Machine learning-based definition of cellular senescence reveals pro-senescence potential implication in lung adenocarcinoma

Ma, L.; Li, H.; Li, Y.; Lin, Z.-A.; Li, J.-Q.; Zhang, Y.-Z.; Zhang, P.; Yao, Z.; Li, J.; Xiong, M.; Cao, Y.; Li, R.; Yang, C.; Tang, X.; Chen, M.; Wang, H.; Zheng, W.; Yang, J.; Wang, X.; Wei, G.-H.; Chen, H.-Z.

doi:10.1101/2025.10.11.681821

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bioRxiv · 10.1101/2025.10.11.681821

Machine learning-based definition of cellular senescence reveals pro-senescence potential implication in lung adenocarcinoma

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Abstract

Despite growing evidence implicating cellular senescence in tumor progression, methodological challenges in objectively quantifying senescent cell burden across cancer types continue to limit mechanistic studies and clinical translation. To address this, we developed the Predictive Cellular Senescence Model (PreCSenM), a machine learning-based tool that assigns a CS score by integrating senescence-associated features across 888 samples. Benchmarking analyses confirmed that PreCSenM markedly outperforms existing methodologies in reliably predicting senescent states within both normal and cancerous transcriptomic datasets. In lung adenocarcinoma (LUAD), PreCSenM identified the CS score as a robust predictor of clinical outcomes. Multi-omics analyses further revealed that lower CS levels correlate with decreased genomic stability and enhanced immune responses, aligning with clinical observations. Notably, drug discovery using PreCSenM identified histone deacetylase inhibitors (HDACis) as potent inducers of CS in LUAD. Transcriptional and epigenetic profiling of HDACi-treated cells pinpointed FOSB as a core transcription factor driving CS, and FOSB knockdown blocked HDACi-induced senescence. Overall, our study establishes PreCSenM as a multidimensional senescence quantification tool, bridging computational prediction with clinical relevance and mechanistic validation to enable senescence-directed therapies in precision oncology.

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Ma, L., Li, H., Li, Y., Lin, Z.-A., Li, J.-Q., Zhang, Y.-Z., Zhang, P., Yao, Z., Li, J., Xiong, M., Cao, Y., Li, R., Yang, C., Tang, X., Chen, M., Wang, H., Zheng, W., Yang, J., Wang, X., Wei, G.-H., Chen, H.-Z.. 2025-10-13. Machine learning-based definition of cellular senescence reveals pro-senescence potential implication in lung adenocarcinoma. https://doi.org/10.1101/2025.10.11.681821

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