Single-cell, multi-region profiling of the macaque brain across the lifespan

Yang, W.; Watkins, K. L.; DeCasien, A. R.; O'Neill, M. B.; Bohlen, M. O.; O'Day, D. R.; Duran, M.; Qiu, C.; Meleshko, A.; Vo, A.; Menke, M.; Calderon, D.; Cayo Biobank Research Unit,; Sallet, J.; Higham, J. P.; Martinez, M. I.; Trapnell, C.; Starita, L. M.; Montague, M. J.; Platt, M.; Chiou, K. L.; Shendure, J.; Snyder-Mackler, N.

doi:10.1101/2025.10.31.685880

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bioRxiv · 10.1101/2025.10.31.685880

Single-cell, multi-region profiling of the macaque brain across the lifespan

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Abstract

Brain aging is a complex process with profound health and societal consequences. However, the molecular and cellular pathways that govern its temporal progression-along with any cell type-, region-, and sex-specific heterogeneity in such progression-remain poorly defined. Here, we present a transcriptomic atlas of 5.3 million cells from 582 samples spanning 11 brain regions of 55 rhesus macaques (29 female, 26 male), aged 5 months (early life) to 21 years (late adulthood). We annotate 12 major cell classes and 225 subclusters, including region-specific subtypes of excitatory and inhibitory neurons, astrocytes, and ependymal cells. We identify a vulnerable excitatory neuron population in the superficial cortical lamina and a cortical interneuron population that are less abundant later in life, along with subtle, region-specific, age-associated compositional differences in subpopulations of microglia and oligodendrocytes, whose detection required single-cell resolution. Finally, we chart convergent and divergent age-associated molecular signatures across brain regions and cell classes-where some of these signatures are sex-specific and could underlie sex biases in neurological disorders. We find that age-associated transcriptional programs not only overlap substantially with those seen in Alzheimers disease (AD), but also unfold along distinct temporal trajectories across brain regions, suggesting that aging and AD may share molecular roots that emerge at different life stages and in region-specific, sex-specific windows of vulnerability. This work provides a temporal, regional, and sex-stratified atlas of the aging primate brain, offering insights into cell type-specific vulnerabilities and regional heterogeneity with translational human relevance.

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Yang, W., Watkins, K. L., DeCasien, A. R., O'Neill, M. B., Bohlen, M. O., O'Day, D. R., Duran, M., Qiu, C., Meleshko, A., Vo, A., Menke, M., Calderon, D., Cayo Biobank Research Unit,, Sallet, J., Higham, J. P., Martinez, M. I., Trapnell, C., Starita, L. M., Montague, M. J., Platt, M., Chiou, K. L., Shendure, J., Snyder-Mackler, N.. 2025-11-01. Single-cell, multi-region profiling of the macaque brain across the lifespan. https://doi.org/10.1101/2025.10.31.685880

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