title: High-throughput small molecule screen identifies inhibitors of aberrant chromatin accessibility.
abstract: Mutations in chromatin-modifying proteins and transcription factors are commonly associated with a wide variety of cancers. Through gain- or loss-of-function, these mutations may result in characteristic alterations of accessible chromatin, indicative of shifts in the landscape of regulatory elements genome-wide. The identification of compounds that reverse a specific chromatin signature could lead to chemical probes or potential therapies. To explore whether chromatin accessibility could serve as a platform for small molecule screening, we adapted formaldehyde-assisted isolation of regulatory elements (FAIRE), a chemical method to enrich for nucleosome-depleted genomic regions, as a high-throughput, automated assay. After demonstrating the validity and robustness of this approach, we applied this method to screen an epigenetically targeted small molecule library by evaluating regions of aberrant nucleosome depletion mediated by EWSR1-FLI1, the chimeric transcription factor critical for the bone and soft tissue tumor Ewing sarcoma. As a class, histone deacetylase inhibitors were greatly overrepresented among active compounds. These compounds resulted in diminished accessibility at targeted sites by disrupting transcription of EWSR1-FLI1. Capitalizing on precise differences in chromatin accessibility for drug discovery efforts offers significant advantages because it does not depend on the a priori selection of a single molecular target and may detect novel biologically relevant pathways.
authors.affiliation: Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27302; Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27302;
authors.forename: Samantha G
authors.initials: SG
authors.lastname: Pattenden
authors.affiliation: Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599; Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599; Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599;
authors.forename: Jeremy M
authors.initials: JM
authors.lastname: Simon
authors.affiliation: Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599; Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599;
authors.forename: Aminah
authors.initials: A
authors.lastname: Wali
authors.affiliation: Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27302; Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27302;
authors.forename: Chatura N
authors.initials: CN
authors.lastname: Jayakody
authors.affiliation: Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599; Department of Pediatrics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599;
authors.forename: Jacob
authors.initials: J
authors.lastname: Troutman
authors.affiliation: Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599;
authors.forename: Andrew W
authors.initials: AW
authors.lastname: McFadden
authors.affiliation: Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599; Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599;
authors.forename: Joshua
authors.initials: J
authors.lastname: Wooten
authors.affiliation: Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27302; Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27302;
authors.forename: Cameron C
authors.initials: CC
authors.lastname: Wood
authors.affiliation: Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27302; Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27302;
authors.forename: Stephen V
authors.initials: SV
authors.lastname: Frye
authors.affiliation: Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27302; Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27302;
authors.forename: William P
authors.initials: WP
authors.lastname: Janzen
authors.affiliation: Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599; Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599; Department of Pediatrics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599; Carolina Center for Genome Sciences, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 ian_davis@med.unc.edu.
authors.forename: Ian J
authors.initials: IJ
authors.lastname: Davis
mesh_terms: D000970:Antineoplastic Agents / Q000302:isolation & purification / Q000494:pharmacology; D001859:Bone Neoplasms / Q000473:pathology; D045744:Cell Line, Tumor; D002843:Chromatin / Q000187:drug effects* / Q000648:ultrastructure; D015195:Drug Design; D004353:Drug Evaluation, Preclinical; D057166:High-Throughput Screening Assays / Q000379:methods*; D056572:Histone Deacetylase Inhibitors / Q000302:isolation & purification / Q000494:pharmacology; D006657:Histones / Q000378:metabolism; D061307:Human Umbilical Vein Endothelial Cells; D006801:Humans; D006877:Hydroxamic Acids / Q000494:pharmacology; D007211:Indoles / Q000494:pharmacology; D058990:Molecular Targeted Therapy; D009707:Nucleosomes / Q000648:ultrastructure; D015514:Oncogene Proteins, Fusion / Q000037:antagonists & inhibitors* / Q000235:genetics; D000077767:Panobinostat; D010654:Phenylbutyrates / Q000494:pharmacology; D012512:Sarcoma, Ewing / Q000473:pathology; D054852:Small Molecule Libraries; D014158:Transcription, Genetic / Q000187:drug effects*; D000077337:Vorinostat
chemical_list: D000970:Antineoplastic Agents; D002843:Chromatin; C576197:EWSR1-FLI1 fusion protein, human; D056572:Histone Deacetylase Inhibitors; D006657:Histones; D006877:Hydroxamic Acids; D007211:Indoles; D009707:Nucleosomes; C529674:OSU-HDAC42 compound; D015514:Oncogene Proteins, Fusion; D010654:Phenylbutyrates; D054852:Small Molecule Libraries; D000077337:Vorinostat; D000077767:Panobinostat
keywords: Ewing sarcoma; FAIRE; chromatin; high throughput screening; histone deacetylase inhibitor