Gene regulatory network inference from CRISPR perturbations in primary CD4+ T cells elucidates the genomic basis of immune disease

Joshua S Weinstock; Maya M Arce; Jacob W Freimer; Mineto Ota; Alexander Marson; Alexis Battle; Jonathan K Pritchard

doi:10.1016/j.xgen.2024.100671

Gene regulatory network inference from CRISPR perturbations in primary CD4⁺ T cells elucidates the genomic basis of immune disease

Cell Genom. 2024 Nov 13;4(11):100671. doi: 10.1016/j.xgen.2024.100671. Epub 2024 Oct 11.

Authors

Joshua S Weinstock¹, Maya M Arce², Jacob W Freimer³, Mineto Ota³, Alexander Marson⁴, Alexis Battle⁵, Jonathan K Pritchard⁶

Affiliations

¹ Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
² Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
³ Department of Genetics, Stanford University, Stanford, CA 94305, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA.
⁴ Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, CA 94143, USA; Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA 94129, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA. Electronic address: [email protected].
⁵ Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA; Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD, USA; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA; Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA. Electronic address: [email protected].
⁶ Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA, USA. Electronic address: [email protected].

Abstract

The effects of genetic variation on complex traits act mainly through changes in gene regulation. Although many genetic variants have been linked to target genes in cis, the trans-regulatory cascade mediating their effects remains largely uncharacterized. Mapping trans-regulators based on natural genetic variation has been challenging due to small effects, but experimental perturbations offer a complementary approach. Using CRISPR, we knocked out 84 genes in primary CD4⁺ T cells, targeting inborn error of immunity (IEI) disease transcription factors (TFs) and TFs without immune disease association. We developed a novel gene network inference method called linear latent causal Bayes (LLCB) to estimate the network from perturbation data and observed 211 regulatory connections between genes. We characterized programs affected by the TFs, which we associated with immune genome-wide association study (GWAS) genes, finding that JAK-STAT family members are regulated by KMT2A, an epigenetic regulator. These analyses reveal the trans-regulatory cascades linking GWAS genes to signaling pathways.

Keywords: CRISPR; GWAS; RNA-seq; T cells; gene regulatory networks; immunology; inbornb errors of immunity; network inference.

MeSH terms

Bayes Theorem
CD4-Positive T-Lymphocytes* / immunology
CD4-Positive T-Lymphocytes* / metabolism
CRISPR-Cas Systems
Clustered Regularly Interspaced Short Palindromic Repeats / genetics
Gene Regulatory Networks*
Genome-Wide Association Study*
Histone-Lysine N-Methyltransferase / genetics
Histone-Lysine N-Methyltransferase / metabolism
Humans
Immune System Diseases / genetics
Immune System Diseases / immunology
Transcription Factors / genetics

Substances

Transcription Factors
Histone-Lysine N-Methyltransferase

Grants and funding

R35 GM139580/GM/NIGMS NIH HHS/United States