Comparative Single Cell Transcriptome Analysis of c-Met Receptor Expressing and Non-Expressing Projection Neurons in the Developing Frontal and Visual Cortices

Single cell transcriptomic analyses in adult mice show that cortical projection neuron (PN) subclasses exhibit heterogenous gene expression profiles that reflect their projection targets, and laminar and areal positions. Further analyses revealed that PNs within the same subclass also exhibit transcriptomic heterogeneity. The MET receptor tyrosine kinase, a regulator of synapse maturation, is expressed in a subpopulation of select cortical PN subclasses, providing an experimental model to address transcriptomic heterogeneity within PN subclasses. Single cell RNA sequencing and smFISH identified transcriptomic differences between Met+ and Met- PN populations in the mouse visual and frontal cortices during the early phase of synapse formation and dendritic growth. Analyses confirmed enrichment of Met in select PN subclasses and further identified astrocytes as the major source of its ligand, Hgf. No genes were expressed uniquely in Met+ or Met- PNs within a subclass; rather, there were graded differences in gene expression between the populations. While the identity of differentially expressed genes varied between subclass and cortical area, there was a consistent overrepresentation of genes associated with axon growth, and synapse structure, development and function, with a subset associated with the MET interactome. Further, expression differences in genes associated with maturation indicate less mature excitatory synapses and spines in the Met+ population at this age. These findings suggest that Met+ neurons do not represent a functional subtype within a PN subclass. Rather, the data are consistent with converging lines of biochemical and electrophysiological evidence that MET contributes to asynchronous maturation of developing cortical circuits. Overall design: P7-P9 frontal and visual cortices were microdissected and analyzed using 10X scRNA sequencing