Transcriptome of Layer 3 Pyramidal Neurons in the Cortical Visuospatial Working Memory Network: Regional Variation and Alterations in Schizophrenia

Deficits in visuospatial working memory (VSWM) is a common symptom of schizophrenia (SZ). VSWM depends on coordinated information transfer across a hierarchical network of cortical regions in the dorsal visual stream, including dorsolateral prefrontal cortex (DLPFC), posterior parietal cortex, PPC), and primary visual cortex (V1). Alterations in excitatory layer 3 pyramidal neurons (L3PNs), a primary source of cortico-cortical projections, are associated with VSWM deficits in SZ. Markers of activity in GABA neurons, which receive excitation from L3PNs, are lower in SZ, with greater alterations in PPC and V1 than in DLPFC. However, this pattern is opposite that of morphological alterations associated with lower L3PN activity in SZ, which are greater in DLPFC than in V1. To resolve conflicting findings, we first (study 1) used qPCR to quantify the specificity of alterations in activity-dependent GABA neuron transcripts in individuals with SZ (n=41) and UCs (n=43) in 2 zones of the DLPFC containing GABA neurons, which either did (superficial zone) or did not (deep zone) receive excitation from L3PNs. Levels of GABA activity-dependent markers were only lower in the superficial zone in SZ, suggesting these alterations reflect L3PN hypoactivity. Next, we sampled pools of 100 L3PNs in SZ (n=39) and UC subjects by laser capture microdissection from the DLPFC, PPC, and V1. L3PN samples underwent RNA-sequencing and were analyzed to identify (study 2) differences in gene expression (GE) and alternative splicing (AS) between SZ and UC subjects. GE alterations in SZ were similar across regions but were greatest in V1, intermediate in PPC, and lowest in DLPFC L3PNs. In L3PNs of each region, oxidative phosphorylation genes (markers of neuronal activity) were downregulated, whereas postsynaptic genes were upregulated in SZ, which may suggest transcriptome alterations in L3PNs are compensatory. Although few AS differences were evident in SZ, regional differences in AS (study 3) were preserved between SZ and UC subjects and associated with genes involved in synaptic neurotransmission and morphology, suggesting AS differences could influence regional differences in excitatory drive to, and morphological alterations in, L3PNs. Together these findings suggest lower L3PN activity may contribute to lower activity-dependent marker levels in GABA neurons.