ChemPerturb-Seq Screen to Identify Small Molecules Enhancing Human Beta Cell Survival After Subcutaneous Transplantation

Although high throughput/content chemical screens have been employed to characterize cellular response to small molecules treatment, traditional chemical screens have only focused on a single assay per screen, making them labor intensive and costly. Here, we combined a chemical screen with scRNA-seq to perform Chemical Perturb-Seq (ChemPerturb-Seq), enabling a systematic analysis of cellular responses and molecular changes of human beta cells upon individual hormone treatments. Furthermore, we developed an AI-powered website, ChemPerturbDB, which provides user friendly open-access analysis of this extensive dataset. Next, we performed an in vivo barcoded screen and developed a hormone cocktail, including Insulin growth factor-1, Lipotropin, and Prostaglandin E2. Pre-conditioning human beta cells and primary islets with this hormone cocktail significantly enhanced their function and survival when transplanted subcutaneously to female, but not to male mice. Combining scRNA-seq and ChemPerturb-seq, we identified two additional moleculeshormones, serotonin and histamine, that promote the function of human islets when transplanted subcutaneously to male mice. Together, we not only generated a comprehensive ChemPerturb-Seq dataset, which can be utilized to systematically investigate the effects of hormones on human beta cells, but also developed hormone cocktails that enhance the survival of human beta cells following subcutaneous transplantation. With further validation, this, which could be applied to improve the current FDA-approved islet transplantation procedure. Overall design: Multiplexed scRNA-seq analysis of human EndoC-betaH1 cells treated with different small molecules from an in-house small molecule screening library