An atlas of healthy and injured cell states and niches in the human kidney (Version 1.5)

Understanding kidney health and disease relies upon defining the complexity of cell types and states, their associated molecular profiles, and interactions within tissue neighborhoods. We have applied single-cell and single-nucleus assays to a broad spectrum of healthy reference and disease kidneys. This has provided a high-resolution cellular atlas that includes rare and novel cell populations. We further identify and define cellular states altered in kidney injury, encompassing cycling, adaptive or maladaptive repair, transitioning and degenerative states affecting several nephron segments. These analyses further define biological pathways relevant to injury niches, including signatures underlying the transition from reference to predicted maladaptive states that are associated with a decline in kidney function during chronic kidney disease. Our collaborative efforts across the Kidney Precision Medicine Project (KPMP), the Human BioMolecular Atlas Program (HuBMAP) and the Human Cell Atlas consortia aim to generate a comprehensive human kidney cell atlas that includes injury and disease-relevant cell states and neighborhoods as a valuable resource to the research community. Here we provide an expanded data set from that published previously (Lake et al., Nature 2023) that includes additional KPMP biopsy data.