Abstract B14: A novel role for BRD9 in regulating cellular growth and DNA damage response pathways
Authors: Vallaster Caroline , Gharadaghi Farzin , Cocozaki Alexis , Jacques Kelly , Price Brendan , Guichard Sylvie 
Published: April 2017

Abstract
Bromodomain containing protein BRD9 has been identified as a component of the SWI/SNF chromatin remodeling complex. Next generation sequencing studies have revealed that SWI/SNF is the most highly perturbed chromatin remodeling complex in cancer with subunit mutations present in approximately 20% of all tumor types. SWI/SNF has been implicated as both tumor suppressor and oncogenic driver in diverse contexts. For example, the catalytic subunit SMARCA4 functions as an oncogenic driver, essential for the maintenance of hematologic malignancies such as leukemia. In contrast, loss of function of the ATPase subunit SMARCA4 and the ARID1a subunit precipitate loss of tumor suppressor activity and are apparent in lung and ovarian subtypes. However, the role of BRD9 has not been clearly delineated. Clinical data indicates that testicular germ cell cancer (66%) and esophageal cancer (18%) bear a hemizygous deletion of BRD9 conferring HETLOSS status. Loss of BRD9 heterozygosity leading to enhanced tumorigenic potential is a hallmark of tumor suppressors. This highlights a novel role for this bromodomain protein in regulating the process of oncogenesis.
Here we demonstrate shRNA-mediated knockdown of BRD9 enhances clonogenic potential of solid tumor cancer cell lines, while expression of wild-type BRD9 in a HETLOSS cell line abrogates colony formation. Collectively, our data suggests BRD9 functions as a regulator of cellular growth. We examined if SWI/SNF chromatin remodeling activity was dependent on BRD9 status and how this correlated with the growth phenotype. Nucleosome accessibility was significantly decreased when BRD9 was depleted indicating chromatin exists in a more compacted conformation. However, BRD9 knockdown does not result in alterations in assembly or stability of the SWI/SNF complex. Though loss of BRD9 does not perturb SWI/SNF dynamics, it may be required for complex recruitment to chromatin directly or by tethering through protein-protein interactions. Identification of novel BRD9-interacting proteins that target recruitment was carried out by proteomic survey. Analysis of the study revealed enrichment of proteins involved in DNA damage repair pathways. Using a double strand break reporter, we examined if BRD9 depletion perturbed homology-directed or non-homologous end joining repair pathways. Knockdown of BRD9 increased NHEJ-associated reporter activity but had subtle effect on homology-directed repair events. BRD9 colocalizes with γH2AX foci upon damage but this colocalization is lost upon depletion of BRD9.
We propose that BRD9 is necessary for recruitment of SWI/SNF to sites of damage, to permit chromatin expansion and assembly of homology-directed repair factors. However, knockdown of BRD9 may shift the balance and favor interactions of non-homologous end joining pathway players to sites of damage, resulting in enhanced error-prone repair and ultimately leading to oncogenic transformation. Collectively, this work highlights a novel and previously unidentified role for BRD9 in DNA damage pathways and identifies a potential vulnerability in NHEJ dependence that may be therapeutically targeted.
Citation Format: Caroline Vallaster, Farzin Gharadaghi, Alexis Cocozaki, Kelly Jacques, Brendan Price, Sylvie Guichard. A novel role for BRD9 in regulating cellular growth and DNA damage response pathways [abstract]. In: Proceedings of the AACR Special Conference on DNA Repair: Tumor Development and Therapeutic Response; 2016 Nov 2-5; Montreal, QC, Canada. Philadelphia (PA): AACR; Mol Cancer Res 2017;15(4_Suppl):Abstract nr B14.