Reeve, R. E. | Search bioRxiv

bioRxiv2026

Circadian Dysregulation in Aging Alters Senescence and Inflammatory Pathways in a Sex- and Time-of-Day Dependent Manner

The circadian rhythm orchestrates gene expression and critical physiological processes but becomes disrupted with aging, contributing to disease. How this disruption interacts with cellular senescence--a key driver of aging pathology--remains poorly defined. We studied renal gene expression at four timepoints over 24hrs in 6- and 24-month-old genetically diverse UM-HET3 mice of both sexes and performed complementary analyses in synchronized fibroblasts sampled at seven timepoints. Aging dysregulated core clock relationships, including loss of the canonical anti-phase expression between Bmal1 and Per2. Senescence-associated genes were not static but exhibited pronounced oscillations, with senescence phenotypes varying by sex and time of day. Differential expression analysis revealed immune activation, metabolic rewiring, and epigenetic changes that were sex- and time-dependent. Variance analysis uncovered increased transcriptional noise in aging, particularly in circadian-regulated pathways such as RNA splicing, ribosome biogenesis, and TOR signaling. Single-nucleus RNA-Seq identified two cell populations lacking the normal Bmal1-Cdkn1a expression relationship: one senescent-like and another profibrotic, revealing distinct cell states linked to circadian dysregulation. Fibroblasts recapitulated key age-related circadian changes seen in the kidneys, including phase shifts in mTOR and oxidative phosphorylation. Together, this work demonstrates that senescence phenotypes are dynamic, sex-specific, and time-of-day dependent, and introduces a new framework for detecting senescent cells based on circadian gene relationships. These findings underscore the need to integrate temporal context into aging research and therapeutic strategies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=185 HEIGHT=200 SRC="FIGDIR/small/709919v1_ufig1.gif" ALT="Figure 1"> View larger version (86K): org.highwire.dtl.DTLVardef@247e70org.highwire.dtl.DTLVardef@1e8f66borg.highwire.dtl.DTLVardef@18a0673org.highwire.dtl.DTLVardef@ad91d7_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2025

T-regulatory cell protection of progenitor cells from CD4+ T-cell-mediated cytotoxicity is essential for endogenous mouse digit-tip regeneration.

Regeneration of amputated digit tips in humans and mice relies on osteoclast-dependent bone erosion coupled with osteoblast-mediated bone replacement. Currently, little is known of the impact of lymphoid immune cells, i.e., T cells, B cells, and NK cells, on digit-tip regeneration. Using lymphoid-deficient mutant mice, we revealed lymphoid immunity as a net negative regulator of regeneration. CD8+ cells are thought to negatively regulate fracture repair; however, we showed that adoptive cell transfer (ACT) of CD8+ T cells into lymphoid-deficient hosts did not impact regeneration. In contrast, ACT of CD4+ T cells potently inhibited regeneration via osteoclast and osteoblast progenitor-cell cytotoxicity. CD4+ T-cell-mediated inhibition of regeneration was rescued by supplementation with T regulatory cells or recombinant RANKL, a mediator of osteoclast differentiation. ACT of IFN-{gamma}-deficient CD4+ T cells abolished cytotoxic activity and rescued regeneration. Future strategies protecting endogenous progenitor cells could enhance human tissue repair and autologous stem-cell therapies. One sentence summaryEndogenous progenitor cells are vulnerable to CD4+ T-cell-mediated cytotoxicity during digit-tip regeneration and require T-regulatory-cell-mediated protection from autoimmune attack. HighlightsO_LIDigit-tip regeneration is enhanced with the loss of lymphoid immunity. C_LIO_LIRegeneration requires T regulatory cells (T-regs) for maintenance of osteoclastogenesis when other lymphoid cells are present. C_LIO_LIT-regs enhance regeneration in the absence of lymphoid immunity during the anabolic phase. C_LIO_LILike thymic NK cells, CD4+ T cells and not CD8+ T cells are responsible for inhibition of regeneration. C_LIO_LIRANKL is essential to the rate-limiting catabolic phase of digit-tip regeneration. C_LIO_LIBoth T-regs and recombinant RANKL can rescue CD4+ T-cell inhibition. C_LIO_LIGenetic knockout of key cytotoxicity genes (IFN{gamma}, Prf1, and TNF) in immune-competent mice enhances regeneration. C_LIO_LICD4+ T-cell ACT induces both apoptosis and necroptosis. C_LIO_LICD4+ T-cell cytotoxicity is dependent on IFN{gamma}. C_LI

developmental biology↗