Biology subjects

Sheehan, S.

Publications and source records attributed to Sheehan, S..

4 recordsLinked to original sources

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↗

bioRxiv2023

A machine learning approach for quantifying age-related histological changes in the mouse kidney.

The ability to quantify aging-related changes in histological samples is important, as it allows for evaluation of interventions intended to effect health span. We used a machine learning architecture that can be trained to detect and quantify these changes in the mouse kidney. Using additional held out data, we show validation of our model, correlation with scores given by pathologists using the Geropathology Research Network aging grading scheme, and its application in providing reproducible and quantifiable age scores for histological samples. Aging quantification also provides the insights into possible changes in image appearance that are independent of specific geropathology-specified lesions. Furthermore, we provide trained classifiers for H&E-stained slides, as well as tutorials on how to use these and how to create additional classifiers for other histological stains and tissues using our architecture.This architecture and combined resources allow for the high throughput quantification of mouse aging studies in general and specifically applicable to kidney tissues.

pathology↗

bioRxiv2021

3-hydroxyanthranilic acid - a new metabolite for healthy lifespan extension

The metabolism of tryptophan to nicotinamide adenine dinucleotide (NAD+) through the kynurenine pathway is increasingly linked to aging and age-associated disease. Kynurenine pathway enzymes and metabolites influence a range of molecular processes critical to healthy aging, including regulation of inflammatory and immune responses, cellular redox homeostasis, and energy production. Aberrant kynurenine metabolism is observed during normal aging and has been implicated in a range of age-associated pathologies, including chronic inflammation, atherosclerosis, neurodegeneration, and cancer. In previous work, we and others identified three genes--kynu-1, tdo-2, and acsd-1--encoding kynurenine pathway enzymes for which decreasing expression extends lifespan in invertebrate models. Here we report that knockdown of haao-1, a fourth kynurenine pathway gene encoding the enzyme 3-hydroxyanthranilic acid dioxygenase (HAAO), extends lifespan by ~30% and delays age-associated decline in health in Caenorhabditis elegans. This lifespan extension is mediated by increased physiological levels of the HAAO substrate 3-hydroxyanthranilic acid (3HAA). 3HAA increases resistance to oxidative stress during aging by directly degrading hydrogen peroxide and activating the Nrf2/SKN-1 oxidative stress response. Aging mice fed a diet supplemented with 3HAA are similarly long-lived. Our results identify HAAO and 3HAA as novel therapeutic targets for age-associated disease. This works provides a foundation for more detailed examination of the molecular mechanisms underlying the benefits of 3HAA, and how these mechanisms interact with other interventions both within and beyond the kynurenine pathway. We anticipate that these findings will bolster growing interest in developing pharmacological strategies to target tryptophan metabolism to improve health aging.

molecular biology↗

bioRxiv2018

Genome assembly and gene expression in the American black bear provides new insights into the renal response to hibernation.

The prevalence of chronic kidney disease (CKD) is rising worldwide and 10-15% of the global population currently suffers from CKD and its complications. Given the increasing prevalence of CKD there is an urgent need to find novel treatment options. The American black bear (Ursus americanus) copes with months of lowered kidney function and metabolism during hibernation without the devastating effects on metabolism and other consequences observed in humans. In a biomimetic approach to better understand kidney adaptations and physiology in hibernating black bears, we established a high-quality genome assembly. Subsequent RNA-Seq analysis of kidneys comparing gene expression profiles in black bears entering (late fall) and emerging (early spring) from hibernation identified 169 protein-coding genes that were differentially expressed. Of these, 101 genes were downregulated and 68 genes were upregulated after hibernation. Fold changes ranged from 1.8-fold downregulation (RTN4RL2) to 2.4-fold upregulation (CISH). Most notable was the upregulation of cytokine suppression genes (SOCS2, CISH, and SERPINC1) and the lack of increased expression of cytokines and genes involved in inflammation. The identification of these differences in gene expression in the black bear kidney may provide new insights in the prevention and treatment of CKD.

genomics↗