The Human Cell Atlas from a cell census to a unified foundation model

• 成果类型: Review
• 署名作者: Rood, Jennifer E.; Wynne, Samantha; Robson, Lucia; Hupalowska, Anna; Randell, John; Teichmann, Sarah A.; Regev, Aviv
• 署名单位: Roche Holding; Genentech; Roche Holding USA; University of Cambridge
• 刊物名称: Nature
• ISSN/ISSBN: 0028-1560
• DOI: 10.1038/s41586-024-08338-4
• 发表日期: 2025-01-30
• 页码: 1065-1071
• 关键词: common coordinate framework; expression; biology; genome; seq

摘要

With the convergence of notable advances in molecular and spatial profiling methods and new computational approaches taking advantage of artificial intelligence and machine learning, the construction of cell atlases is progressing from data collection to atlas integration and beyond. Here, we explore five ways in which cell atlases, including the Human Cell Atlas, are already revealing valuable biological insights, and how they are poised to provide even greater benefits in the coming years. In particular, we discuss cell atlases as censuses of cells; as 3D maps of cells in the body, across modalities and scales; as maps connecting genotype causes to phenotype effects; as 4D maps of development; and, ultimately, as foundation models of biology unifying all of these aspects and helping to transform medicine.