title: Loss of tumor suppressor KDM6A amplifies PRC2-regulated transcriptional repression in bladder cancer and can be targeted through inhibition of EZH2.
abstract: Trithorax-like group complex containing KDM6A acts antagonistically to Polycomb-repressive complex 2 (PRC2) containing EZH2 in maintaining the dynamics of the repression and activation of gene expression through H3K27 methylation. In urothelial bladder carcinoma,KDM6A(a H3K27 demethylase) is frequently mutated, but its functional consequences and therapeutic targetability remain unknown. About 70% ofKDM6Amutations resulted in a total loss of expression and a consequent loss of demethylase function in this cancer type. Further transcriptome analysis found multiple deregulated pathways, especially PRC2/EZH2, inKDM6A-mutated urothelial bladder carcinoma. Chromatin immunoprecipitation sequencing analysis revealed enrichment of H3K27me3 at specific loci inKDM6A-null cells, including PRC2/EZH2 and their downstream targets. Consequently, we targeted EZH2 (an H3K27 methylase) and demonstrated thatKDM6A-null urothelial bladder carcinoma cell lines were sensitive to EZH2 inhibition. Loss- and gain-of-function assays confirmed that cells with loss of KDM6A are vulnerable to EZH2. IGFBP3, a direct KDM6A/EZH2/H3K27me3 target, was up-regulated by EZH2 inhibition and contributed to the observed EZH2-dependent growth suppression inKDM6A-null cell lines. EZH2 inhibition delayed tumor onset inKDM6A-null cells and caused regression ofKDM6A-null bladder tumors in both patient-derived and cell line xenograft models. In summary, our study demonstrates that inactivating mutations ofKDM6A, which are common in urothelial bladder carcinoma, are potentially targetable by inhibiting EZH2.
authors.affiliation: Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.|Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.|NUS Graduate School for Integrative Sciences and Engineering, 28 Medical Drive, Singapore 117456, Singapore.
authors.forename: Lian Dee
authors.identifier: 0000-0001-5838-2804
authors.initials: LD
authors.lastname: Ler
authors.affiliation: Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857, Singapore.|Centre for Computational Biology, Duke-NUS Medical School, Singapore 169857, Singapore.
authors.forename: Sujoy
authors.identifier: 0000-0002-7601-165X
authors.initials: S
authors.lastname: Ghosh
authors.affiliation: Centre for Computational Biology, Duke-NUS Medical School, Singapore 169857, Singapore.
authors.forename: Xiaoran
authors.initials: X
authors.lastname: Chai
authors.affiliation: Department of Pathology, Singapore General Hospital, Singapore, Singapore.
authors.forename: Aye Aye
authors.identifier: 0000-0002-9116-2325
authors.initials: AA
authors.lastname: Thike
authors.affiliation: Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.|Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.
authors.forename: Hong Lee
authors.initials: HL
authors.lastname: Heng
authors.affiliation: Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.|Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.
authors.forename: Ee Yan
authors.identifier: 0000-0001-8614-1979
authors.initials: EY
authors.lastname: Siew
authors.affiliation: Cancer Science Institute of Singapore, National University of Singapore, Centre for Life Sciences, Singapore 117456, Singapore.
authors.forename: Sucharita
authors.initials: S
authors.lastname: Dey
authors.affiliation: Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.|Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.
authors.forename: Liang Kai
authors.identifier: 0000-0002-0687-3510
authors.initials: LK
authors.lastname: Koh
authors.affiliation: Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.|Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.
authors.forename: Jing Quan
authors.identifier: 0000-0003-3732-8707
authors.initials: JQ
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authors.affiliation: Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.|Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.
authors.forename: Weng Khong
authors.identifier: 0000-0003-4391-1130
authors.initials: WK
authors.lastname: Lim
authors.affiliation: Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.|Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.
authors.forename: Swe Swe
authors.initials: SS
authors.lastname: Myint
authors.affiliation: Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.|Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.
authors.forename: Jia Liang
authors.initials: JL
authors.lastname: Loh
authors.affiliation: Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.|Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.
authors.forename: Pauline
authors.identifier: 0000-0001-9367-0000
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authors.affiliation: Department of Pathology, Singapore General Hospital, Singapore, Singapore.
authors.forename: Xin Xiu
authors.identifier: 0000-0003-0583-2319
authors.initials: XX
authors.lastname: Sam
authors.affiliation: Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.|Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.
authors.forename: Dachuan
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authors.affiliation: Department of Pathology, Singapore General Hospital, Singapore, Singapore.
authors.forename: Tony
authors.initials: T
authors.lastname: Lim
authors.affiliation: Department of Pathology, Singapore General Hospital, Singapore, Singapore.
authors.forename: Puay Hoon
authors.identifier: 0000-0002-1052-8605
authors.initials: PH
authors.lastname: Tan
authors.affiliation: Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.|Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.
authors.forename: Sanjanaa
authors.initials: S
authors.lastname: Nagarajan
authors.affiliation: Department of Urology, Singapore General Hospital, Outram Road, Singapore 169608, Singapore.
authors.forename: Christopher Wai Sam
authors.initials: CW
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authors.affiliation: Department of Urology, Singapore General Hospital, Outram Road, Singapore 169608, Singapore.
authors.forename: Henry
authors.initials: H
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authors.affiliation: Department of Urology, Singapore General Hospital, Outram Road, Singapore 169608, Singapore.
