A team led by bioengineers at the University of California San Diego has developed a genome-scale reference map that details how individual genes control the functions and identities of human stem cells. This open-access resource could help researchers build virtual cell models for complex diseases, as well as design patient-specific treatments for these diseases.
The study was published in Nature Biotechnology .
"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.
This is the first genome-scale map of gene function in human induced pluripotent stem cells, which are adult cells that have been reprogrammed back into an embryonic-like state and can turn into any type of cell in the body, such as muscle, heart, skin or bone. Such a reference map is needed because the vast majority of what human genes actually do inside these cells remains a mystery.
To build this comprehensive reference 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. This allowed them to isolate previously hidden metabolic and self-renewal genes. The map enabled researchers to uncover previously unrecognized cell regulators and confirm their roles experimentally. For example, they identified a specific gene, called DBR1, as the main regulator for RNA editing — specifically, the conversion of adenosine to inosine.
The team envisions that this open-access map could serve as a resource for streamlining and accelerating biomedical research.
"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."
"We are grateful for the support of the NIH, especially the Bridge2AI program and NHGRI," Mali said. "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."
The map is accessible at https://y-doctor.github.io/KOLF2.1J_Perturbation_Cell_Atlas/ .
Full study: " A genome-scale CRISPRi perturbation atlas of human induced pluripotent stem cells. " First authors of the study are Sami Nourreddine and Yesh Doctor, UC San Diego. Additional co-authors on the study 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 (senior author).
This work was supported by the National Institutes of Health (grants OT2OD032742, R01CA310063 and R01HG012351), the California Institute for Regenerative Medicine (grant DISC4-19271), the Department of Defense (grant W81XWH-22-1-0401) and University of California San Diego institutional funds.
Disclosures: Prashant Mali is a scientific cofounder of Shape Therapeutics, Boundless Biosciences, Navega Therapeutics, Pi Bio and Engine Biosciences. The terms of these arrangements have been reviewed and approved by the University of California San Diego in accordance with its conflict-of-interest policies. Trey Ideker is a cofounder, advisor and holder of equity for Data4Cure and Serinus Biosciences and he is an advisor and shareholder for Ideaya BioSciences. The terms of these arrangements have been reviewed and approved by University of California San Diego in accordance with its conflict-of-interest policies. The Nevan Krogan laboratory has received research support from Vir Biotechnology, F. Hoffmann-La Roche and Rezo Therapeutics. Nevan Krogan has a financially compensated consulting agreement with Maze Therapeutics, is the president and is on the board of directors of Rezo Therapeutics and is a shareholder in Tenaya Therapeutics, Maze Therapeutics, Rezo Therapeutics, GEn1E Lifesciences and Interline Therapeutics. Emma Lundberg is a cofounder of GenBio.ai and an advisor for the Chan-Zuckerberg Initiative Foundation, Element Biosciences, Cartography Biosciences, Pfizer and Pixelgen Technologies. The remaining authors declare no competing interests.
