A Brain Anti-Senescence Transcriptional Program Triggered by Hypothalamic-Derived Exosomal microRNAs

Abstract

In contrast to the hypothesis that aging results from cell-autonomous deterioration processes, the programmed longevity theory proposes that aging arises from a partial inactivation of a "longevity program" aimed at maintaining youthfulness in organisms. Supporting this hypothesis, age-related changes in organisms can be reversed by factors circulating in young blood. Concordantly, the endocrine secretion of exosomal microRNAs (miRNAs) by hypothalamic neural stem cells (htNSCs) regulates the aging rate by enhancing physiological fitness in young animals. However, the specific molecular mechanisms through which hypothalamic-derived miRNAs exert their anti-aging effects remain unexplored. Using experimentally validated miRNA-target gene interactions and single-cell transcriptomic data of brain cells during aging and heterochronic parabiosis, we identify the main pathways controlled by these miRNAs and the cell-type-specific gene networks that are altered due to age-related loss of htNSCs and the subsequent decline in specific miRNA levels in the cerebrospinal fluid (CSF). Our bioinformatics analysis suggests that these miRNAs modulate pathways associated with senescence and cellular stress response, targeting crucial genes such as Cdkn2a, Rps27, and Txnip. The oligodendrocyte lineage appears to be the most responsive to age-dependent loss of exosomal miRNA, leading to significant derepression of several miRNA target genes. Furthermore, heterochronic parabiosis can reverse age-related upregulation of specific miRNA-targeted genes, predominantly in brain endothelial cells, including senescence promoting genes such as Cdkn1a and Btg2. Our findings support the presence of an anti-senescence mechanism triggered by the endocrine secretion of htNSC-derived exosomal miRNAs, which is associated with a youthful transcriptional signature.

Keywords: aging; bioinformatics; exosomes; miRNAs; neural stem cells; transcriptomics.

Figure 1

Shared pathways enriched in htNSC-derived miRNA gene targets suggest a transcriptional anti-aging program operating in young animals. Chord diagram showing Reactome pathways shared by ≥3 htNSCs miRNA-targeted genes. Logarithmic fold change (logFC) in miRNA CSF levels with aging was reported in [5]. Figure was made with SRPlot (http://www.bioinformatics.com.cn/SRplot (accessed on 30 November 2023)).

Figure 2

Age-upregulated htNSC-derived miRNA target genes across the main brain cell classes. Alluvial plot networking htNSC-secreted miRNAs with their target genes upregulated with aging in ≥2 brain cell classes. Statistically significantly upregulated genes determined by single-cell RNA-seq (TPM-based FC ≥ 1.5 and adjusted p-value < 0.05) were extracted from [16].

Figure 3

Interaction network between htNSC-derived miRNAs and their age-upregulated target genes in oligodendrocyte lineage. Regulatory gene network between miRNAs and age-upregulated genes in the oligodendrocyte precursor cells, mature oligodendrocytes, and olfactory ensheathing glia. Statistically significantly upregulated genes determined by single-cell RNA-seq (TPM-based FC ≥ 1.5 and adjusted p-value < 0.05) were extracted from [16]. For genes upregulated in more than one cell type, node size and color represent the greatest change observed.

Figure 4

Heterochronic parabiosis reverse age-dependent upregulation of several target genes of htNSC-secreted exosomal miRNAs. Balloon plot showing the reversal of age-associated upregulation of htNSC-derived miRNA target genes after 4–5 weeks of heterochronic parabiosis. Logarithmic-transformed FCs were downloaded from [16] (aging-associated changes) and [20] (heterochronic parabiosis-associated changes). We used a Benjamini–Hochberg-adjusted p-value < 0.05 thresholding to determine statistically significant differential expression.

Figure 5

htNSC-derived miRNA target genes are widely upregulated in aged hypothalamus. Heatmap highlighting differential expression of htNSC-derived miRNA target genes between young and old female hypothalamus-specific cell types. Color scale indicates the logarithmic-transformed FC. NS = not significant.

Figure 6

Integrative model of the anti-senescence program triggered by htNSC-derived miRNAs with the hallmarks of aging. Aging-dependent inflammation causes htNSC loss and diminished exosomal miRNA secretion. Subsequent loss of decline in the repression of key target genes promotes brain aging through cellular senescence and oxidative stress.