2025 Hyper Recent •CC0 1.0 Universal

This work is dedicated to the public domain. No rights reserved.

Access Preprint From Server
January 22nd, 2025
Version: 1
Rutgers New Jersey Medical School
genomics
biorxiv

Epigenetic mechanisms regulating CD8+ T cell senescence in aging humans

Turano, P. S.Open in Google Scholar•Dewald, H. K.Open in Google Scholar•Akbulut, E.Open in Google Scholar•Vasilopoulos, T.Open in Google Scholar•Fitzgerald-Bocarsly, P.Open in Google Scholar•Herbig, U.Open in Google Scholar•Martinez Zamudio, R. I.Open in Google Scholar

Aging leads to the decline of immunity, rendering the elderly susceptible to infection and disease. In the CD8+ T cell compartment, aging leads to a substantial increase of cells with high levels of senescence-associated beta-galactosidase activity (SA-BGal) and other senescence characteristics, including a pro-inflammatory transcriptome and impaired proliferative potential. Using senescent cell isolation coupled with multiomic profiling, here we characterized the epigenetic mechanisms regulating CD8+ T cell senescence in a cohort of younger and older donors. High levels of SA-BGal activity defined changes to global transcriptomes and chromatin accessibility landscapes, with a minor effect of age. Widespread enhancer remodeling was required for the repression of functional CD8+ T cell genes and upregulation of inflammatory and secretory pathway genes. Mechanistically, the senescence program in CD8+ T cells was controlled by chromatin state-specific transcription factor (TF) networks whose composition was largely insensitive to donor age. Pharmacological inhibition of TF network nodes AP1, KLF5, and RUNX2 modulated the transcriptional output, demonstrating the feasibility of TF network perturbation as an approach to modulate CD8+ T cell senescence. Further, CD8+ T cell senescence gene signatures faithfully predicted refractoriness to chimeric antigen receptor (CAR) T-cell therapy in a cohort of diffuse large B cell lymphomas and were highly enriched in the transcriptomes of peripheral CD8+ T cells of individuals with active systemic lupus erythematosus. Collectively, our findings demonstrate the potential of multiomic profiling in identifying key regulators of senescence across cell types and suggest a critical role of senescent CD8+ T cells in disease progression.