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authors.identifier: 0000-0002-3073-5396
authors.initials: LG
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authors.affiliation: Department of Urology, Singapore General Hospital, Outram Road, Singapore 169608, Singapore.
authors.forename: John
authors.initials: J
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authors.affiliation: Division of Urooncology, Department of Urology, Chang Gung University and Memorial Hospital at LinKou, TaoYuan, Taiwan.
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authors.identifier: 0000-0001-8245-4302
authors.initials: PH
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authors.affiliation: Division of Urooncology, Department of Urology, Chang Gung University and Memorial Hospital at LinKou, TaoYuan, Taiwan.
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authors.identifier: 0000-0001-6154-1220
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authors.affiliation: Division of Urooncology, Department of Urology, Chang Gung University and Memorial Hospital at LinKou, TaoYuan, Taiwan.
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authors.initials: YH
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authors.affiliation: Department of Chemical Engineering and Biotechnology and Graduate Institute of Biochemical and Biomedical Engineering, National Taipei University of Technology, Taipei, Taiwan.
authors.forename: Wen-Hui
authors.identifier: 0000-0002-6021-0451
authors.initials: WH
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authors.affiliation: Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.|Centre for Computational Biology, Duke-NUS Medical School, Singapore 169857, Singapore.
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authors.identifier: 0000-0002-4288-0056
authors.initials: SG
authors.lastname: Rozen
authors.affiliation: Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.|Cancer Science Institute of Singapore, National University of Singapore, Centre for Life Sciences, Singapore 117456, Singapore.|Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore 169610, Singapore.|Genome Institute of Singapore, 60 Biopolis Street Genome, Singapore 138672, Singapore.
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authors.affiliation: Cancer Epigenetics Discovery Performance Unit, Oncology R&D, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA.
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authors.identifier: 0000-0002-3735-6401
authors.initials: CL
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authors.affiliation: Division of Urooncology, Department of Urology, Chang Gung University and Memorial Hospital at LinKou, TaoYuan, Taiwan. teh.bin.tean@singhealth.com.sg songling.poon@gmail.com michael.t.mccabe@gsk.com jacobpang@adm.cgmh.org.tw.
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authors.initials: ST
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authors.affiliation: Cancer Epigenetics Discovery Performance Unit, Oncology R&D, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA. teh.bin.tean@singhealth.com.sg songling.poon@gmail.com michael.t.mccabe@gsk.com jacobpang@adm.cgmh.org.tw.
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authors.identifier: 0000-0001-5715-9563
authors.initials: MT
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authors.affiliation: Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore. teh.bin.tean@singhealth.com.sg songling.poon@gmail.com michael.t.mccabe@gsk.com jacobpang@adm.cgmh.org.tw.|Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.
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authors.affiliation: Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore. teh.bin.tean@singhealth.com.sg songling.poon@gmail.com michael.t.mccabe@gsk.com jacobpang@adm.cgmh.org.tw.|Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.|Cancer Science Institute of Singapore, National University of Singapore, Centre for Life Sciences, Singapore 117456, Singapore.|Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, #07-18, Singapore 138673, Singapore.
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mesh_terms: D000818:Animals; D045744:Cell Line, Tumor; D049109:Cell Proliferation / Q000235:genetics; D000071221:Enhancer of Zeste Homolog 2 Protein / Q000037:antagonists & inhibitors* / Q000378:metabolism; D015972:Gene Expression Regulation, Neoplastic; D056466:Histone Demethylases / Q000378:metabolism*; D018972:Insulin-Like Growth Factor Binding Protein 3 / Q000378:metabolism; D008819:Mice, Nude; D008954:Models, Biological; D009361:Neoplasm Invasiveness; D009687:Nuclear Proteins / Q000378:metabolism*; D063151:Polycomb Repressive Complex 2 / Q000378:metabolism*; D014158:Transcription, Genetic; D001749:Urinary Bladder Neoplasms / Q000235:genetics* / Q000473:pathology; D019459:Urothelium / Q000473:pathology
chemical_list: C515497:IGFBP3 protein, human; D018972:Insulin-Like Growth Factor Binding Protein 3; D009687:Nuclear Proteins; D056466:Histone Demethylases; C523998:KDM6A protein, human; C498409:EZH2 protein, human; D000071221:Enhancer of Zeste Homolog 2 Protein; D063151:Polycomb Repressive Complex 2