Fig. 2: Identifying a transcriptomic cell type that corresponds to von Economo neurons (VENs) in situ.

a Violin plots showing distributions of genes further examined by in situ hybridization (ISH). Each row represents a gene, black dots indicate median gene expression within clusters, and maximum gene expression values are shown on the right-hand side of each row. Gene expression values are displayed on a linear scale. The EXC GABRQ FEZF2 type expresses GABRQ and ADRA1A, previously defined markers of VENs. b Chromogenic single gene ISH from the Allen Human Brain Atlas (http://human.brain-map.org/) for GABRQ and ADRA1A confirms a subset of layer 5b cells expressing these genes have spindle-shaped cell bodies typical of VENs (red arrows). The nearest Nissl-stained section is shown for each ISH image for laminar context. c ISH from the Allen Human Brain Atlas (http://human.brain-map.org/) for genes expressed in other excitatory neuron types revealed by our analyses. Genes are expressed in and around layer 5 of FI but labeled cells lack spindle-shaped cell bodies typical of VENs. Red arrows in the nearest Nissl-stained section for each ISH image show representative examples of cells with VEN morphology in the approximate region highlighted in the neighboring ISH image (red rectangle). Scale bars in b, c low magnification, 150 μm, high magnification 50 μm. d Multiplex fluorescent ISH (top left) and double chromogenic ISH for marker genes of Exc FEZF2 GABRQ. Cells with pyramidal (P), VEN (V), and fork (F) morphologies are indicated by labeled arrows in each image. Scale bars, 10 μm. e Quantification of the proportion of ADRA1A+, POU3F1+ cells with pyramidal vs. VEN morphologies (n = 5 human donors). Cells lacking defining features of these morphological classes were called uncharacterized. Bars show the mean and error bars the standard deviation. Individual data points are overlaid on each bar plot.