Similar Papers

biorxiv
Wed Jul 02 2025
Persistent Activation of Endothelial Cells is Linked to Thrombosis and Inflammation in Cerebral Cavernous Malformation Disease
BACKGROUND: Cerebral cavernous malformations (CCM) are neurovascular lesions that affect both children and adults, and morbidity often results from thrombosis, bleeding, and neurological dysfunction. Studies indicate that inflammation-related activation of endothelial cells contributes significantly to the worsening of CCM disease. This suggests that ongoing vascular inflammation and endothelial d...
Gallego-Gutierrez, H.
•
Frias-Anaya, E.
•
Bui, C.
•
Zhao, L.
...•
Lopez-Ramirez, M. A.
biorxiv
Wed Jul 02 2025
Illuminating the mystery of thylacine extinction: a role for relaxed selection and gene loss
Gene loss shapes lineage-specific traits but is often overlooked in species survival. In this study, we investigate the role of ancestral gene loss using the extinction icon - thylacine (Thylacinus cynocephalus). While studies of neutral genetic variation indicate a population decline before extinction, the impact of thylacine-specific ancestral gene losses remains unexplored. The availability of ...
Salve, B. G.
•
Vijay, N.
biorxiv
Wed Jul 02 2025
Integrative Transcriptomic and Machine Learning Approaches to decipher Mitochondrial Gene Regulation in severe Plasmodium vivax Malaria
Mitochondria in Plasmodium vivax are functionally vital despite possessing a highly reduced genome and differing substantially from the human organelle. Beyond their classical role in energy production, they dynamically coordinate processes like pyrimidine biosynthesis and heme metabolism, adapting their functions across the intra-erythrocytic development cycle (IDC). Their unique architecture and...
Roy, P.
•
Aggarwal, Y.
•
Kochar, S. K.
•
Kochar, D. K.
•
Das, A.
biorxiv
Wed Jul 02 2025
An optimised computational approach for the identification of somatic structural variants in cancer
Structural variants play a critical role in tumorigenesis. At present, these events are most commonly identified using short-read whole-genome sequencing data, and a number of computational tools are available for this purpose. Consensus approaches have been used to improve precision, but may reduce sensitivity. The optimal number and combination of callers remains unclear, in part due to the lack...
Waise, S.
•
Mensah, N.
•
Lesluyes, T.
•
Demeulemeester, J.
...•
Van Loo, P.
biorxiv
Wed Jul 02 2025
Language models learn to represent antigenic properties of human influenza A(H3) virus
Given that influenza vaccine effectiveness depends on a good antigenic match between the vaccine and circulating viruses, it is important to assess the antigenic properties of newly emerging variants continuously. With the increasing application of real-time pathogen genomic surveillance, a key question is if antigenic properties can reliably be predicted from influenza virus genomic information. ...
Durazzi, F.
•
Koopmans, M.
•
Fouchier, R. A. M.
•
Remondini, D.
biorxiv
Wed Jul 02 2025
Multi-omic identification of key transcriptional regulatory programs during endurance exercise training in rats
Transcription factors (TFs) play a key role in regulating gene expression. We conducted an integrated analysis of chromatin accessibility, DNA methylation, mRNA expression, protein abundance and phosphorylation across eight tissues in fifty rats of equally represented sexes following endurance exercise training (EET) to identify coordinated epigenomic and transcriptional changes and determine key ...
Smith, G. R.
•
Zhao, B.
•
Lindholm, M. E.
•
Raja, A.
...•
Sealfon, S. C.
biorxiv
Wed Jul 02 2025
spRefine Denoises and Imputes Spatial Transcriptomics with a Reference-Free Framework Powered by Genomic Language Model
The analysis of spatial transcriptomics is hindered by high noise levels and missing gene measurements, challenges that are further compounded by the higher cost of spatial data compared to traditional single-cell data. To overcome this challenge, we introduce spRefine, a deep learning framework that leverages genomic language models to jointly denoise and impute spatial transcriptomic data. Our r...
Liu, T.
•
Huang, T.
•
Jin, W.
•
Chu, T.
...•
Zhao, H.
biorxiv
Wed Jul 02 2025
microRNA-206 is a reproducibly sensitive and specific plasma biomarker of amyotrophic lateral sclerosis
Amyotrophic lateral sclerosis (ALS) is a devastating and fatal neurodegenerative disease with no current therapeutic to modify disease progression. Reliable biomarkers for ALS are essential for improving diagnosis and evaluating therapeutic efficacy. We combined small-RNA sequencing from a discovery cohort of ALS patients and healthy controls with sequencing data from a previously published ALS co...
Henderson, B. W.
•
Roberts, B. S.
•
Kolodziejczak, S.
•
Cohcran, M.
•
Myers, R. M.
biorxiv
Wed Jul 02 2025
Perplexity as a Metric for Isoform Diversity in the Human Transcriptome
Long-read sequencing (LRS) has revealed a far greater diversity of RNA isoforms than earlier technologies, increasing the critical need to determine which, and how many, isoforms per gene are biologically meaningful. To define the space of relevant isoforms from LRS, many existing analysis pipelines rely on arbitrary expression cutoffs, but a single threshold cannot accommodate the broad variabili...
Schertzer, M. D.
•
Park, S. H.
•
Su, J.
•
Sheynkman, G. M.
•
Knowles, D. A.
biorxiv
Wed Jul 02 2025
Haplotype-Resolved DNA Methylation at the APOE Locus identifies Allele-Specific Epigenetic Signatures Relevant to Alzheimer's Disease Risk
The APOE gene encodes a key lipid transport protein and plays a central role in Alzheimer\'s disease (AD) pathogenesis. Three common APOE alleles, {epsilon}2 (rs7412(C>T), {epsilon}3 (reference), and {epsilon}4 (rs429358(T>C)), arise from two coding variants in exon 4 and confer distinct AD risk profiles, with {epsilon}4 increasing risk and {epsilon}2 providing protection. The {epsilon}3-linked AP...
Genner, R. M.
•
Meredith, M.
•
Moller, A.
•
Weller, C.
...•
Billingsley, K. J.