title: Chem-seq permits identification of genomic targets of drugs against androgen receptor regulation selected by functional phenotypic screens.
abstract: Understanding the mechanisms by which compounds discovered using cell-based phenotypic screening strategies might exert their effects would be highly augmented by new approaches exploring their potential interactions with the genome. For example, altered androgen receptor (AR) transcriptional programs, including castration resistance and subsequent chromosomal translocations, play key roles in prostate cancer pathological progression, making the quest for identification of new therapeutic agents and an understanding of their actions a continued priority. Here we report an approach that has permitted us to uncover the sites and mechanisms of action of a drug, referred to as "SD70," initially identified by phenotypic screening for inhibitors of ligand and genotoxic stress-induced translocations in prostate cancer cells. Based on synthesis of a derivatized form of SD70 that permits its application for a ChIP-sequencing-like approach, referred to as "Chem-seq," we were next able to efficiently map the genome-wide binding locations of this small molecule, revealing that it largely colocalized with AR on regulatory enhancers. Based on these observations, we performed the appropriate global analyses to ascertain that SD70 inhibits the androgen-dependent AR program, and prostate cancer cell growth, acting, at least in part, by functionally inhibiting the Jumonji domain-containing demethylase, KDM4C. Global location of candidate drugs represents a powerful strategy for new drug development by mapping genome-wide location of small molecules, a powerful adjunct to contemporary drug development strategies.
authors.affiliation: Howard Hughes Medical Institute,Department of Medicine, School of Medicine.
authors.forename: Chunyu
authors.initials: C
authors.lastname: Jin
authors.affiliation: Howard Hughes Medical Institute,Department of Medicine, School of Medicine.
authors.forename: Liuqing
authors.initials: L
authors.lastname: Yang
authors.affiliation: Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158;Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158; and.
authors.forename: Min
authors.initials: M
authors.lastname: Xie
authors.affiliation: Howard Hughes Medical Institute,Department of Medicine, School of Medicine.
authors.forename: Chunru
authors.initials: C
authors.lastname: Lin
authors.affiliation: Howard Hughes Medical Institute,Department of Medicine, School of Medicine,Bioinformatics and Systems Biology Graduate Program, and.
authors.forename: Daria
authors.initials: D
authors.lastname: Merkurjev
authors.affiliation: Department of Urology, School of Medicine, University of California, Davis, Sacramento, CA 95817.
authors.forename: Joy C
authors.initials: JC
authors.lastname: Yang
authors.affiliation: Howard Hughes Medical Institute,Department of Medicine, School of Medicine.
authors.forename: Bogdan
authors.initials: B
authors.lastname: Tanasa
authors.affiliation: Howard Hughes Medical Institute,Department of Medicine, School of Medicine,Department/School of Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093;
authors.forename: Soohwan
authors.initials: S
authors.lastname: Oh
authors.affiliation: Howard Hughes Medical Institute,Department of Medicine, School of Medicine.
authors.forename: Jie
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Howard Hughes Medical Institute,Department of Medicine, School of Medicine.
authors.forename: Kenneth A
authors.initials: KA
authors.lastname: Ohgi
authors.affiliation: Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158;Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158; and.
authors.forename: Hongyan
authors.initials: H
authors.lastname: Zhou
authors.affiliation: Howard Hughes Medical Institute,Department of Medicine, School of Medicine.
authors.forename: Wenbo
authors.initials: W
authors.lastname: Li
authors.affiliation: Department of Urology, School of Medicine, University of California, Davis, Sacramento, CA 95817.
authors.forename: Christopher P
authors.initials: CP
authors.lastname: Evans
authors.affiliation: Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158;Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158; and mrosenfeld@ucsd.edu sheng.ding@gladstone.ucsf.edu.
authors.forename: Sheng
authors.initials: S
authors.lastname: Ding
authors.affiliation: Howard Hughes Medical Institute,Department of Medicine, School of Medicine, mrosenfeld@ucsd.edu sheng.ding@gladstone.ucsf.edu.
authors.forename: Michael G
authors.initials: MG
authors.lastname: Rosenfeld
mesh_terms: D059002:Androgen Receptor Antagonists / Q000494:pharmacology*; D000818:Animals; D000970:Antineoplastic Agents; D045744:Cell Line, Tumor; D004252:DNA Mutational Analysis / Q000379:methods; D016503:Drug Delivery Systems / Q000379:methods*; D006801:Humans; D008297:Male; D051379:Mice; D009363:Neoplasm Proteins / Q000235:genetics* / Q000378:metabolism; D011471:Prostatic Neoplasms / Q000188:drug therapy / Q000235:genetics* / Q000378:metabolism; D011944:Receptors, Androgen / Q000235:genetics* / Q000378:metabolism; D014178:Translocation, Genetic; D023041:Xenograft Model Antitumor Assays / Q000379:methods*
chemical_list: D059002:Androgen Receptor Antagonists; D000970:Antineoplastic Agents; D009363:Neoplasm Proteins; D011944:Receptors, Androgen
keywords: histone demethylase; transcription