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Series GSE150955 Query DataSets for GSE150955
Status Public on Dec 02, 2020
Title ALC1 and PARP activities coordinate chromatin accessibility and viability in homologous recombination deficient cells (ATAC-seq)
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The response to Poly (ADP-ribose) polymerase inhibitors (PARPi) is dictated by homologous recombination (HR) DNA repair mechanisms and the abundance of lesions that trap PARP enzymes on chromatin. It remains unclear, however, if the established role of PARP in promoting chromatin accessibility impacts viability in these settings. Using a CRISPR based screen, we identify the PAR-binding Snf2-like ATPase, ALC1 as a key determinant of PARPi toxicity in HR-deficient cells. ALC1 loss reduced viability of BRCA mutant cells and enhanced their sensitivity to PARPi by up to 250-fold, while overcoming several known resistance mechanisms. ALC1 loss was not epistatic to other repair pathways that execute the PARPi response. Instead, ALC1 deficiency reduced chromatin accessibility concomitant with a decrease in the association of repair factors. This resulted in an accumulation of replication associated DNA damage and a reliance on HR. These findings establish PAR-dependent chromatin remodeling as a mechanistically distinct aspect of PARPi responses, implicating ALC1 inhibition as a new approach to overcome therapeutic resistance in HR-deficient cancers.
 
Overall design ATAC seq profiles of DLD1 BRCA2-/- cells and UWB1.29 cells expressing either sgRNA for a Negative control (ctrl) or for ALC1. DLD1 cells were also treated with either DMSO or 5uM Olaparib(PARPi) for 4hrs. UWB1.289 cells were treated with either DMSO or 1uM talizoparib (PARPi) for 4 hours
 
Contributor(s) Zhou Y, Verma P, Faryabi RB, Greenberg R
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Submission date May 20, 2020
Last update date Dec 05, 2020
Contact name Robert Babak Faryabi
E-mail(s) faryabi@pennmedicine.upenn.edu
Phone 215-573-8220
Organization name University of Pennsylvania
Department Pathology
Lab Faryabi Lab
Street address Room 553 BRB II/III, 421 Curie Boulevard
City Philadelphia
State/province Pennsylvania
ZIP/Postal code 19104
Country USA
 
Platforms (1)
GPL21697 NextSeq 550 (Homo sapiens)
Samples (22)
GSM4561820 DLD1 BRCA2-/- sgNeg_rep1
GSM4561821 DLD1 BRCA2-/- sgNeg_rep2
GSM4561822 DLD1 BRCA2-/- sgNeg_rep3
Relations
BioProject PRJNA634143
SRA SRP262520

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Supplementary file Size Download File type/resource
GSE150955_RAW.tar 2.9 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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