A molecularly defined and spatially resolved cell atlas of the whole mouse brain

Abstract

In mammalian brains, tens of millions to billions of cells form complex interaction networks to enable a wide range of functions. The enormous diversity and intricate organization of cells in the brain have so far hindered our understanding of the molecular and cellular basis of its functions. Recent advances in spatially resolved single-cell transcriptomics have allowed systematic mapping of the spatial organization of molecularly defined cell types in complex tissues. However, these approaches have only been applied to a few brain regions and a comprehensive cell atlas of the whole brain is still missing. Here, we imaged a panel of >1,100 genes in ~8 million cells across the entire adult mouse brain using multiplexed error-robust fluorescence in situ hybridization (MERFISH) and performed spatially resolved, single-cell expression profiling at the whole-transcriptome scale by integrating MERFISH and single-cell RNA-sequencing (scRNA-seq) data. Using this approach, we generated a comprehensive cell atlas of >5,000 transcriptionally distinct cell clusters, belonging to ~300 major cell types, in the whole mouse brain with high molecular and spatial resolution. Registration of the MERFISH images to the common coordinate framework (CCF) of the mouse brain further allowed systematic quantifications of the cell composition and organization in individual brain regions defined in the CCF. We further identified spatial modules characterized by distinct cell-type compositions and spatial gradients featuring gradual changes in the gene-expression profiles of cells. Finally, this high-resolution spatial map of cells, with a transcriptome-wide expression profile associated with each cell, allowed us to infer cell-type-specific interactions between several hundred pairs of molecularly defined cell types and predict potential molecular (ligand-receptor) basis and functional implications of these cell-cell interactions. These results provide rich insights into the molecular and cellular architecture of the brain and a valuable resource for future functional investigations of neural circuits and their dysfunction in diseases.

Single-cell DNA Methylome and 3D Multi-omic Atlas of the Adult Mouse Brain

“…In addition, remarkable cellular diversity is observed in nontelencephalic regions (TH, HY, MB, HB, Fig 2d, e, Extended Data Fig. 5), a common feature observed in other single-cell brain atlases that investigate various molecular modalities [7][8][9]12 .…”

“…After strict quality control, this single-cell RNA-seq (scRNA-seq) dataset established a cell type taxonomy that categorized 4.3 million cells into 5,200 cell clusters, 1,045 supertypes, 306 subclasses, 32 classes, and 7 divisions. Brain-wide MERFISH datasets 7,8 were utilized to incorporate various aspects into the cluster annotation, including spatial distribution, neurotransmitter identity, marker genes, and existing cell-type knowledge 30 .…”

“…To increase spatial resolution and investigate whether the observed methylation spatial pattern corresponds to actual transcriptomic diversity, we employed the MERFISH technology, which enables in situ profiling of hundreds of genes' expression in brain sections 2,8,33 . We designed a 500-gene panel (Legend on next page) (Supplementary Table 6) selected based on cell type and spatial diversity in gene body hypomethylation across the brain (Methods) and profiled six coronal sections corresponding to our mC and m3C brain slices (Extended Data Fig.…”

“…The mouse brain is a complex organ composed of millions of cells forming hundreds of anatomical structures that exhibit diverse cell types [4][5][6][7][8][9] . This cellular and spatial diversity is stringently controlled by epigenetic mechanisms [10][11][12] .…”

High affinity of β-amyloid proteins to cerebral capillaries: implications in chronic lead exposure-induced neurotoxicity in rats

“…In addition, Pb exposure is known to damage the cerebral vasculature [ 41 , 43 , 60 ]. Noticeably also, brain endothelial cells are regionally heterogenous, rendering them more diverse in response to Pb exposure [ 5 ], this regional heterogeneity is even greater in neuronal cells [ 72 ]. Hence, it is possible that the spatial cellular heterogeneity also contributed to LRP1 alterations in the frontal cortex capillaries and hippocampal parenchyma by Pb, but not in others.…”