Abstract B007: Endogenous retrotransposable elements induction in SMARCA4-deficient ovarian cancer is associated with immunomodulatory changes in the tumor microenvironment
Authors: Brodeur Melica N. , Sun Siyu , Zhu Yingjie , Greenbaum Benjamin , Weigelt Britta , Zamarin Dmitriy 
Published: December 2022

Abstract
Introduction: Ovarian cancer (OC) is the most lethal gynecologic cancer, and there is an urgent need to develop new therapies. Patient responses to immune checkpoint blockade have overall been disappointing, which is likely due to the immunosuppressive tumor microenvironment (TME) of most OCs that may be in part under the influence of epigenetic regulation. There is evidence that OCs that harbor loss-of-function mutations in the SWI/SNF chromatin remodeling complex catalytic subunit, SMARCA4, may be more immunogenic and amenable to immunotherapy, however the mechanisms by which this occurs is unclear. Proposed mechanisms include de-methylation of normally silenced noncoding elements. The aim of our study is to investigate the epigenetic changes of retrotransposable elements (RTEs) induced by SMARCA4 mutations that modulate the TME. Experimental Procedures: Stable isogenic SMARCA4-knockout (KO) murine (ID8) and human (OAW28) OC models were generated using CRISPR-Cas9 lentiviral transduction and clonal selection. Transcriptomic analyses of these cells were performed using RNA sequencing using ribosomal depletion protocol and validated using qRT-PCR. Moreover, differentially expressed coding genes in RNA sequencing were identified according to fold change between KO and control cells of RPKM (Reads Per Kilobase of transcript, per Million mapped reads) values. Gene Ontology enrichment analysis was then performed to identify the most altered pathways. Results: CRISPR-Cas9 KO of SMARCA4 in OC cells led to an increased fraction of reads coming from repetitive elements (repeatome). Within the repeatome, short interspersed nuclear elements (SINEs) have increased fraction of mapped reads in KO compared to wildtype OAW28 cells. Quantification analyses of known repeats demonstrate significant upregulation of endogenous retroviruses (ERVs) in KO compared to control ID8 cells. Certain RTEs known to be associated with viral mimicry and increased immunogenicity were upregulated in KO cells. Top 10 upregulated genes were significantly enriched in pathways related to interferon and viral responses. Further quantification analyses demonstrated that the dsRNA sensing pathway was activated in SMARCA4-deficient OCs leading to downstream increase in interferon-response genes. Knockdown of dsRNA sensor mitochondrial antiviral signaling protein (MAVS) downregulates the SMARCA4 loss-induced interferon-response activation. Conclusion: De-repression of normally silenced RTEs and subsequent increased immunogenicity of SMARCA4-deficient OCs suggest a potential new immunomodulatory biomarker for targeted therapy investigation. A mechanistic understanding of the role of SMARCA4 in OCs enhances our knowledge of the epigenetic processes that govern immune-stimulating responses in the TME. Studies are underway to explore combination epigenetic therapy and immunotherapy in these cancers.
Citation Format: Melica N. Brodeur, Siyu Sun, Yingjie Zhu, Benjamin Greenbaum, Britta Weigelt, Dmitriy Zamarin. Endogenous retrotransposable elements induction in SMARCA4-deficient ovarian cancer is associated with immunomodulatory changes in the tumor microenvironment. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr B007.