Genome-Scale CRISPRi Atlas Maps Gene Function Across 2.5 Million Human iPSCs

A team led by bioengineers at the University of California San Diego查看公司主页 has developed a genome-scale reference map detailing how individual genes control the functions and identities of human stem cells, publishing the work in Nature Biotechnology. The open-access resource is the first genome-scale map of gene function in human induced pluripotent stem cells查看药品详情 (iPSCs) — adult cells reprogrammed back into an embryonic-like state that can become any cell type in the body, including muscle, heart, skin or bone.

"The result is a kind of reference atlas; it's a way to look up what perturbing almost any gene does to a stem cell's behavior, measured here as the impact on its whole transcriptome," said study senior author Prashant Mali, professor in the Shu Chien-Gene Lay Department of Bioengineering at the UC San Diego Jacobs School of Engineering.

The effort addresses a fundamental gap: the vast majority of what human genes actually do inside these cells remains a mystery, according to the researchers.

CRISPRi Perturbation Across 11,692 Genes

To build the map, the team used CRISPR technology to systematically switch off 11,692 expressed genes one by one, then measured the effect on cellular transcriptomes across more than 2.5 million single cells. By compiling these data, the researchers grouped related genes and cellular components together based on shared molecular traits and functions.

That clustering allowed them to isolate previously hidden metabolic and self-renewal genes. The map also enabled the team to uncover previously unrecognized cell regulators and confirm their roles experimentally. As one example, they identified a gene called DBR1 (搜索)搜索该靶点 as the main regulator for RNA editing — specifically, the conversion of adenosine to inosine.

A Hypothesis Engine for Target Discovery

The team envisions the open-access map as a resource for streamlining and accelerating biomedical research, including the design of patient-specific treatments for complex diseases and the construction of virtual cell models.

"The map we generated works as a hypothesis engine — it's a starting point for what a given gene does and which genes might be worth pursuing as targets to drive differentiation into cell states of interest," said study co-first author Yesh Doctor, a bioengineering PhD student in Mali's lab. "Scientists can use it to look up the functions of genes and build hypotheses on them instead of having to run the experiments themselves."

Mali framed the resource as groundwork for computational approaches as well. "These comprehensive, genome-scale screens enable generation of reference maps that are not just invaluable for basic science discovery, but also an important resource for powering future computational and AI tools for genotype-phenotype prediction, one of the central pursuits in genetics research," he said, acknowledging support from the NIH, particularly the Bridge2AI program and NHGRI.

The study, titled "A genome-scale CRISPRi perturbation atlas of human induced pluripotent stem cells查看药品详情," lists Sami Nourreddine and Yesh Doctor as first authors. Additional co-authors include Amir Dailamy, Yi-Hung Lee, Jan N. Hansen, Rebecca Chinn, Antoine Forget, Benjamin Polacco, Monita Muralidharan, Alina Sigaeva, Sushant Sunder, Emily Pan, Jiahao Gao, Jake Y. Chen, Timothy Clark, Jillian Parker, Kirsten Obernier, Christian Metallo, Trey Ideker, Emma Lundberg, Nevan Krogan and Prashant Mali as senior author.

The work was supported by the National Institutes of Health查看公司主页 (grants OT2OD032742, R01CA310063 and R01HG012351), the California Institute for Regenerative Medicine (搜索)搜索该公司 (grant DISC4-19271), the Department of Defense (搜索)搜索该词条 (grant W81XWH-22-1-0401) and University of California San Diego查看公司主页 institutional funds. The map is accessible at https://y-doctor.github.io/KOLF2.1J_Perturbation_Cell_Atlas/.