Abstract B05: Induction of DNA damage in high-grade serous carcinoma induces type I interferon signaling

Abstract

Purpose: Current immunotherapy response rates in high-grade serous carcinoma (HGSC) of the ovary, fallopian tube, and peritoneum are 10-15%. We sought to determine if decreasing levels of the DNA damage repair protein DEK or inhibiting its downstream effector aurora kinase A (AURKA) induces type I interferon (IFN-I) signaling to improve the immune sensing of HGSC. Experimental Procedures: RNA-Seq analysis was performed on HGSC cell lines with stable expression of shRNA targeting DEK (shDEK) or control. Gene expression patterns were analyzed by gene set enrichment analysis and confirmed by RT-PCR. As AURKA/B were identified to be downregulated by shDEK, cell lines were treated with aurora kinase inhibitors and analyzed for DNA damage and apoptosis. IFN-I signature transcripts were analyzed by RT-PCR following shDEK therapy or aurora kinase inhibitor therapy compared to controls. Tumor-infiltrating lymphocyte (TIL) profiles in HGSC from The Cancer Genome Atlas (TCGA) were characterized. Using the ID8 immunocompetent ovarian cancer mouse model, IFN-I signature transcripts were quantified after transfection with siRNA targeting Dek or control without or with overexpression of the DNA damage sensing protein Sting. In vivo studies were performed by injecting ID8 cells intraperitoneally and then treating with the AURKA inhibitor alisertib, anti-PD-L1 antibody, combination therapy or control. TILs were analyzed by flow cytometry. Results: RNA-Seq analysis identified interferon-alpha response as an upregulated pathway in the setting of DEK deficiency. In vitro validation revealed that decreasing DEK levels increases IFN-I signaling. RNA-Seq analysis also showed decreased AURKA/B following shDEK treatment. A positive correlation between DEK and AURKA/B transcript levels was also found in primary patient samples. AURKA/B inhibitor therapy resulted in increased DNA damage and apoptosis, and increased IFN-I signature gene transcripts including IFNB1, IFNA4, ISG15, and MX1. TCGA analysis showed that elevated levels of IFN-I genes including chemokines CXCL9 and CXCL10 are correlated with TIL subsets essential for antitumor immunity. In ID8 cells, Dek-deficiency enhanced Sting-mediated induction of Ifnb1, Cxcl9, and Cxcl10. In the ID8 in vivo studies, AURKA inhibitor therapy resulted in increased TCRβ and TCRγδ TIL subpopulations. Combinatorial therapy animal studies are ongoing. Conclusions: Decreasing levels of the DNA damage repair protein DEK or inhibiting its effector AURKA/B induces DNA damage and increases IFN-I signaling in both HGSC cells lines and primary patient samples. Our TCGA analysis supports the hypothesis that IFN-I signaling is pivotal for the HGSC immunogenicity. Inhibition of AURKA in the ID8 mouse model system results in a shift in the immune phenotype, and further preclinical combinatorial studies are under way. Our results identify a new synthetic immune toxicity combination by priming HGSC with AURKA-targeted therapy with the goal of increasing immunotherapy responses. Citation Format: Danielle E. Bolland, Yuning Hao, Yee Sun Tan, Jake Reske, Lijun Tan, Ronald L. Chandler, Yuying Xie, Yu L. Lei, Karen McLean. Induction of DNA damage in high-grade serous carcinoma induces type I interferon signaling [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research; 2019 Sep 13-16, 2019; Atlanta, GA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(13_Suppl):Abstract nr B05.

CIRCNV: Detection of CNVs Based on a Circular Profile of Read Depth from Sequencing Data

“…For the CNVs detected by the CIRCNV method, we further find that these CNVs contain many biological genes associated with ovarian cancer. For instance, the CNVs detected in sample EGAR00001004802_2053_1 contain cancer-associated genes such as ELOVL7 [10] located at 5q12.1, IFNB1 [44] located at 9p21.3, BAG1 [45] located at 9p21.1, RECK [46] located at 9p13.3, DAPK1 [47], CTSL [48], and CCRK [49] located at 9q21.33, SYK [50] located at 9q22.2, and NR4A3 [51] and TMEFF1 [52] located at 9q22.33. Similarly, the CNVs detected in sample EGAR00001004836_2561_1 also contain many cancer-associated genes, such as CD80 [53], GSK3B [54], FSTL1 [55], CASR [56], PARP9 [57], and PARP15 [58] located at 3q13.33.…”