Abstract 216: Functional annotations of membrane transport genes using genetic perturbation screens

Dysregulation of membrane transport and ion channels genes have been associated with through their role in cellular communication, regulation of cell size through osmoregulation and inflammation. However, a systematic profiling of the biological functions that are affected downstream of ion channels is not well studied due to challenges in monitoring their activity. Depleting known ligand-gated and voltage-gated ion channels has been shown to have a distinct phenotypic signature in HCT116 colorectal cells which is associated with their size and collective arrangement. These results were based on data from a genome-wide image-based siRNA screen where more than 500 million cells were segmented, and their shape and organisation were quantified. Single cells data were aggregated for each gene to capture cell heterogeneity and partial penetrance effects resulting in more than 1700 features per gene. Predictions of multiple functions for each gene were generated using KCML, a machine learning platform that automatically links gene perturbation phenotypes to molecular and biological function. Here we analysed the predicted functions for known ligand-gated and voltage-gated ion channel genes using KCML. Top predicted functions included ubiquitin protein ligase activity, phosphatase activity, stress-activated protein kinase signalling cascade, positive regulation of inflammatory response and cellular response to starvation. To validate these predictions, we applied KCML to independent genome-wide CRISPR screens measuring cell viability in 60 cancer cell lines from different tissue types. We focused on the functional association between ion channels and inflammatory response which is well recognised. We confirmed the prediction of 62/86 ion channel genes role in positive regulation of inflammatory response based on viability phenotypes. Many of these genes are documented to play a role in inflammation but has not annotated with inflammatory function in the gene ontology including GAS1, CHRNA2, and TMEM37. Pathway analysis revealed that seven of these genes are associated with gastric acid secretion (p-value =3.4E-5) including KCNQ1 gene that its loss that has been linked to the expression of inflammatory genes in colon cancer and worse patient outcomes. These results show that a comprehensive analysis of gene perturbation screens utilising siRNA or CRISPR technologies allows functional annotation of different roles for known ion channel genes. In particular, we identify 62 ion channel genes to be associated with inflammation and therefore would be promising therapeutic targets in colorectal cancer. Citation Format: Heba Sailem. Functional annotations of membrane transport genes using genetic perturbation screens [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 216.