DNA methylation in Uropathology

Transcription

1 DNA methylation in Uropathology Clinical significance Rui Henrique, MD, PhD Director, Department of Pathology Difrector, Department of Education Senior Researcher, Cancer Biology and Epigenetics Group Portuguese Oncology Institute of Porto & Guest Full Professor of Pathology and Oncobiology Department of Pathology and Molecular Immunology Institute of Biomedical Sciences Abel Salazar University of Porto 1 Porto, Portugal

2 DNA methylation in Uropathology Clinical significance Conflicts of interest statement For the purposes of this presentation and its content, I declare that I have no conflicts of interest 2

3 DNA methylation in Uropathology Clinical significance Outline Epigenetic-based biomarkers Prostate cancer: early detection and risk stratification Urothelial carcinoma: upper and lower tract cancer detection Renal cell carcinoma: assessing prognosis Testicular cancer: TGCT subtype discrimination and risk assessment 3

4 DNA methylation in Uropathology Is there a need for new biomarkers? Urological tumors are curable if detected at its earliest stages (organ-confined) Advanced disease (locally or sistemically) is associated with significant morbidity and mortality Cancer Site 5-year relative survival by stage at diagnosis (%) Localized Regional Distant Prostate Bladder Kidney US National Cancer Institute 4

5 DNA methylation in Uropathology Is there a need for new biomarkers? However, early stage disease is mostly clinically silent, requiring the use of tests which, ideally, should be able to detect cancer-specific alterations The distinction of benign from malignant lesions remains challenging in a significant proportion of cases There is a need for molecular markers Epigenetic-based markers 5

6 Epigenetics Regulatory mechanisms not directly involving the underlying coding sequence, displaying a flexible and reversible event with high impact on tumorigenesis (Baylin & Jones, 2011). 6

7 DNA methylation and cancer CpG dinucleotides CpG islands Clusters of CpG dinucleotides in small stretches of DNA (0.5-4 kb in length), usually > 60% GC content. According to computer prediction by bioinformatics, there are at least 20,000 CpG islands: ~ 60 % in promoter regions ~ 30 % in coding sequences ~ 10 % in other regions 7 GONZALGO et al. J UROL, 2003

8 Epigenetic-based cancer biomarkers Advantages of epigenetic-based biomarkers They often precede the emergence of the malignant phenotype early cancer detection They may be detected in clinical samples, including those obtained by exfoliative cytology, endoscopic brush techniques, and biopsy, as well as urine, saliva, feces, plasma and sputum non- or minimally invasive molecular detection They may detect cancer relapse before it manifests with clinical symptoms or on imaging during routine patient follow-up. They may predict response to specific anti-cancer drugs 8

9 DNA methylation-based biomarkers for urological cancer

10 10 DNA methylation in prostate cancer Early detection and risk stratification

11 11 DNA methylation in prostate cancer Early detection and risk stratification

12 DNA methylation in prostate cancer Early detection and risk stratification Multigene methylation analysis enhances the rate of cancer detection, keeping high specificity and PPV, and increasing the NPV of the assay. 12

13 DNA methylation in prostate cancer Early detection and risk stratification Methylation assay: GSTP1, APC & RARB2 GS 7 No PCa The ProCaM assay displays higher predictive accuracy than currently used parameters to decide a prostate biopsy and identifies a larger number of cases with high Gleason score ( 7) 13

14 DNA methylation in prostate cancer Early detection and risk stratification Methylation assay: GSTP1 & APC 14

15 DNA methylation in prostate cancer Early detection and risk stratification Methylation assay: GSTP1, APC & RASSF1A ConfirmMDx 15

16 DNA methylation in prostate cancer Early detection and risk stratification Promoter methylation of micrornas for detection and prognostication of prostate cancer 16 Human Methylation 450 BeadChip results

17 DNA methylation in prostate cancer Early detection and risk stratification MiR-193b me outperforms other reported methylation biomarkers, including GSTP1, RARβ2 and APC (AUC= ) (without prostatic massage) and FDA-approved biomarkers: serum PSA (AUC= ), prostate health index (AUC= ) and urinary PCA3 (AUC= ). 17 Torres-Ferreira & Ramalho-Carvalho et al. Mol Cancer, 2017

18 DNA methylation in prostate cancer Early detection and risk stratification mir and mir-34b/c high methylation levels independently associate with worse outcome 18 Torres-Ferreira & Ramalho-Carvalho et al. Mol Cancer, 2017

19 Epigenetic biomarkers for prostate cancer management - 19

20 DNA methylation in urothelial carcinoma Detection of lower and upper tract tumors Aims Validate mir-129-2me and mir-663ame as malignancy biomarkers in large series of UC, encompassing BUC and UTUC tissues Assess the performance in detecting UC in voided urine samples 20

21 21 Padrão et al, Br J Cancer 2017

22 DNA methylation in urothelial carcinoma Detection of lower and upper tract tumors Tissue Urine mir-129-2me and mir-663ame accurately identifies urothelial malignancy in urine samples This panel might be useful for complementing other epigenetic biomarkers for noninvasive detection and/or monitoring of UC patients. 22 Padrão et al. Br J Cancer 2017

