Comparative cellular analysis of motor cortex in human, marmoset and mouse

Abstract

The primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally conserved across mammals1. Here, using high-throughput transcriptomic and epigenomic profiling of more than 450,000 single nuclei in humans, marmoset monkeys and mice, we demonstrate a broadly conserved cellular makeup of this region, with similarities that mirror evolutionary distance and are consistent between the transcriptome and epigenome. The core conserved molecular identities of neuronal and non-neuronal cell types allow us to generate a cross-species consensus classification of cell types, and to infer conserved properties of cell types across species. Despite the overall conservation, however, many species-dependent specializations are apparent, including differences in cell-type proportions, gene expression, DNA methylation and chromatin state. Few cell-type marker genes are conserved across species, revealing a short list of candidate genes and regulatory mechanisms that are responsible for conserved features of homologous cell types, such as the GABAergic chandelier cells. This consensus transcriptomic classification allows us to use patch–seq (a combination of whole-cell patch-clamp recordings, RNA sequencing and morphological characterization) to identify corticospinal Betz cells from layer 5 in non-human primates and humans, and to characterize their highly specialized physiology and anatomy. These findings highlight the robust molecular underpinnings of cell-type diversity in M1 across mammals, and point to the genes and regulatory pathways responsible for the functional identity of cell types and their species-specific adaptations.

A multimodal cell census and atlas of the mammalian primary motor cortex

“…Correspondence matrices show that the mouse MERFISH-based spatial transcriptomic taxonomy 41 , the transcriptomic-epigenomic integrated mouse molecular taxonomies using either SCF or LIGER 37 and the human and marmoset transcriptomic taxonomies 38 all aligned largely consistently with the mouse consensus transcriptomic taxonomy (Fig. 9e, Extended Data Fig.…”

“…1d) between marmoset and mouse. However, this probably reflects that rare non-neuronal cells in human (n = 40 nuclei) were under-sampled compared with marmoset (n = 463) and mouse (n = 2,329), and average expression was not adequately estimated 38 .…”

“…We describe a synthesis of eleven companion studies through a coordinated multi-laboratory effort. In these studies, we derive a cross-species consensus molecular taxonomy of cell types using scRNA-seq or single-nucleus RNA sequencing (snRNA-seq), DNA methylation and chromatin accessibility data [37][38][39][40] . In mouse, we map the spatial cellular organization by multiplexed error-robust fluorescence in situ hybridization (MERFISH) 41 , characterize morphological and electrophysiological properties by multimodal profiling using patch clamp recording, biocytin staining and scRNA-seq (Patch-seq) 42,43 , describe the cellular input-output wiring diagrams by anterograde and retrograde tracing 44 , identify glutamatergic neuron axon projection patterns by Epi-retro-seq 45 , Retro-MERFISH 41 and single-neuron complete morphology reconstruction 46 , and describe transgenic driver lines targeting glutamatergic cell types on the basis of marker genes and lineages 47 .…”

“…This integrated taxonomy linked RNA transcripts with epigenomic marks identifying potential cell-type-specific cis-regulatory elements (CREs) and transcriptional regulatory networks. Similarly, we established M1 cell-type taxonomies for human (127 t-types) and marmoset (94 t-types) by unsupervised clustering of snRNA-seq data, followed by integration with epigenomic datasets 38 .…”

“…Patch-seq also enables direct comparison of the morpho-electric properties of homologous cell types across species. Here we analysed the gigantocellular Betz cells found in M1 of primates and large carnivores, which are predicted to be in the L5 ET subclass 38 , as are the mouse corticospinal-projecting L5 ET neurons. We first created a joint embedding of excitatory neurons in mouse, macaque and human, which showed strong homology across all three species for the L5 ET subclass (Fig.…”