Epigenome-Wide DNA Methylation Profiling Identifies Differential Methylation Biomarkers in High-Grade Bladder Cancer.
Epigenetic changes, including CpG island hypermethylation, occur frequently in bladder cancer (BC) and may be exploited for BC detection and distinction between high-grade (HG) and low-grade (LG) disease. Genome-wide methylation analysis was performed using Agilent Human CpG Island Microarrays to determine epigenetic differences between LG and HG cases. Pathway enrichment analysis and functional annotation determined that the most frequently methylated pathways in HG BC were enriched for anterior/posterior pattern specification, embryonic skeletal system development, neuron fate commitment, DNA binding, and transcription factor activity. We identified 990 probes comprising a 32-gene panel that completely distinguished LG from HG based on methylation. Selected genes from this panel, EOMES, GP5, PAX6, TCF4, and ZSCAN12, were selected for quantitative polymerase chain reaction-based validation by MethyLight in an independent series (n=84) of normal bladder samples and LG and HG cases. GP5 and ZSCAN12, two novel methylated genes in BC, were significantly hypermethylated in HG versus LG BC (P≤.03). We validated our data in a second independent cohort of LG and HG BC cases (n=42) from The Cancer Genome Atlas (TCGA). Probes representing our 32-gene panel were significantly differentially methylated in LG versus HG tumors (P≤.04). These results indicate the ability to distinguish normal tissue from cancer, as well as LG from HG, based on methylation and reveal important pathways dysregulated in HG BC. Our findings were corroborated using publicly available data sets from TCGA. Ultimately, the creation of a methylation panel, including GP5 and ZSCAN12, able to distinguish between disease phenotypes will improve disease management and patient outcomes.
Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 60 Murray St., Toronto, Ontario, Canada, M5T 3L9; Department of Laboratory Medicine and Pathobiology, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada, M5S 1A1. Electronic address: olkhov@lunenfeld.ca.
Ekaterina
E
Olkhov-Mitsel
Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 60 Murray St., Toronto, Ontario, Canada, M5T 3L9; Department of Laboratory Medicine and Pathobiology, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada, M5S 1A1. Electronic address: savio@lunenfeld.ca.
Andrea J
AJ
Savio
Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 60 Murray St., Toronto, Ontario, Canada, M5T 3L9; Department of Laboratory Medicine and Pathobiology, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada, M5S 1A1. Electronic address: kenjkron@gmail.com.
Ken J
KJ
Kron
Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 60 Murray St., Toronto, Ontario, Canada, M5T 3L9. Electronic address: pethev@aol.com.
Vaijayanti V
VV
Pethe
Department of Surgery and Surgical Oncology, Division of Urology, The Princess Margaret Cancer Centre, University Health Network, 610 University Ave., Toronto, Ontario, Canada, M5G 2M9. Electronic address: thomas.hermanns@usz.ch.
Thomas
T
Hermanns
Department of Surgery and Surgical Oncology, Division of Urology, The Princess Margaret Cancer Centre, University Health Network, 610 University Ave., Toronto, Ontario, Canada, M5G 2M9. Electronic address: neil.fleshner@uhn.ca.
Neil E
NE
Fleshner
Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 60 Murray St., Toronto, Ontario, Canada, M5T 3L9; Department of Surgery and Surgical Oncology, Division of Urology, The Princess Margaret Cancer Centre, University Health Network, 610 University Ave., Toronto, Ontario, Canada, M5G 2M9. Electronic address: basvanrhijn@hotmail.com.
Bas W
BW
van Rhijn
Department of Laboratory Medicine and Pathobiology, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada, M5S 1A1; Department of Pathology, University Health Network, 200 Elizabeth St., Toronto, Ontario, Canada, M5G 2C4. Electronic address: theodorus.vanderkwast@uhn.ca.
Theodorus H
TH
van der Kwast
Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 60 Murray St., Toronto, Ontario, Canada, M5T 3L9; Department of Surgery, Division of Urology, Sinai Health System, 600 University Ave., Toronto, Ontario, Canada, M5G 1X5. Electronic address: azlotta@mtsinai.on.ca.
Alexandre R
AR
Zlotta
Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 60 Murray St., Toronto, Ontario, Canada, M5T 3L9; Department of Laboratory Medicine and Pathobiology, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada, M5S 1A1; Department of Pathology, University Health Network, 200 Elizabeth St., Toronto, Ontario, Canada, M5G 2C4. Electronic address: bapat@lunenfeld.ca.
Bharati
B
Bapat