Unveiling the cell-type-specific landscape of cellular senescence through single-cell transcriptomics using SenePy

Mark A. Sanborn (), Xinge Wang, Shang Gao, Yang Dai and Jalees Rehman ()
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Mark A. Sanborn: College of Medicine
Xinge Wang: College of Medicine
Shang Gao: College of Medicine
Yang Dai: University of Illinois Chicago
Jalees Rehman: College of Medicine

Nature Communications, 2025, vol. 16, issue 1, 1-19

Abstract: Abstract Senescent cells accumulate in most tissues with organismal aging, exposure to stressors, or disease progression. It is challenging to identify senescent cells because cellular senescence signatures and phenotypes vary widely across distinct cell types and tissues. Here we developed an analytical algorithm that defines cell-type-specific and universal signatures of cellular senescence across a wide range of cell types and tissues. We utilize 72 mouse and 64 human weighted single-cell transcriptomic signatures of cellular senescence to create the SenePy scoring platform. SenePy signatures better recapitulate in vivo cellular senescence than signatures derived from in vitro senescence studies. We use SenePy to map the kinetics of senescent cell accumulation in healthy aging as well as multiple disease contexts, including tumorigenesis, inflammation, and myocardial infarction. SenePy characterizes cell-type-specific in vivo cellular senescence and could lead to the identification of genes that serve as mediators of cellular senescence and disease progression.

Date: 2025
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DOI: 10.1038/s41467-025-57047-7

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