Age-associated alterations in pro-inflammatory gene expression in humans

National Institute On Aging

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Abstract

The goal of the first phase of GESTALT was to obtain transcriptomic, proteomic and epigenomic data from 11 purified immune cell subsets obtained from peripheral blood. Sample collection for this phase was completed in February 2020. While the last sets of samples were being collected we began to analyze RNA, protein, DNA methylation and ATAC-Seq data from the first 54 samples. During FY21 we accomplished the following: - we combined methylation, other epigenetic marks, ChIP-Seq and gene expression data into a manuscript describing cellular identity of 6 immune cell types from human blood. the revised re-submission is in place. - Age-associated changes in DNA methylation were identified for each cell type. Motif analysis showed that sites of age-associated hypomethylation in most cell types were enriched for the binding site of ARNT, the heterodimeric partner of hypoxia-induced factor 1a. These analyses were completed during FY21 and a manuscript is being prepared for submission. It is expected to be submitted within FY21. - Age-associated changes in chromatin structure were evaluated in monocytes using a cohort of 21 individuals from GESTALT. To determine functional consequences of these age-related changes we carried out stimulation studies using LPs as an activator and analyzed cytokine and chemokine expression using multi-parameter flow cytometry. One of the interesting observations was that a subset of older individuals constitutively express IL-1b and IL-6, indicative of ongoing NF-kB activation. In these subjects further LPS treatment does not induce higher levels of these inflammatory cytokines. These data are being prepared for publication. - We assayed DNA methylation and transcriptional changes that accompany differentiation of naive lymphocytes to memory lymphocytes. Hypomethylation, rather than hypermethylation, featured prominently during this transition in all three adaptive lineages (B cells, CD4+ and CD8+ T cells). Remarkably, sites of differentiation-induced hypomethylation were enriched for motifs of the transcription factor ARNT. Amongst these changes we clearly distinguished those that were common to all lymphocytes and those that occurred specifically in B versus T cells. We extended these studies to include ATAC-Seq changes that occur upon differentiation of naive to memory cells. - To complement ATAC-Seq data from naive and memory human B cells, we carried out cell activation studies. RNA-Seq was used to identify genes whose expression is changed by differentiation to memory cells. Relationships between altered DNA methylation, chromatin structure changes and inducible gene expression are being assembled into a manuscript. - We completed studies of human wound healing. - we initiated studies of COVID patient samples.