A Perturb-seq screen guided by species divergence uncovers pathways for collateral artery formation
Year: 2026
Type: preprint
Abstract: Collateral arteries are natural bypasses that can reroute blood flow around arterial blockages, limiting tissue injury during stroke and coronary artery disease. Despite their clinical effectiveness, therapeutic strategies to stimulate collateral artery growth remain unavailable due to our limited understanding of their developmental mechanisms. Remarkably, guinea pigs display exceptionally dense collateral artery networks across various organs, resulting in complete resistance to ischemic damage in the brain and heart. In this study, we compared single-cell RNA sequencing (scRNA-seq) from guinea pig and mouse tissues to identify endothelial cell (EC) gene expression patterns associated with extensive collateral artery development. We then developed an in vivo Perturb-seq platform in mice to test whether genes differentially expressed in guinea pigs influence artery EC specification. This pipeline identified artery repressors that were downregulated in guinea pigs and increased pial collateral abundance when inhibited in mice. Downstream analysis suggests that artery repressors, including WNT and hypoxia response genes, function in two capillary EC subsets— Esm1+ pre-artery and Apln+ angiogenic tip cells. Reduced activity of these repressors allows more ECs to acquire arterial identity, potentiating collateral artery formation. Collectively, our study establishes a strategy for discovering the genes underlying species-specific traits, suggests that guinea pigs have collaterals due to decreased activity of artery inhibitor pathways and hypoxia responses, and identifies novel targets for stimulating collateral artery formation ( Graphical abstract ). Abstract Figure
Authors: Xiaochen Fan, Ronghao Zhou, Brian C. Raftrey, Pamela E. Rios Coronado, Emily Trimm, Erin Clancy, Xinhong Chen, Jamie Bozeman, Maggie S. Chen, Shoxruxxon Alimukhamedov, Juan Alcocer, Idalina Bonham, Stuti Agarwal, Alina Isakova, Vinicio A. de Jesus Perez, Chong Y. Park, Timothy F. Shay, Viviana Gradinaru, Thomas Quertermous, Jesse M. Engreitz, Kristy Red-Horse
Institutions: Stanford Cardiovascular Institute, Stanford University, Lucile Packard Children's Hospital, Stanford Medicine, Institute for Stem Cell Biology and Regenerative Medicine, California Institute of Technology, California State Polytechnic University, Howard Hughes Medical Institute, Broad Institute
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
Awards: Intersecting clinical, genomic, and experimental investigation to understand the mechanisms and impact of coronary artery patterning, Engineered AAV Identification, Validation, and Dissemination Pipeline for Brain Cell Type-Specific Manipulation Across Species, Mechanotransduction and transcriptional regulation during artery development, Scaled identification of receptor-targeted AAVs for potent and cell type-specific transgene delivery, Institutional Training Grant in Genome Science, Identifying causal gene programs for vascular disease using high throughput CRISPR genomics, Stanford Center for Connecting DNA Variants to Function and Phenotype
OpenAlex ID: W7160182804