Transcriptomic diversity of cell types across the adult human brain

Abstract

The human brain directs a wide range of complex behaviors ranging from fine motor skills to abstract intelligence and emotion. However, the diversity of cell types that support these skills has not been fully described. Here we used high-throughput single-nucleus RNA sequencing to systematically survey cells across the entire adult human brain in three postmortem donors. We sampled over three million nuclei from approximately 100 dissections across the forebrain, midbrain, and hindbrain. Our analysis identified 461 clusters and 3313 subclusters organized largely according to developmental origins. We found area-specific cortical neurons, as well as an unexpectedly high diversity of midbrain and hindbrain neurons. Astrocytes also exhibited regional diversity at multiple scales, comprising subtypes specific to the telencephalon and to more precise anatomical locations. Oligodendrocyte precursors comprised two distinct major types specific to the telencephalon and to the rest of the brain. Together, these findings demonstrate the unique cellular composition of the telencephalon with respect to all major brain cell types. As the first single-cell transcriptomic census of the entire human brain, we provide a resource for understanding the molecular diversity of the human brain in health and disease.

Transcriptomic cytoarchitecture reveals principles of human neocortex organization

“…S12E ). By contrast, areal variation in protoplasmic, but not ILM or fibrous astrocytes, was apparent and this was consistent with previous reports describing brain-wide astrocyte heterogeneity ( 20 , 50 ) and variation in astrocytes across cortical and hippocampal areas in mouse ( 51 ). Interestingly, protoplasmic astrocytes from ACC grouped together on the UMAP and expressed distinct areal markers ( NRP2, NR4A3 , and LGR6 ) ( Fig.…”

“…Single cell and spatial transcriptomic technologies have recently provided new and powerful means to define cortical cellular diversity and spatial organization and compare across cortical areas and species (11)(12)(13)(14)(15)(16)(17)(18)(19). Applied to human (11,20), marmoset (12), and mouse primary motor cortex (15,16,19), single cell RNA-seq revealed a complex, hierarchical cell type architecture based on gene expression signatures that is quite well conserved across species except at the finest cell type cluster distinctions (16). These studies established a subclass level of the hierarchy consisting of 24 well-defined neuronal and nonneuronal types with highly conserved identities across species, distinct laminar patterning and correlated phenotypic properties including cellular anatomy, physiology and broad projection targets (Table S1).…”

Integrative single-cell characterization of hypothalamus sex-differential and obesity-associated genes and regulatory elements

“…Similarly, the recent study by Siletti et al,. in which ~3.4 million nuclei from 106 sections of three human adult brains were sequenced, observed a large number of oligodendrocytes (~600K) despite the fact that they isolated neurons by FACS with NeuN (similar to what was done here) aiming to collect 90% neurons and 10% non-neuronal cells 119 . This might be due to human neurons being sensitive to nuclear permeabilization or samples being collected post-mortem when nucleus neurons are the most sensitive to hypoxia 120 as well as the age of donors (Supplemental Table 1).…”

deCLUTTER2+pipeline to analyze calcium traces in a novel stem cell model for ventral midbrain patterned astrocytes

“…Astrocytes are a highly heterogeneous cell type based on their morphology, transcriptome, and physiology (Batiuk et al, 2020; Bayraktar et al, 2020; Oberheim et al, 2009; Pestana et al, 2020; Siletti et al, 2022). They elicit heterogeneous responses to injury and functionally specialize to their surrounding tissue (Bugiani et al, 2022).…”

“…They elicit heterogeneous responses to injury and functionally specialize to their surrounding tissue (Bugiani et al, 2022). Astrocytes residing in the ventral midbrain are physiologically distinct from, e.g., astrocytes in the cortex and hippocampus (Siletti et al, 2022; Xin et al, 2019). Additionally, ventral midbrain astrocytes alleviate neuronal α-synuclein pathology, which is one of the main pathological hallmarks of PD (Yang et al, 2022).…”