Sex-specific gene and isoform expression characterizes hippocampal aging in rhesus macaques

Abstract

Aging produces widespread transcriptomic alterations that extend beyond changes in gene expression to include changes at the isoform level. Declining splicing fidelity, including increased intron retention and aberrant isoform expression, has been proposed to contribute to cellular dysfunction; however, the extent and biological significance of isoform-specific changes in the aging brain remain poorly understood. Age-related cognitive decline has also been associated with neuroinflammation and the development of a chronic inflammatory state, or ''inflammaging,'' within the brain. Here, we used short- and long-read RNA sequencing to characterize gene- and isoform-level changes associated with hippocampal aging across sex in 24 rhesus macaques. We identified 594 age-associated differential isoform expression events, comprising both shared and sex-specific changes. Inflammatory pathways, including TNF- -- NF-{kappa}B signaling, interferon responses, and complement pathways, were enriched across both sexes. Weighted gene co-expression network analysis (WGCNA) further identified sex-specific modules associated with inflammatory, glial, mitochondrial, and hormone-responsive processes. Notably, several age-associated changes were detected at the isoform level despite limited or absent corresponding gene-level differences, highlighting transcript-level regulation as an additional dimension of brain aging that may be overlooked by gene-level analyses. To investigate the relationship between aging and Alzheimer's disease (AD), we independently performed WGCNA on the rhesus macaque cohort and a publicly available human hippocampal AD single-nucleus RNA-sequencing dataset (GSE268609). Cross-species module preservation and gene overlap analyses identified shared genes between age-associated and AD-associated networks, with pathway enrichment implicating glial function, inflammation, and mitochondrial biology. Together, these findings highlight sex-associated differences in hippocampal transcriptomic aging, underscore the importance of isoform-level regulation, and identify shared transcriptional signatures between normal aging and AD-associated pathways.