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bioRxiv · 10.1101/2025.05.16.654528

ER-Localized Ceramide Accumulation Due to Disrupted CERT Transport Contributes to Replicative Senescence

Chitkara, S.·Gozali, N.·Kuzmin, A.·Pliss, A.·Prasad, P.·Sancak, Y.·Atilla-Gokcumen, G. E.
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Abstract

Ceramides regulate diverse cellular processes through compartment-specific accumulation. While mitochondrial ceramide accumulation promotes apoptosis, its regulation and function during senescence remain incompletely understood. Here, we integrate lipidomics, transcriptomics, Raman spectroscopy and biochemical characterizations to define sphingolipid remodeling in replicative senescence. Senescent cells exhibit elevated ceramide levels and depletion of very-long-chain sphingomyelins, despite unaltered sphingomyelin synthase 1 expression, implicating impaired ceramide-sphingomyelin turnover. Pharmacological inhibition of ceramide transfer protein (CERT), the ER-to-Golgi ceramide transporter, phenocopies this sphingolipid remodeling and enhances senescence markers, suggesting disrupted ceramide trafficking as a driver of senescence. Raman spectroscopy suggests ceramide accumulation localized to the ER, with no enrichment at mitochondria, consistent with a non-apoptotic phenotype. Analysis of ER-enriched fractions confirm increased ceramide levels in ER fractions of senescent cells. Mechanistically, ceramide accumulation at the ER can contribute to ER stress, a key component of the senescence program. These findings identify altered ceramide trafficking as a contributor to ER stress and highlight ER-localized ceramide as a critical component of senescence-associated sphingolipid remodeling. SignificanceHow ceramides function during replicative senescence has remained poorly understood. In this study, we demonstrate that senescent cells accumulate ceramides at the endoplasmic reticulum (ER), revealing a fundamentally different mode of ceramide regulation and function in senescence. By integrating lipidomics, enzymatic assays, Raman-BCA imaging, and biochemical assays, we show that impaired ER-to-Golgi ceramide transport leads to ER-localized ceramide retention. Disrupting ceramide trafficking through inhibition of the ceramide transfer protein CERT phenocopies senescence-associated lipid remodeling and enhances senescence markers, establishing altered ceramide transport as a mechanistic contributor to this process. These findings link impaired ceramide trafficking to replicative senescence and suggest that ceramide function in senescence is linked to its retention at the ER.

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Chitkara, S., Gozali, N., Kuzmin, A., Pliss, A., Prasad, P., Sancak, Y., Atilla-Gokcumen, G. E.. 2025-05-19. ER-Localized Ceramide Accumulation Due to Disrupted CERT Transport Contributes to Replicative Senescence. https://doi.org/10.1101/2025.05.16.654528

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