Integrated single cell and unsupervised spatial transcriptomic analysis defines molecular anatomy of the human dorsolateral prefrontal cortex

Abstract

The molecular organization of the human neocortex has been historically studied in the context of its histological layers. However, emerging spatial transcriptomic technologies have enabled unbiased identification of transcriptionally-defined spatial domains that move beyond classic cytoarchitecture. Here we used the Visium spatial gene expression platform to generate a data-driven molecular neuroanatomical atlas across the anterior-posterior axis of the human dorsolateral prefrontal cortex (DLPFC). Integration with paired single nucleus RNA-sequencing data revealed distinct cell type compositions and cell-cell interactions across spatial domains. Using PsychENCODE and publicly available data, we map the enrichment of cell types and genes associated with neuropsychiatric disorders to discrete spatial domains. Finally, we provide resources for the scientific community to explore these integrated spatial and single cell datasets at research.libd.org/spatialDLPFC/.

Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments

“…For example, using data from the 10x Genomics Visium Spatial Gene Expression platform, a Samui user can annotate at the cell (segmented cells/points on the image), spot (55 μm circles), or spatial domain (polygons) level ( Figure 2a ). Annotation can also be done using data acquired from the 10x Genomics Visium Spatial Proteogenomics platform, which generates multiplex images of fluorescently-labeled proteins paired with gene expression [23].…”

“…Visium Spatial Proteogenomics (Visium-SPG) Data. Full-resolution IF images, filtered spaceranger output, and annotations were obtained from [23] (https://github.com/LieberInstitute/spatialDLPFC). Primary antibodies were for four brain cell-type marker proteins, NeuN for neurons, TMEM119 for microglia, GFAP for astrocytes, and OLIG2 for oligodendrocytes.…”

“…Samui is available at https://samuibrowser.com (v1.0.0-next.7). The 10x Genomics Visium data was obtained from [23, 26]. The source MERFISH data is available from the Vizgen Data Release Program [27, 28].…”

escheR: Unified multi-dimensional visualizations with Gestalt principles

“…In a recent study investigating the molecular organization of human dorsolateral prefrontal cortex [16], two schizophrenia risk genes, membrane-bound ligand ephrin A5 ( EFNA5 ) and ephrin type-A receptor 5 ( EPHA5 ), were identified to colocalize via cell-cell communication analysis. In addition, data suggested Layer 6 was the most highly co-localized layer compared to other cortex layers.…”

“…We provide an R package, escheR, implementing these ideas, which is built on the state-of-the-art data visualization framework ggplot2 in the R programming language. The traditional visualization displays the colocalization plot of the expression of two genes EFNA5 and EPHA5 (A) and the spatial domains from the dorsolateral prefrontal cortex (DLPFC) in postmorteum human brain [16] (B) side-by-side, creating challenges to cognitively connecting colocalization status to spatial domains. (C) The watercolor effect enables displaying spatial domains by color-coding only outlines of circles.…”