Mapping the functional impact of non-coding regulatory elements in primary T cells through single-cell CRISPR screens

Medientyp: E-Artikel

Titel: Mapping the functional impact of non-coding regulatory elements in primary T cells through single-cell CRISPR screens

Beteiligte: Alda-Catalinas, Celia; Ibarra-Soria, Ximena; Flouri, Christina; Gordillo, Jorge Esparza; Cousminer, Diana; Hutchinson, Anna; Sun, Bin; Pembroke, William; Ullrich, Sebastian; Krejci, Adam; Cortes, Adrian; Acevedo, Alison; Malla, Sunir; Fishwick, Carl; Drewes, Gerard; Rapiteanu, Radu

Erschienen: Springer Science and Business Media LLC, 2024

Sprache: Englisch

DOI: 10.1186/s13059-024-03176-z

ISSN: 1474-760X

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Beschreibung: Abstract Background Drug targets with genetic evidence are expected to increase clinical success by at least twofold. Yet, translating disease-associated genetic variants into functional knowledge remains a fundamental challenge of drug discovery. A key issue is that the vast majority of complex disease associations cannot be cleanly mapped to a gene. Immune disease-associated variants are enriched within regulatory elements found in T-cell-specific open chromatin regions. Results To identify genes and molecular programs modulated by these regulatory elements, we develop a CRISPRi-based single-cell functional screening approach in primary human T cells. Our pipeline enables the interrogation of transcriptomic changes induced by the perturbation of regulatory elements at scale. We first optimize an efficient CRISPRi protocol in primary CD4+ T cells via CROPseq vectors. Subsequently, we perform a screen targeting 45 non-coding regulatory elements and 35 transcription start sites and profile approximately 250,000 T -cell single-cell transcriptomes. We develop a bespoke analytical pipeline for element-to-gene (E2G) mapping and demonstrate that our method can identify both previously annotated and novel E2G links. Lastly, we integrate genetic association data for immune-related traits and demonstrate how our platform can aid in the identification of effector genes for GWAS loci. Conclusions We describe “primary T cell crisprQTL” — a scalable, single-cell functional genomics approach for mapping regulatory elements to genes in primary human T cells. We show how this framework can facilitate the interrogation of immune disease GWAS hits and propose that the combination of experimental and QTL-based techniques is likely to address the variant-to-function problem.

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