Research Paper Volume 14, Issue 5 pp 2174—2193

Increased DNA methylation, cellular senescence and premature epigenetic aging in guinea pigs and humans with tuberculosis

Carly A. Bobak1, *, , Abhimanyu2,3,4, *, , Harini Natarajan5, , Tanmay Gandhi6,7, , Sandra L. Grimm6,7, , Tomoki Nishiguchi2,3,4, , Kent Koster8, , Santiago Carrero Longlax2,3,4, , Qiniso Dlamini9, , Jacquiline Kahari9, , Godwin Mtetwa9, , Jeffrey D. Cirillo8, , James O’Malley1,10, #, , Jane E. Hill11, #, , Cristian Coarfa6,7, #, , Andrew R. DiNardo2,3,4, #, ,

  • 1 Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
  • 2 The Global Tuberculosis Program, Baylor College of Medicine, Houston, TX 77030, USA
  • 3 William Shearer Center for Human Immunobiology, Texas Children's Hospital, Houston, TX 77030, USA
  • 4 Immigrant and Global Health, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
  • 5 Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH 03755, USA
  • 6 Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
  • 7 Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, TX 77030, USA
  • 8 Department of Microbial Pathogenesis and Immunology, Texas A&M University Health, Bryan, TX 77807, USA
  • 9 Baylor-Swaziland Children’s Foundation, Mbabane, Swaziland
  • 10 The Dartmouth Institute, Dartmouth College, Hanover, NH 03755, USA
  • 11 Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, BC, Canada
* Co-first authors contributing equally
# Co-senior authors contributing equally

Received: December 23, 2021       Accepted: February 22, 2022       Published: March 7, 2022
How to Cite

Copyright: © 2022 Bobak et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


Background: Tuberculosis (TB) is the archetypical chronic infection, with patients having months of symptoms before diagnosis. In the two years after successful therapy, survivors of TB have a three-fold increased risk of death.

Methods: Guinea pigs were infected with Mycobacterium tuberculosis (Mtb) for 45 days, followed by RRBS DNA methylation analysis. In humans, network analysis of differentially expressed genes across three TB cohorts were visualized at the pathway-level. Serum levels of inflammation were measured by ELISA. Horvath (DNA methylation) and RNA-seq biological clocks were used to investigate shifts in chronological age among humans with TB.

Results: Guinea pigs with TB demonstrated DNA hypermethylation and showed system-level similarity to humans with TB (p-value = 0.002). The transcriptome in TB in multiple cohorts was enriched for DNA methylation and cellular senescence. Senescence associated proteins CXCL9, CXCL10, and TNF were elevated in TB patients compared to healthy controls. Humans with TB demonstrate 12.7 years (95% CI: 7.5, 21.9) and 14.38 years (95% CI: 10.23–18.53) of cellular aging as measured by epigenetic and gene expression based cellular clocks, respectively.

Conclusions: In both guinea pigs and humans, TB perturbs epigenetic processes, promoting premature cellular aging and inflammation, a plausible means to explain the long-term detrimental health outcomes after TB.


DE: Differential expression; DHG: Differential hypermethylated genes; DMCs: Differentially methylated CpG sites; DMRs: Differentially methylated regions; DNA: Deoxyribonucleic acid; FC: Fold change; FDR: False discovery rate; GEO: Gene Expression Omnibus; GO: Gene Ontology; GSEA: Gene set enrichment analysis; HR: Hazard Ratio; HIV: Human Immuno-deficiency virus; LCMV: Lymphocytic choriomeningitis virus; LTBI: Latent Tuberculosis Infection; MSigDB: Molecular Signature Database; Mtb: Mycobacterium Tuberculosis; NCBI: National Center for Biotechnology Information; NES: Normalized enrichment scores; OS: Oxidative-stress; OSIS: Oxidative-stress induced senescence; PBMCs: Peripheral blood mononuclear cells; PCR: Polymerase chain reaction; RNA: Ribonucleic acid; RRBS: Representation bisulfite sequencing; SA-PE: Streptavidin-phycoerythrin; SASP: Senescence associated secretory pathway; TF: Transcription factors.