UC San Diego researchers develop genome-scale map of human stem cell genes

A team of bioengineers at the University of California San Diego has unveiled a genome-scale reference map detailing the functions of nearly every gene in human stem cells, marking a significant leap in understanding cellular biology and its implications for disease research. This open-access resource, developed using CRISPR technology, systematically analyzed the effects of silencing 11,692 expressed genes across 2.5 million single cells, offering a comprehensive framework for studying gene behavior and its impact on cellular identity.

The study, led by Prashant Mali, professor in the Shu Chien-Gene Lay Department of Bioengineering at UC San Diego’s Jacobs School of Engineering, represents the first genome-scale map of gene function in human induced pluripotent stem cells (iPSCs). These cells, reprogrammed from adult cells into an embryonic-like state, can differentiate into any cell type in the body, making them critical for regenerative medicine and disease modeling. The map, published in *Nature Biotechnology*, provides a "reference atlas" for researchers to explore how gene perturbations influence cellular processes, from self-renewal to metabolic regulation.

By leveraging CRISPR-based screening, the team identified previously unknown regulators of stem cell behavior, including the gene DBR1, which plays a central role in RNA editing. The research also revealed hidden metabolic and self-renewal pathways, offering new targets for therapeutic interventions. "This map works as a hypothesis engine," said Mali, emphasizing its potential to accelerate biomedical research by allowing scientists to "look up the functions of genes and build hypotheses without running experiments themselves."

The project’s scale and methodology set it apart from earlier efforts. Using single-cell RNA sequencing, the researchers measured transcriptomic changes across millions of cells, enabling them to group genes by shared molecular traits. This approach uncovered gene networks and functional modules that were previously obscured, such as the role of the Integrator complex in RNA processing, where MIT researchers identified a 15th component, C7orf26, through similar CRISPR-based analyses.

While the UC San Diego study focused on iPSCs, parallel efforts by MIT’s Jonathan Weissman and colleagues expanded the scope to all expressed human genes. Their work, published in *Cell*, utilized a scaled-up version of the Perturb-seq method to map genotype-phenotype relationships across 2.5 million cells. This approach not only identified gene functions but also revealed insights into aneuploidy, mitochondrial stress responses, and the evolutionary rationale for mitochondrial DNA’s independent genome.

The findings align with broader initiatives like the MorPhiC Consortium, a project involving 12 institutions, including Memorial Sloan Kettering Cancer Center, which aims to systematically silence every protein-coding gene to decipher its role in development and disease. Researchers at MSK have developed a "knockout village" technique to study gene functions in parallel, using barcoded stem cells to track developmental vulnerabilities. This collaborative effort underscores the growing consensus that large-scale, open-access resources are essential for advancing precision medicine.

The UC San Diego map, accessible online, is already being integrated into computational tools for genotype-phenotype prediction, a key goal of the National Human Genome Research Institute (NHGRI). "These screens enable reference maps that are invaluable for basic science and future AI-driven research," Mali noted. The project’s success highlights the transformative potential of CRISPR and single-cell technologies in unraveling the complexities of the human genome, paving the way for targeted therapies and personalized treatments for conditions ranging from cancer to neurodegenerative diseases.