EPIKOL, a chromatin-focused CRISPR/Cas9-based screening platform to identify cancer-specific epigenetic vulnerabilities

Dysregulation of the epigenome due to alterations in chromatin modifier proteins commonly contribute to malignant transformation. To interrogate the roles of epigenetic modifiers in cancer cells, we generated an epigenome-wide CRISPR-Cas9 knockout library (EPIKOL) that targets a wide-range of epigenetic modifiers and their cofactors. We conducted eight screens in two different cancer types and showed that EPIKOL performs with high efficiency in terms of sgRNA distribution and depletion of essential genes. We discovered novel epigenetic modifiers that regulate triple-negative breast cancer and prostate cancer cell fitness. We confirmed the growth-regulatory functions of individual candidates, including SS18L2 and members of the NSL complex (KANSL2, KANSL3, KAT8) in triple negative breast cancer cells. Overall, we show that EPIKOL, a focused sgRNA library targeting approximately 800 genes, can reveal epigenetic modifiers that are essential for cancer cell fitness under in vitro and in vivo conditions and enable identification of novel anti-cancer targets. Due to its comprehensive epigenome-wide targets and relatively high number of sgRNAs per gene, EPIKOL will facilitate studies examining functional roles of epigenetic modifiers in a wide range of contexts, such as screens in primary cells, patient-derived xenografts as well as in vivo models. Epigenome-focused CRISPR/Cas9 Screens to identify genes whose mutations cause fitness defects in prostate and triple-negative breast cancer. 4 cells lines per cancer type were screened. For each screen, initial and final timepoint samples were collected and sequenced as triplicates. For in vivo screen, initial pellet from MDA-MB-231 cells were collected and triplicate tumors were collected and sequenced for week2 and week4 after implantation. To understand transcriptomic changes upon SS18L2 knockout, cells infected with either NT1 or SS18L2 guide carrying viruses were collected as triplicates on day 6 post-transduction.