Summary
Complex gene regulatory networks ensure that important genes are expressed at precise levels. When gene expression is sufficiently perturbed it can lead to disease. To understand how gene expression disruptions percolate through a network, we must first map connections between regulatory genes and their downstream targets. However, we lack comprehensive knowledge of the upstream regulators of most genes. Here we developed an approach for systematic discovery of upstream regulators of critical immune factors – IL2RA, IL-2, and CTLA4 – in primary human T cells. Then, we mapped the network of these regulators’ target genes and enhancers using CRISPR perturbations, RNA-Seq, and ATAC-Seq. These regulators form densely interconnected networks with extensive feedback loops. Furthermore, this network is highly enriched for immune-associated disease variants and genes. These results provide insight into how immune-associated disease genes are regulated in T cells and broader principles about the structure of human gene regulatory networks.
Highlights
A systematic approach to identify upstream regulators of key immune genes in primary human cells
Comprehensive RNA-Seq and ATAC-Seq perturbation maps after KO of individual discovered regulators
Analysis uncovers a highly interconnected regulatory network of enhancers and genes in T cells
This network is highly enriched for immune disease variants and genes shedding light on the trans-regulatory connections among key immune genes in health and disease
Competing Interest Statement
A.M. is cofounder, member of the Boards of Directors and member of Scientific Advisory Boards of Spotlight Therapeutics and Arsenal Biosciences. A.M. has served as an advisor to Juno Therapeutics, was a member of the scientific advisory board at PACT Pharma and was an advisor to Trizell. A.M. has received honoraria from Merck and Vertex, a consulting fee from AlphaSights, and is an investor in and informal advisor to Offline Ventures. A.M. owns stock in Arsenal Biosciences, Spotlight Therapeutics and PACT Pharma. The Marson lab has received research support from Juno Therapeutics, Epinomics, Sanofi, GlaxoSmithKline, Gilead and Anthem. W.J.G. is a consultant for 10x Genomics, which has licensed IP associated with ATAC-seq. W.J.G. has additional affiliations with Guardant Health (consultant) and Protillion Biosciences (cofounder and consultant). J.W.F., O.S., J.K.P., and A. M. are listed as inventors on a patent application related to this work.