Comprehensive in situ mapping of human cortical transcriptomic cell types

Abstract

The ability to spatially resolve the cellular architecture of human cortical cell types over informative areas is essential to understanding brain function. We combined in situ sequencing gene expression data and single-nucleus RNA-sequencing cell type definitions to spatially map cells in sections of the human cortex via probabilistic cell typing. We mapped and classified a total of 59,816 cells into all 75 previously defined subtypes to create a first spatial atlas of human cortical cells in their native position, their abundances and genetic signatures.

Conservation and divergence in cortical cellular organization between human and mouse revealed by single-cell transcriptome imaging

“…1D). The excitatory-to-inhibitory neuron ratio was 2:1 in human, in line with recent independent measurements (9,11) and substantially lower than the 6:1 ratio observed in mouse (Fig. 1D).…”

“…Among inhibitory neurons, VIP and LAMP5 were enriched in upper layers (L1-L3) while PVALB and SST were broadly distributed from L2 to L6 (Fig. 2, A middle and B middle) (8,9). Notably, at the cluster level, inhibitory neurons also adopted a pronounced laminar organization, with many inhibitory clusters being primarily restricted to one cortical layer, or even a sub-portion of a layer (Fig.…”

“…Next, we performed dimensionality reduction using principal component analysis (PCA), restricted to the 30 principal components (PCs) with the highest eigenvalues, and finally visualized using a 2D UMAP embedding (55). In the UMAP space, the batch effect between MERFISH experiments was further eliminated using Canonical Correlation Analysis (CCA) which was implemented in Seurat V3 (9). To identify transcriptionally distinct cell clusters, we performed graph-based Leiden (56) community detection (k=15; resolution=0.5) in the 30 PCs-space.…”

“…Recent single-cell RNA sequencing analysis has revealed a high diversity of transcriptionally distinct cell populations in the human MTG (8), a model system for studying human cortex because fresh surgical tissues are often available for this brain region. Combination of single-cell RNA sequencing with microdissection (8), and more recently an in situ sequencing study targeting 120 genes (9), have revealed the laminar organization of these transcriptionally defined neuronal cell types, in particular the excitatory neuronal cell types, in the human MTG. However, a systematic understanding of the spatial relationship and cell-cell interactions among this high diversity of cell types is still lacking.…”

Developmental landscape of human forebrain at a single-cell level unveils early waves of oligodendrogenesis

“…To determine the exact spatial location of the first waves of OL lineage cells, we performed In Situ Sequencing (Gyllborg et al, 2020; Ke et al, 2013) on an entire PCW 8 forebrain, with 10μm thick coronal sections covering both ventral and dorsal regions and spanning three regions in the anterior-posterior axis (Figure 7A-E, S6 and S7). In particular, we applied hybridization-based In Situ Sequencing (HybISS) (Gyllborg et al, 2020) that has an increased signal-to-noise ratio and performs well for in situ mapping of human cell types (Langseth et al, 2021). We targeted 50 genes which characterize subsets of the populations identified_by scRNA-seq and scATAC-Seq (Figure 7D, E and S7A-D) and used pciSeq (Qian et al, 2020) for cellular assignment.…”