An integrated transcriptomic analysis of brain aging and strategies for healthy aging

Abstract

Background: It is been noted that the expression levels of numerous genes undergo changes as individuals age, and aging stands as a primary factor contributing to age-related diseases. Nevertheless, it remains uncertain whether there are common aging genes across organs or tissues, and whether these aging genes play a pivotal role in the development of age-related diseases.

Methods: In this study, we screened for aging genes using RNAseq data of 32 human tissues from GTEx. RNAseq datasets from GEO were used to study whether aging genes drives age-related diseases, or whether anti-aging solutions could reverse aging gene expression.

Results: Aging transcriptome alterations showed that brain aging differ significantly from the rest of the body, furthermore, brain tissues were divided into four group according to their aging transcriptome alterations. Numerous genes were downregulated during brain aging, with functions enriched in synaptic function, ubiquitination, mitochondrial translation and autophagy. Transcriptome analysis of age-related diseases and retarding aging solutions showed that downregulated aging genes in the hippocampus further downregulation in Alzheimer's disease but were effectively reversed by high physical activity. Furthermore, the neuron loss observed during aging was reversed by high physical activity.

Conclusion: The downregulation of many genes is a major contributor to brain aging and neurodegeneration. High levels of physical activity have been shown to effectively reactivate these genes, making it a promising strategy to slow brain aging.

Keywords: aging gene; brain aging; neurodegenerative diseases; retard aging; transcriptome.

FIGURE 1

Alteration of gene expression levels is different between brain and body tissues during aging. (A) Heat map of r-values of each gene to age. Gene expression profiles of tissues were downloaded from GTEX, and the association of gene levels to age were calculated by Pearson correlation analysis. Each row represents one gene, while each column represents one tissue. (B) Heat map of r-values between tissues. Aging transcriptomes of each tissue (each column of panel A) was compared to the other tissues using Pearson correlation analysis.

FIGURE 2

Knockdown of downregulated aging genes accelerates stress-induced senescence. (A) The number of group down aging genes in each group. Venn diagrams of negative aging genes in group i to iv, respectively, with the number of group down aging genes in the center. (B,C) The expression levels of GPCPD1 and TMEM169 are downregulated in stress induced senescent cell. Neuroblastoma cell SH-SY5Y were treated with 25 μg/mL bleomycin (BLM) for 72 h, and senescence was detected by SA-β-gal staining (B), GPCPD1 and TMEM169 were detected by qRT-PCR (C). (D,E) The experiments of panels (B,C) have been repeated in A549 cell. (F–H) GPCPD1 and TMEM169 depletion promotes stress-induced senescence. GPCPD1 and TMEM169 were depleted by siRNAs in A549 cells (F), and cells were treated with BLM for 72 h. SA-β-gal staining was performed (G), and the positive cell rates were counted (H). Student’s t-test, *p < 0.05; **p < 0.01; ***p < 0.001.

FIGURE 3

Enriched function of group down aging genes in three groups. (A) Top 10 biological processes enriched by group i down aging genes. (B) The most enriched four categories of biological process in group i. (C) All of the biological processes enriched by group ii down aging genes. (D) Top 10 biological processes enriched by group iii down aging genes. (E) The overlapped biological processes enriched in both group i and iii. (F–H) Top 10 or all of the KEGG pathways enriched in group i, ii, and iii, respectively.

FIGURE 4

Group up aging genes and enriched functions. (A–D) The number of group up aging genes in each group. Venn diagrams of positive aging genes in group i to iv respectively, with group up aging genes listed. (E–G) Enriched biological processes of group up aging genes from group i-iii. (H) KEGG pathways enriched by group up aging genes from group iii.

FIGURE 5

Aging genes in AD and PD patients. (A) The proportions of upregulated aging genes that further upregulated in corresponding tissues of AD patients. (B) The proportions of downregulated aging genes that further downregulated in corresponding tissues of AD patients. (C,D) Top 10 of enriched biological processes or KEGG pathways of aging and AD downregulated genes in hippocampus (genes in the 44.3% in panel B). (E,F) Same analysis as panels (A,B) in indicated tissues of PD patients.

FIGURE 6

Effects of retard aging solutions on aging and AD gene expression. (A,B) Proportion of reversed aging up (A) or down (B) genes by indicating retard aging solutions in indicating tissues. (C) High physical activity rescues downregulated aging genes in hippocampus. The gene level-age r-values of downregulated aging genes in hippocampus were displayed in green bars. The log₂FC of corresponding genes in high physical activity individuals versus low ones were displayed in purple (p < 0.05) or gray (p > 0.05). (D) Proportion of AD up- or downregulated genes reversed by high or moderate physical activity in hippocampus. (E) High physical activity rescues AD downregulated genes in hippocampus. In each analysis, aging genes that did not detected in the corresponding retarding aging solutions were excluded.

FIGURE 7

High level exercise reverses hippocampus aging. (A) Neuron cells decreased in hippocampus during aging. Cell dissection were performed with hippocampus bulk sequence data from GTEx using CIBERSORTx. (B) High level exercise increases the proportion of neuron cells. Cell dissection were performed with RNAseq data from physical activity study (GSE110298) using CIBERSORTx. (C,D) High level exercise reversed negative aging genes in neuron and oligodendrocyte cells of hippocampus. Cell type-specific gene expression profiles of hippocampus from GTEx and GSE110298 were generated by “high-resolution expression imputation” function of CIBERSORTx. Exercise reversed negative aging genes in neuron or oligodendrocyte were showed respectively (p < 0.05, fold > 1.1). (E,F) Enriched biological process and KEGG pathways by reversed genes in neuron. (G,H) Enriched biological process and KEGG pathways by reversed genes in oligodendrocyte. Student’s t-test, *p < 0.05; **p < 0.01; ***p < 0.001.