Abstract

CRISPR screens have become the primary discovery engine in modern biology. However, many screening workflows are still performed in cancer cell lines and coupled to simplistic read-outs such as cellular fitness. At Aelian, we combine CRISPR screening with single-cell RNA sequencing, leveraging two transformative technologies to enable genetic screening for complex phenotypes. We utilize the CRISPR screening workflow to map the impact of thousands of genetic perturbations on the global transcriptome at single-cell resolution, thus effectively establishing a paradigm for next generation CRISPR screens. Our powerful approach has broad applications in identifying novel drug targets or elucidating unknown mechanisms of actions of drugs. Primary human T cells are currently of great interest in the scientific community. They are not only key players in autoimmunity, but also represent attractive targets for immunotherapy of cancer. To enable the discovery of novel targets in immunology and immunotherapy, we built a workflow that utilizes T cells from peripheral blood and allows functional genomic screens in these cells. Our first proof-of-concept experiment was performed to identify cells involved in the differentiation of T cells from naïve to effector cells. Different stages of cellular differentiation could be captured using transcriptomic signatures that were partly inferred from the literature and partly created de novo. Importantly, several gene KOs introduced in a pooled fashion using CRISPR/Cas9 accumulated in distinct subpopulations, suggesting that these genes represent key drivers of T cell differentiation.