Systematic Perturb-seq to discover endothelial cell programs related to CAD v2

Linking variants from genome-wide association studies (GWAS) to underlying mechanisms of disease remains a challenge1,4,6. For some diseases, a successful strategy has been to look for cases where multiple GWAS loci contain genes that act in the same biological pathway1–6. However, our knowledge of which genes act in which pathways is incomplete, particularly for cell-type specific pathways or understudied genes. Here we introduce a method to connect GWAS variants to functions, which links variants to genes using epigenomic data, links genes to pathways de novo using Perturb-seq, and integrates these data to identify convergence of GWAS loci onto pathways. We apply this approach to study the role of endothelial cells in genetic risk for coronary artery disease (CAD), and discover that 43 CAD GWAS signals converge on the cerebral cavernous malformations (CCM) signaling pathway. Two regulators of this pathway, CCM2 and TLNRD1,are each linked to a CAD risk variant, regulate other CAD risk genes, and affect atheroprotective processes in endothelial cells. These results suggest a model where CAD risk is driven in part by the convergence of causal genes onto a particular transcriptional pathway in endothelial cells, highlight shared genes between common and rare vascular diseases (CAD and CCM), and identify TLNRD1 as a new, previously uncharacterized member of the CCM signaling pathway. This approach will be widely useful for linking variants to functions for other common polygenic diseases. Note: The list of authors for this protocol does not include all authors of the accompanying manuscript, only those who played a role in developing and executing the Perturb-seq method. For a complete list of manuscript authors, see the Manuscript Citation. Notes are provided to indicate which authors are best to contact for questions regarding specific methods.