Multi-scale CRISPR screens in primary T cells to characterize genetic variants driving autoimmune disease

Autoimmune diseases (AIDs) affect almost 400 million people worldwide, and currently have no known cure.

Genome-wide association studies (GWAS) have identified genetic variants linked to an increased risk of developing AIDs, with the potential to pinpoint molecular processes causal to AID and targets for novel interventions.

While many GWAS variants overlap cis-regulatory elements (CREs) such as enhancers or open chromatin, identifying causal variants has remained a challenge due to the large number of variants and their frequent co-inheritance.

Here, I will perform multiple CRISPR screens on primary T cells, key cell types in autoimmunity, to interrogate disease-associated variants and pinpoint genomic regions which contribute to AID development.

I will first identify genes which when perturbed drive AID-relevant T-cell phenotypes, then perturb CREs overlapping AID-associated variants adjacent to these genes and examine the same phenotypes.

To understand the mechanisms of functional CREs/variants, I will combine CRISPR perturbations with single-cell sequencing in primary T cells.

Finally, using CRISPR base editing, I will insert precise AID-associated variants and measure their impact on single-cell transcriptomics and T-cell phenotypes.

This study will develop a pipeline for the scalable identification of disease-relevant genes, CREs, and causal variants, elucidating the complex mechanisms underlying AIDs and identifying target genes for novel therapies.