23 DNA methylation in renal cell carcinoma Biomarkers for prognosis MicroRNA-30a and renal cancer Critical role in autophagy (inhibition of the process) interfering with the efectiveness of sorafenib in RCC treatment (Zheng et al., 2015). mirna-30a is significantly downregulated in RCC tissues compared to adjacent normal kidney tissues (Zheng et al., 2015). Low expression levels associate with advanced TNM stage, high pathologic grade and shorter overall survival in ccrcc patients (Wang et al., 2017). Metastatic ccrccs disclose lower mirna-30a expression compared to non-metastatic ccrccs, correlating with worse survival (Heinzelmann et al., 2011). 23

24 DNA methylation in renal cell carcinoma Biomarkers for prognosis mir-30a promoter methylation is significantly higher in ccrcc, correlating inversely with expression mir-30a promoter methylation accurately discriminates ccrcc from normal renal tissue 24 Barros-Silva D et al., manuscript in preparation

25 DNA methylation in renal cell carcinoma Biomarkers for prognosis Higher mir-30a promoter methylation and lower expression levels associate with worse disease-free and disease-specific survival, in tissue samples 25 Barros-Silva D et al., manuscript in preparation

26 DNA methylation in renal cell carcinoma Biomarkers for prognosis Patients with ccrcc disclose higher mir-30a promoter methylation levels compared to controls, in urine Patients with metastatic ccrcc at diagnosis or which develop metastatic disease, display higher mir-30a promoter methylation levels than patients without metastasis, in urine 26 Barros-Silva D et al., manuscript in preparation

27 DNA methylation in renal cell carcinoma Biomarkers for prognosis Higher mir-30a promoter methylation levels in urine of ccrcc patients associates with worse metastasis-free survival 27 Barros-Silva D et al., manuscript in preparation

28 DNA methylation in TGCT Subtype discrimination and risk stratification 11 28

29 DNA methylation in TGCT Subtype discrimination and risk stratification Evaluate a panel of promoter methylation of five gene in TGCT subtypes and assess their potential as biomarkers for subtype discrimination, as well as identify differences among TGCT subtypes. Can gene promoter methylation: CRIPTO HOXA9 MGMT RASSF1A SCGB3A1 Distinguish TGCT from normal testicular tissue? Discriminate among TGCT subtypes? Associate with prognosis? Costa et al., Epigenomics (in press)

30 DNA methylation in TGCT Subtype discrimination and risk stratification Patients & Tissue Samples HISTOLOGIC TYPE NUMBER OF CASES Pure Seminoma 76 Pure Embryonal Carcinoma 10 Pure Postpubertal-Type Yolk- Sac Tumor Pure Choriocarcioma 0 Pure Postpubertal-Type Teratoma 4 Mixed Germ Cell Tumors 56 Prepubertal-Type Yolk-Sac Tumor 4 Prepubertal-Type Teratoma 11 0 Total: 161 TGCT samples Period: Testicular tissues from patients without TGCT: 16 Testicular inflammatory disease Benign pathology Mixed SE 19 Mixed Embryonal Carcinoma 42 Mixed Postpubertal-Type Yolk-Sac Tumor 36 Mixed Choriocarcinoma 14 Mixed Postpubertal-Type Teratoma 37 Total: 238 components samples of GCNISrelated TGCT 30 Costa et al., Epigenomics (in press)

31 DNA methylation in TGCT Subtype discrimination and risk stratification CRIPTO, HOXA9, MGMT and SCGB3A1 methylation levels are significantly higher in GCNIS-related TGCT components compared to controls. 31 Costa et al., Epigenomics (in press)

32 DNA methylation in TGCT Subtype discrimination and risk stratification Specific gene methylation panels discriminate NST from controls (CRIPTO/HOXA9/SCGB3A1) or from SE (HOXA9/RASSF1A) 32 Costa et al., Epigenomics (in press)

33 DNA methylation in TGCT Subtype discrimination and risk stratification CRIPTO, MGMT and RASSF1A methylation levels are significantly higher in SE as component of mixed TGCT than in pure SE MGMT methylation levels are significantly higher in EmbrCa as component of mixed TGCT than in pure EmbrCa 33 Costa et al., Epigenomics (in press)

34 DNA methylation in TGCT Subtype discrimination and risk stratification HOXA9, RASSF1A and SCGB3A1 display significantly higher promoter methylation levels in stage III disease HOXA9 and SCGB3A1 methylation levels were significantly higher in poor prognosis group (IGCCCG Classification) 34 Costa et al., Epigenomics (in press)

35 35 Methylation in Uropathology Clinical significance

36 Acknowledgements Portuguese Oncology Institute of Porto Cancer Biology & Epigenetics Group Research Centre Department of Pathology Department of Urology Department of Epidemiology University of Minho School of Medicine Life and Health Sciences Research Institute ICVS/3B s EpiDiaCan Johns Hopkins University Head & Neck Cancer Research Division The Norwegian Radium Hospital Department of Molecular Oncology Centre for Cancer Biomedicine IDIBELL Programa d'epigenètica i Biologia del Càncer 36