Naz, H. | Search bioRxiv

bioRxiv2025

Core Activation Program and Selective Regional Responsiveness of Microglia in Aging and Parabiosis

Aging is associated with immune dysregulation in brain and is the biggest risk factor for many neurodegenerative diseases whereas rejuvenation interventions can mediate beneficial effects. Microglia are considered as a major player in the development of neurodegenerative disease yet, the molecular changes underlying brain aging and rejuvenation remain poorly understood at the single cell level. We identified and benchmarked several reproducible microglial states and a core set of genes leading to microglia activation in the mice brain. We investigated microglial heterogeneity and studied the impact of aging and parabiosis-mediated exposure of young and old blood on microglia subpopulations across four different brain regions including cerebellum, cortex, hippocampus, and striatum. We revealed region-specific differences in microglia subpopulation composition and age-related changes, with cerebellum and striatum displaying the most distinctive profiles and dynamic shifts compared to other brain regions. We consistently observed cerebellum as the most responsive, while striatum appeared distinctive by its minimal responsiveness to these interventions. Our findings highlighted the role of microglia in brain regional vulnerability and provided a foundation for microglia-targeted treatment for modulating brain aging. HighlightsO_LIDefined the composition of different microglial populations reproducible in aging and parabiosis, benchmarking a reference for the field. C_LIO_LIUncovered an under-appreciated core activation gene signature of microglia shared in all reactive states and regions during normal aging and old blood-induced aging. C_LIO_LIIdentified region-specific gene expression changes and associated biological processes in microglia during aging and parabiosis C_LIO_LIDiscovered microglial regional selectivity in response to aging and parabiosis, showing cerebellum as the most sensitive region and the striatum as the least affected. C_LI

neuroscience↗

bioRxiv2025

Single nucleus multiomic atlas of human dorsal root ganglia reveals the contribution of non-neuronal cell types to pain

Sensory neurons residing in dorsal root ganglia (DRG) transmit sensory information such as pain, itch, touch, pressure and bodily position to the central nervous system. The activity of sensory neurons is regulated by non-neuronal cell types in the DRG, including satellite glial cells (SGCs), immune cells and fibroblasts. Dysregulated gene expression in DRG cells contributes to sensory nervous system disorders such as chronic pain. Understanding the genetic underpinnings of these conditions requires dissecting transcriptional regulation in human tissue. In this study, we profiled transcriptomic and chromatin accessibility landscapes from postmortem human DRG (hDRG) samples at single-nucleus level. We demonstrate that sequencing depth significantly impacts downstream analysis, with deeper sequencing yielding more detected cells and features, improved data integration, refined clustering and annotation, and more accurate scientific interpretations. We identified nine major cell types, defined their molecular signatures, and mapped cis-regulatory landscapes. Integration of gene expression with chromatin accessibility enabled peak-gene association and transcriptional network analyses, revealing transcription factors, their target genes, regulatory elements and potential partners that cooperatively drive cell-type-specific gene expression programs. This integrative approach identified cell types, genes, and cis-regulatory regions potentially driving pain conditions. Our unbiased genome-wide analysis not only recovered known pain-related genes but also highlighted novel candidate genes and regulatory regions implicated in pain mechanisms. Importantly, our results demonstrate that non-neuronal cells, including endothelial cells, fibroblasts, macrophages, and SGCs, play critical roles in pain pathogenesis and should be investigated as therapeutic targets. One Sentence SummaryOur work provides a comprehensive single-nucleus multi-omic atlas of human dorsal root ganglia, uncovering novel cell-type-specific regulatory mechanisms and candidate therapeutic targets for pain, thereby directly advancing translational insights into human sensory disorders and chronic pain pathogenesis.

neuroscience↗