An Intrinsic-hoc Framework for Heterogeneous Cellular Senescence Elucidation Using Deep Graph Representation Learning and Experimental Validation

Ma, A.; Cheng, H.; Vanegas, N. D. P.; Ghobashi, A.; Chen, H.; Rodriguez, J.; Rosas, L.; Wang, C.; Shao, J.; Jiang, Y.; Wang, X.; Rahman, I.; Lugo-Martinez, J.; Li, D.; Pryhuber, G. S.; Bar-Joseph, Z.; Eickelberg, O.; Konigshoff, M.; Chung, D.; Chen, R.; Finkel, T.; Mora, A.; Rojas, M.; Ma, Q.

doi:10.1101/2025.07.01.662364

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bioRxiv · 10.1101/2025.07.01.662364

An Intrinsic-hoc Framework for Heterogeneous Cellular Senescence Elucidation Using Deep Graph Representation Learning and Experimental Validation

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Abstract

Cellular senescence is a primordial driver of tissue and organ aging, and the accumulation of senescent cells (SnCs) has been implicated in numerous age-related diseases. A major barrier to studying senescence is the rarity and heterogeneity of SnCs, which are not a uniform population but instead comprise diverse senotypes shaped by cell-of-origin and microenvironmental context. Such heterogeneity exceeds what classical senescence hallmarks can resolve at single-cell resolution, motivating the need for computational frameworks that can capture senotype-level diversity intrinsically. Here, we introduce DeepSAS, a deep graph representation learning framework that robustly identifies cell-type-specific SnCs and their senescence-associated genes (SnGs). DeepSAS incorporates a heterogeneous graph that integrates intracellular transcriptional states with intercellular communication cues, enabling the joint inference of senescent cells and senescence-linked genes through attention-based contrastive learning. Applied to public healthy eye and lung atlases, DeepSAS identified SnCs whose proportions positively correlate with aging. From in-house idiopathic pulmonary fibrosis (IPF) patient scRNA-seq data, DeepSAS detected 1,678 SnCs (out of 24,125 cells) and 263 SnGs across 26 cell types, including 43 SnGs that are uniquely associated with a single cell type. We generated high-resolution Xenium spatial transcriptomics data to further validate SnGs in IPF, revealing NFE2L2 as a SnG specifically enriched in CTHRC1+ fibroblasts. Notably, the ex vivo bleomycin-induced senescence in human precision-cut lung slice (hPCLS) samples similarly identified NFE2L2 as an SnG in CTHRC1+ fibroblasts, albeit with stronger transcriptional signals, suggesting mechanistic differences in senescence cells associated with chronic and acute injury. Overall, DeepSAS uncovers distinct senescence programs and infers cell-type-specific SnGs that are difficult to resolve using existing marker-based approaches. We believe it offers a generalizable and translationally relevant strategy for advancing senescence biology and therapeutic development.

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Ma, A., Cheng, H., Vanegas, N. D. P., Ghobashi, A., Chen, H., Rodriguez, J., Rosas, L., Wang, C., Shao, J., Jiang, Y., Wang, X., Rahman, I., Lugo-Martinez, J., Li, D., Pryhuber, G. S., Bar-Joseph, Z., Eickelberg, O., Konigshoff, M., Chung, D., Chen, R., Finkel, T., Mora, A., Rojas, M., Ma, Q.. 2025-07-04. An Intrinsic-hoc Framework for Heterogeneous Cellular Senescence Elucidation Using Deep Graph Representation Learning and Experimental Validation. https://doi.org/10.1101/2025.07.01.662364

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