Transcriptomic profiles of aging in purified human immune cells

Lindsay M. Reynolds, Jingzhong Ding, Jackson R. Taylor, Kurt Lohman, Nicola Soranzo, Alberto de la Fuente, Tie Fu Liu, Craig Johnson, R. Graham Barr, Thomas C. Register, Kathleen M. Donohue, Monica V. Talor, Daniela Cihakova, Charles Gu, Jasmin Divers, David Siscovick, Gregory Burke, Wendy Post, Steven Shea, David R. JacobsIna Hoeschele, Charles E. McCall, Stephen B. Kritchevsky, David Herrington, Russell P. Tracy, Yongmei Liu

Research output: Contribution to journalArticle

Abstract

Background: Transcriptomic studies hold great potential towards understanding the human aging process. Previous transcriptomic studies have identified many genes with age-associated expression levels; however, small samples sizes and mixed cell types often make these results difficult to interpret. Results: Using transcriptomic profiles in CD14+ monocytes from 1,264 participants of the Multi-Ethnic Study of Atherosclerosis (aged 55-94 years), we identified 2,704 genes differentially expressed with chronological age (false discovery rate, FDR = 0.001). We further identified six networks of co-expressed genes that included prominent genes from three pathways: protein synthesis (particularly mitochondrial ribosomal genes), oxidative phosphorylation, and autophagy, with expression patterns suggesting these pathways decline with age. Expression of several chromatin remodeler and transcriptional modifier genes strongly correlated with expression of oxidative phosphorylation and ribosomal protein synthesis genes. 17% of genes with age-associated expression harbored CpG sites whose degree of methylation significantly mediated the relationship between age and gene expression (p < 0.05). Lastly, 15 genes with age-associated expression were also associated (FDR = 0.01) with pulse pressure independent of chronological age. Comparing transcriptomic profiles of CD14+ monocytes to CD4+ T cells from a subset (n = 423) of the population, we identified 30 age-associated (FDR < 0.01) genes in common, while larger sets of differentially expressed genes were unique to either T cells (188 genes) or monocytes (383 genes). At the pathway level, a decline in ribosomal protein synthesis machinery gene expression with age was detectable in both cell types. Conclusions: An overall decline in expression of ribosomal protein synthesis genes with age was detected in CD14+ monocytes and CD4+ T cells, demonstrating that some patterns of aging are likely shared between different cell types. Our findings also support cell-specific effects of age on gene expression, illustrating the importance of using purified cell samples for future transcriptomic studies. Longitudinal work is required to establish the relationship between identified age-associated genes/pathways and aging-related diseases.

Original languageEnglish (US)
Article number333
JournalBMC genomics
Volume16
Issue number1
DOIs
StatePublished - Dec 12 2015

Keywords

  • Aging
  • Autophagy
  • Methylation
  • Mitochondrial ribosome
  • Monocyte
  • Oxidative phosphorylation
  • Protein synthesis
  • Ribonucleoprotein complex
  • T cell
  • Transcriptome
  • Translation

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

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    Reynolds, L. M., Ding, J., Taylor, J. R., Lohman, K., Soranzo, N., de la Fuente, A., Liu, T. F., Johnson, C., Barr, R. G., Register, T. C., Donohue, K. M., Talor, M. V., Cihakova, D., Gu, C., Divers, J., Siscovick, D., Burke, G., Post, W., Shea, S., ... Liu, Y. (2015). Transcriptomic profiles of aging in purified human immune cells. BMC genomics, 16(1), [333]. https://doi.org/10.1186/s12864-015-1522-4