Abstract 4616: Exploring the role of interferon and innate immune regulators in outlier cancer cell line survival

Abstract

Abstract We conducted an outlier dependence analysis using functional genomic screening data generated by groups at the Dana-Farber Cancer Institute and Broad Institute. These genome-wide knockdown (shRNA) and knockout (CRISPR-Cas9) screens seek to discover genetic vulnerabilities, or “Achilles’ heels“, across hundreds of cancer cell lines. The most recent version of the gene knockdown screen includes over 500 total cell lines, allowing overall and lineage-specific outliers to be assessed. Taking advantage of the relatively large number of cell lines in this data set, our study parallels “exceptional responder” patient studies derived from clinical trials, with the goal of finding a small number of cell lines that are acutely dependent on certain genes for survival. These outlier cell lines could then be profiled to search for a common genetic factor or gene expression signature that can be used to predict sensitivity to the knockdown of the gene(s) in question. Strong, specific genetic dependencies have the potential to generate novel, hypothesis-driven therapeutic strategies that can be further tested experimentally. Initially, we focused on the lung cancer cell lines profiled in the knockdown screen. We used an unbiased approach to investigate genes with the most pronounced outlier patterns across these lung lines. One of the top genes in our analysis encodes the RNA-editing enzyme ADAR1, which has a role in epigenetically altering double-strand RNA sequences. ADAR1 encodes a protein that catalyzes adenosine-to-inosine editing in RNA. This RNA editing function has been studied in the context of suppressing innate immune sensing, as endogenous RNA is edited to avoid detection by intracellular sensors that activate the type I interferon pathway after encountering unedited RNA from infecting viruses. ADAR1 homozygous mutant patients and mouse models each display greatly increased interferon levels and activation of downstream interferon-induced gene expression, further supporting the role of ADAR1 to suppress interferon activation and autoimmunity. Importantly, outlier cell lines sensitive to ADAR1 knockdown are also sensitive to knockdown of ISG15, which similarly suppresses interferon signaling, and show greatly increased survival after IFNAR1 knockdown, a positive regulator of interferon signaling. We next mined genome-wide CRISPR-Cas9 knockout screens and found a pancreatic cell line that is also dependent on ADAR1 and ISG15 for survival. Likewise, knockout of IFNAR1 or any gene along the IFNAR1-JAK-STAT pathway enhances survival in this cell line. These converging data suggest a link between the interferon pathway and vulnerability to knockdown of ADAR1 or ISG15. While no common mutations or genomic changes were found in the outlier cell lines, we have uncovered a shared gene expression signature. We are continuing to study the mechanisms that cause these cell lines to be acutely dependent on ADAR1 and ISG15. Citation Format: Hugh S. Gannon, Michael Kiessling, Francisca Vazquez, William Hahn, Matthew Meyerson. Exploring the role of interferon and innate immune regulators in outlier cancer cell line survival [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4616. doi:10.1158/1538-7445.AM2017-4616