Whole-genome CRISPR screening identifies genetic manipulations to reduce immune rejection of stem cell-derived islets

Human embryonic stem cells (hESCs) provide opportunities for cell replacement therapy of insulin-dependent diabetes. Therapeutic quantities of human stem cell-derived islets (SC-islets) can be produced by directed differentiation. However, preventing allo-rejection and recurring autoimmunity, without the use of encapsulation or systemic immunosuppressants, remains a challenge. An attractive approach is to transplant SC-islets, genetically modified to reduce the impact of immune rejection. To determine the underlying forces that drive immunogenicity of SC-islets in inflammatory environments, we performed single-cell RNA sequencing (scRNA-seq) and whole-genome CRISPR screen of SC-islets under immune interaction with allogeneic peripheral blood mononuclear cells (PBMCs). Data analysis points to “alarmed” populations of SC-islets that upregulate genes in the interferon (IFN) pathway. The CRISPR screen in vivo confirms that targeting IFNγ-induced mediators has beneficial effects on SC-islet survival under immune attack. Manipulating the IFN response by depleting chemokine ligand 10 (CXCL10) in SC-islet grafts confers improved survival against allo-rejection compared with wild-type grafts in humanized mice. These results offer insights into the nature of immune destruction of SC-islets during allogeneic responses and provide targets for gene editing. • IFN pathway induction sets the fate of SC-islets under allogeneic immune challenge • “Alarm” genes drive immunogenicity of SC-islets • Genetically modified SC-islets were generated and evaluated for hypo-immunogenicity • CXCL10 depletion can reduce immune activation and SC-islet graft rejection Using single-cell transcriptomics and whole-genome CRISPR screening, Sintov and colleagues find gene perturbation targets that can promote immune evasion of SC-islets in allogeneic transplantations. One of these targets, the early inflammatory response chemokine CXCL10, was depleted in SC-islets, which resulted in partial immune evasion in vitro and in vivo .