Identification of senescent cell subpopulations by CITE-seq analysis

Cellular senescence, a state of indefinite growth arrest, is closely associated with aging and age-related diseases. Deciphering the heterogeneity within senescent cell populations and identifying therapeutic targets are paramount for mitigating senescence-related pathologies. In this study, proteins on the surface of senescent cells were identified using mass spectrometry, and a subset of them was used for single-cell CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by Sequencing) analysis. Among seven clusters of senescent cells identified, cluster 1 was characterized by high levels of CD109 and CD112 on the plasma membrane, and cluster 2 by high levels of CD44, CD73, CD49a, and CD54 on the plasma membrane. The transcriptomes of cluster 1 revealed cells in which translation was reduced, proteolysis was increased, and SASP factors including IL1B, GDF15, CCL13, and CCL2 were expressed. The transcriptomes of cluster 2 revealed cells that expressed a different subset of SASP factors such as VEGFA, IL13, IL15, FGF2, and FGF7, as well as extracellular matrix remodeling factors. Our study highlights the heterogeneity of senescent cells and represents the first attempt to explore the potential of cell surface proteins as tools for differentiating senescent cell programs and subclasses, paving the way for targeted therapeutic strategies in disorders exacerbated by senescence.