseases.
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Affiliation(s)
- Daniela Barros-Silva
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua António Bernardino Almeida, 4200-072 Porto, Portugal.
| | - C Joana Marques
- Genetics, Department of Pathology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal.
- I3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua António Bernardino Almeida, 4200-072 Porto, Portugal.
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal.
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS)-University of Porto, 4050-313 Porto, Portugal.
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Rua António Bernardino Almeida, 4200-072 Porto, Portugal.
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS)-University of Porto, 4050-313 Porto, Portugal.
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23
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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 2018; 9:167. [PMID: 29415999 PMCID: PMC5833437 DOI: 10.1038/s41419-017-0241-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 12/10/2017] [Accepted: 12/18/2017] [Indexed: 12/14/2022]
Abstract
Upregulation of MYC and miRNAs deregulation are common in prostate cancer (PCa). Overactive MYC may cause miRNAs’ expression deregulation through transcriptional and post-transcriptional mechanisms and epigenetic alterations are also involved in miRNAs dysregulation. Herein, we aimed to elucidate the role of regulatory network between MYC and miRNAs in prostate carcinogenesis. MYC expression was found upregulated in PCa cases and matched precursor lesions. MicroRNA’s microarray analysis of PCa samples with opposed MYC levels identified miRNAs significantly overexpressed in high-MYC PCa. However, validation of miR-27a-5p in primary prostate tissues disclosed downregulation in PCa, instead, correlating with aberrant promoter methylation. In a series of castration-resistant PCa (CRPC) cases, miR-27a-5p was upregulated, along with promoter hypomethylation. MYC and miR-27a-5p expression levels in LNCaP and PC3 cells mirrored those observed in hormone-naíve PCa and CRPC, respectively. ChIP analysis showed that miR-27a-5p expression is only regulated by c-Myc in the absence of aberrant promoter methylation. MiR-27a-5p knockdown in PC3 cells promoted cell growth, whereas miRNA forced expression in LNCaP and stable MYC-knockdown PC3 cells attenuated the malignant phenotype, suggesting a tumor suppressive role for miR-27a-5p. Furthermore, miR-27a-5p upregulation decreased EGFR/Akt1/mTOR signaling. We concluded that miR-27a-5p is positively regulated by MYC, and its silencing due to aberrant promoter methylation occurs early in prostate carcinogenesis, concomitantly with loss of MYC regulatory activity. Our results further suggest that along PCa progression, miR-27a-5p promoter becomes hypomethylated, allowing for MYC to resume its regulatory activity. However, the altered cellular context averts miR-27a-5p from successfully accomplishing its tumor suppressive function at this stage of disease.
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Affiliation(s)
- Daniela Barros-Silva
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Master in Oncology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Porto, Portugal
| | - Pedro Costa-Pinheiro
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Henrique Duarte
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Elsa Joana Sousa
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | | | - Inês Graça
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Isa Carneiro
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Master in Oncology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Porto, Portugal
| | - Ana Teresa Martins
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Master in Oncology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Porto, Portugal
| | - Jorge Oliveira
- Department of Urology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - André L Carvalho
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Márcia M Marques
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Barretos School of Health Sciences, Barretos, São Paulo, Brazil
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS)-University of Porto, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal. .,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS)-University of Porto, Porto, Portugal.
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