GESTALT-Genetic and Epigenetic Signatures of Translational Aging Laboratory Testing

National Institute On Aging

Investigators

Linked publications, trials & patents

Abstract

Progress in 2021: 1- GESTALT donors recruitment is still ongoing and donors follow-up visits in years 2 and 4 are also still ongoing. Now, we have 68 donors that completed visit 2 (year 2) and 40 donors that completed visit 3 (year 4). 2-Transcriptome: The RNA sequencing of the immune cells was completed for around 1400 samples. The cell-specific gene expression analysis was determined for 6 immune cells of 50 donors and are part of the manuscript "DNA methylation signatures reveal that distinct combinations of transcription factors specify human immune cell epigenetic identity" that was published in FY 2021 in Immunity. The age-associate changes in gene expression analysis are ongoing and a manuscript is in preparation. 3- Proteome: We studied the proteins present in primary skin fibroblasts collected from 82 GESTALT donor. We identified key pathways associated with skin fibroblast aging, including autophagy, scavenging of reactive oxygen species (ROS), ribosome biogenesis, DNA replication, and DNA repair. This study was published this year in Aging Cell. Proteomic studies of the 13 immune cells (around 1000 sample) from the 99 GESTALT donors was completed and the data analysis is in progress. 4- Epigenetics a. Chromatin Accessibility: Age-associate changes in chromatin accessibility were studied in monocytes and B cells (naive and memory). Monocytes open chromatin studies were performed in 21 donors (young: 20-55year n=12, old: 60-85 years n=9). PCA analysis of differentially open chromatin (DOC) identified three major clusters, only old (n=5), only young (n=7) and old and young together (n=4 O+5 Y). This heterogeneous healthy old population was characterized by significant enrichment of DOC comprising NF-kappaB and ETS motifs. The genes associated with DOCs corresponded to the enrichment of pro-inflammatory pathways involving NF-kappaB and NOD-like receptor signaling, demonstrating heterogenous inflamm-aging process. Furthermore, the monocytes of the 5 old donors show distinct cytokine expression profile in intracellular cytokine assays. Inflammatory cytokines such as IL-6 and IL-1beta were already expressed in the baseline status. However, TNFalpha was neither expressed at the baseline nor after endotoxin activation (LPS). The current analysis of chromatin accessibility variations with DNA methylation, transcriptome, and serum cytokine levels are determined and a manuscript is in preparation. B cell open chromatin studies identified the naive and memory features of lymphocytes such as presence of OCT motif in memory specific open chromatin and ETS in naive B cells. Manuscript describing the lymphocytes differentiation properties is in preparation. b. Methylome: DNA methylation data was obtained from 99 donor and the cell specific methylation was determined. In summary our analysis identified lineage-specific signatures and their relationships to other epigenomic chromatin features. Lineage-specific sites of hypomethylation coincided with enhancer chromatin marks while lineage-specific hypermethylation sites presented only in adaptive immune cells but not the innate ones. We further studied if the cell specific methylation was related to the cell specific gene expression. Our data shows that small portion of cell specific upregulated genes were also hypomethylated in that specific cell type. The cell specific methylation and gene expression manuscript by Roy et al was published in Immunity. In addition to the cell specific methylation studies, age-associate changes in DNA methylation manuscript was submitted for publication. We further assayed DNA methylation and gene expression changes of naive to memory lymphocytes (B, CD4 and CD8 T cells) differentiation. These differentiation studies were accompanied with activation assays and a manuscript is in preparation.