New research reveals the cellular secrets of aging, with cutting-edge single-cell data mapping how neurons, glial cells, and immune systems reshape the aging brain.
Study: Brain-wide cell-type-specific transcriptomic signatures of healthy ageing in mice. Image Credit: Monkey Business Images / Shutterstock
In a recent study published in the journal Nature, scientists from the Allen Institute for Brain Science in the United States investigated how different cell types in the mouse brain change at the genetic level with age. By analyzing over 1.2 million single-cell transcriptomes from young and old mice, the researchers identified key gene expression shifts linked to aging. These shifts highlight specific molecular mechanisms, such as immune activation and structural integrity decline, across various cell types. These findings could help reveal brain regions and cells most affected by aging.
Background
Aging is a natural process marked by cellular and molecular changes that impact overall function. In the brain, aging manifests as altered cell activity, inflammation, and reduced neurogenesis, among other changes. Previous studies have identified general aging markers across tissues and some brain-specific changes. However, given the brain's complexity and its numerous cell types and functions, it remains unclear how specific cell types contribute to aging. Emerging evidence has shown that certain regions, such as the hypothalamus’s third ventricle, serve as focal points for aging-related changes. Recent advances in single-cell transcriptomics have provided unprecedented insights into cellular diversity and allowed researchers to identify changes at high resolution.
While these studies have revealed age-related shifts in neurons and glial cells, comprehensive mapping across the entire brain is lacking. This mapping has now revealed distinct, cell-type-specific aging patterns, including immune activation and neuronal decline. Furthermore, specific changes in smaller, overlooked cell populations and their contribution to brain health and aging remain unexplored. Understanding these dynamics is crucial to uncovering the mechanisms driving age-related cognitive and functional decline and their potential links to neurodegenerative diseases.
About the study
The present study employed single-cell ribonucleic acid sequencing (scRNA-seq) to examine the brains of young (2-month-old) and aged (18-month-old) mice. The researchers targeted 16 key brain regions, encompassing the forebrain, midbrain, and hindbrain. These regions were selected for their involvement in aging and age-related disorders. Using the 10x Genomics platform, the researchers generated a dataset of approximately 1.2 million high-quality single-cell transcriptomes from neurons and non-neuronal cells. Notably, this represents one of the most comprehensive single-cell datasets for aging research to date. Additional cell sorting strategies ensured comprehensive sampling across cell types, and the study included fluorescence-activated cell sorting (FACS) for the unbiased sampling of neurons and other cells.
The Allen Brain Cell Atlas, an open resource developed by the Allen Institute that allows researchers to explore numerous whole-brain datasets, was used to annotate the data. The findings identified 847 cell clusters representing 172 subclasses across 25 cell classes. Furthermore, gene expression changes were modeled using computational methods to detect differentially expressed genes associated with aging. Spatial transcriptomics was also employed to obtain additional validation and visualize gene expression in brain regions of interest.
Numerous other analyses were used to categorize differentially expressed genes by cell class and subclass while distinguishing age-related changes in neurons, glial cells, and other cell types. This included the identification of specific pro-inflammatory microglial clusters and age-depleted neural stem cell populations. Particular attention was given to sparsely distributed populations, such as ependymal cells and tanycytes, specialized glial cells found in the hypothalamus and involved in regulating physiological processes such as energy balance.
Additionally, Gene Ontology or GO enrichment analyses were performed to identify the biological processes impacted by aging, such as immune signaling and neuronal structure maintenance. These analyses uncovered significant losses in neurogenic potential and structural maintenance, especially in tanycytes and neurons near the hypothalamic third ventricle. Key gene expression patterns were identified using in situ hybridization to complement the transcriptomic findings.
Results
The study found that aging leads to significant changes in gene expression across various brain cell types and identified 2,449 differentially expressed genes with unique and common signatures across cell types. Neurons, glial, and vascular cells showed distinct gene expression patterns, with many differentially expressed genes linked to immune activation, structural integrity, and cellular senescence.
Notably, neurons exhibited reduced expression of synaptic signaling and structural genes such as Ccnd2, while microglia displayed increases in inflammatory markers like Ildr2 and Ccl4. Glial cells, such as astrocytes and oligodendrocytes, displayed reduced expression of support-related genes. In contrast, the expression of immune-related genes was higher in microglia, macrophages, and other immune cell types.
Furthermore, region-specific changes were observed to be prominent near the hypothalamic third ventricle, where tanycytes and ependymal cells displayed notable age-associated shifts. These shifts included increased interferon-response signaling and reduced markers for structural maintenance. Similarly, oligodendrocytes in aged brains exhibited altered gene expression patterns, suggesting compromised myelin integrity.
Vascular cells, particularly endothelial cells, also showed aging-related gene expression changes linked to the genes involved in the major histocompatibility complex (MHC) antigen presentation, with evidence of impaired vascular function. Furthermore, the microglial cells in aged brains formed new clusters associated with pro-inflammatory and senescent states. Spatial analyses confirmed increased immune activity localized to subcortical areas, particularly the midbrain and hindbrain.
Conclusions
The results provided a detailed single-cell transcriptomic map of brain aging and uncovered cell-type-specific and region-specific molecular changes linked to aging. These findings highlight the hypothalamus as a hub for aging-related changes, with significant implications for understanding neurodegenerative diseases. Key findings highlighted the roles of immune activation, neuronal decline, and glial dysfunction in aging. These insights set the foundation for exploring how aging influences brain function and its intersection with neurodegenerative diseases.
Journal reference:
- Jin, K., Yao, Z., van Velthoven, C. T. J., Kaplan, E. S., Glattfelder, K., Barlow, S. T., Boyer, G., Carey, D., Casper, T., Chakka, A. B., Chakrabarty, R., Clark, M., Departee, M., Desierto, M., Gary, A., Gloe, J., Goldy, J., Guilford, N., Guzman, J., Hirschstein, D... & Zeng, H.(2025). Brain-wide cell-type-specific transcriptomic signatures of healthy ageing in mice. Nature. DOI:10.1038/s41586024083508, https://www.nature.com/articles/s41586-024-08350-8