Selective vulnerability of supragranular layer neurons in schizophrenia

Abstract

Schizophrenia is one of the most wide-spread mental brain disorders with complex and largely unknown etiology. To characterize the impact of schizophrenia at a cellular level, we performed single nucleus RNA sequencing of >190,000 neurons from the dorsolateral prefrontal cortex of patients with schizophrenia and matched controls (7 vs 11, respectively). In addition, to correlate data with cortical anatomy, >100,000 neurons were analyzed topographically by immunohistochemistry in an extended cohort of cases with schizophrenia and controls (10 vs 10). Compositional analysis of RNA sequencing data revealed reduction in relative abundance across all families of GABAergic neurons and a concomitant increase in principal neurons, which was most pronounced for supragranular subtypes (layers 2-3). Moreover, supragranular subtypes of GABAergic interneurons showed most dramatic transcriptomic changes. These results were substantiated by histological analysis, which revealed a reduction in the density of calretinin, calbindin and parvalbumin GABAergic interneurons particularly in layer 2. Common effect of schizophrenia on supragranular neuronal networks was underlined by downregulation of protein processing genes and upregulation of neuronal development/plasticity genes across supragranular subtypes of principal neurons and GABAergic interneurons. In situ hybridization and spatial transcriptomics further confirmed supragranular layer neuron vulnerability, revealing complexity of schizophrenia-affected cortical circuits. These point towards general network impairment within supragranular layers being a core substrate associated with schizophrenia symptomatology.

Altered resting-state functional connectivity in hiPSC-derived neuronal networks from schizophrenia patients

“…We hypothesize that the differences we observe may be due to an altered plasticity mechanism of reinforcing certain neuronal connections during neurodevelopment, resulting in fewer different configurations strengthened in the SZ condition. This possibility is supported by the fact that genome wide-association studies [49][50][51] and a recent singlenucleus RNA sequencing (snRNAseq) analysis in SZ [52], have evidenced alterations in sequence and expression of several genes implicated in specific synaptic pathways related to plasticity [53].…”

Case-control analysis of single-cell RNA-seq studies

“…Using simple MDS plots and tests, we indeed found that in many cases batch or other technical factors drove expression or compositional differences of the datasets more than the conditions the study was designed to compare. Especially when unbalanced, such factors can significantly distort the results, highlighting the importance of tracking and testing for association with technical and design factors, as was done for instance in (Batiuk et al, 2020). Further methodological developments will be needed to incorporate ability to control and correct for extraneous factors within the comparison tests themselves.…”

“…The impact of the disease in different samples, however, may be heterogeneous, and result in shifts of disease samples along different directions, effectively increasing variability of the expression states in the disease condition ("variance change", Fig. 4C,F) (Batiuk et al, 2020). Such situation is likely to be characteristic of complex spectrum disorders, such as schizophrenia and autism, where understanding of multidirectionality of transcription shifts could help to distinguish subgroups of patients.…”

Cell group analysis reveals changes in upper-layer neurons associated with schizophrenia

“…Our findings of SCZ-associated changes in upper-layer neurons were validated by multiple lines of experiments from other studies. In a recent snRNA-seq study of cortical layers from seven SCZ patients and 11 controls, the selective vulnerability of supragranular layer neurons was revealed in SCZ in terms of dramatic transcriptomic changes and cell proportion changes 47 . A decreased proportion of upper-layer neuron subtypes was also observed in mouse model SCZ-predisposing 22q11.2 microdeletion 48 and human postmortem brains 49,50 .…”