Single-Cell Atlas of Microglia Reveals Conserved and Divergent Cell Populations in Mouse and Human Brain 2255696

Multimodal brain cell atlas across the adult macaque lifespan.

A comprehensive transcriptomic and chromatin accessibility atlas of 8 brain regions of 23 female cynomolgus macaques spanning the adult lifespan, including exceptionally old individuals establishes a foundational framework for understanding the cellular and regulatory architecture of primate brain aging and its links to disease.

Cross-species single-cell atlas of the striatum defines cell-type and subregion disease vulnerabilities.

The striatum is critical for decision-making, movement, and reward processing, functions achieved through subregional cellular and molecular specialization. Striatal cell types and subregions are differentially implicated in neurodegenerative and neuropsychiatric disorders, but the mechanisms underlying these vulnerabilities are poorly understood. Using single-nucleus RNA sequencing across 109 human and 22 mouse samples spanning dorsal and ventral striatum, we provide a comprehensive atlas of subregional neuronal specialization. We define rare neuronal subpopulations and transcriptional gradients along the dorsolateral-ventromedial axis with notable differences between species, suggesting divergent pharmacological targets, connectivity, and disease mechanisms. Integration with genome-wide association and pharmacological studies identifies human-enriched sites of opioid receptor expression and ventral-biased chronic antipsychotic action. Lastly, paired single-cell transcriptomic and somatic trinucleotide repeat expansion measurements identify differences in subregion and neuronal subtype vulnerability in Huntington's disease. Our findings lay the foundation for understanding how striatal cell types and subregions contribute to brain function and neurological disorders.

Somatic mutations reveal the ontogeny of microglia in human ageing.

A roadmap for enriching rare cell populations from human post-mortem brain, demonstrated by 100% microglial purity

Understanding brain disease requires studying the specific cell types that drive each condition: microglia in Alzheimer’s, dopaminergic neurons in Parkinson’s, motor neurons in ALS, and many others. For most of these rare populations, protocols to isolate them from human post-mortem brain at the required purity have never been developed. The shared hurdles are reliable nuclear markers, compatible fluorescent dyes, antibody host-species cross-reactivity, and achieving pure rather than merely enriched populations. Here we present a generalisable roadmap for developing fluorescence-activated nuclear sorting (FANS) protocols for rare cell populations in human brain. We demonstrate it on microglia, reaching 100% purity in cortex and 98% in cerebellum, with the cortex sort simultaneously yielding astrocytes at 93% purity. The roadmap tackles each hurdle including an on-bench antibody labelling step that expands fluorescence channels without cross-reactivity problem and an affordable single-nucleus RNA-seq validation workflow, giving labs a pathway for enriching any rare cell type reliably.

A reference protein atlas of the adult mouse brain vasculature

Current methods for assessing low-abundance proteins in individual cells are limited. As a result, cell functions are often inferred from single-cell RNA sequencing (scRNA-seq) data, which can be misleading due to the poor cross-gene correlation (different genes in the same cells) between messenger RNA (mRNA) and protein levels. To address this issue, we used isolated brain vascular fragments to study the blood–brain barrier. We applied a combination of deep bulk proteomic analysis, a proteomic ruler approach, and scRNA-seq, assuming a high within-gene correlation (same gene in different cells) between mRNA and protein. This approach allowed us to estimate protein copy numbers per cell for 9,940 proteins across eight cell types, including endothelium, smooth muscle, pericytes, fibroblasts, and microglia. We also evaluated protein abundance in astrocyte end-feet attached to the vessel fragments. Our data are available through an Online Database, providing a searchable resource and reference protein atlas for future studies of neurovascular proteomics in health and disease.

VINE-seq and MultiVINE-seq for single-nucleus and multiome profiling of the brain vasculature.