Transcriptomic and genetic analysis suggests a role for mitochondrial dysregulation in schizophrenia

Abstract Schizophrenia is an often devastating disorder characterized by persistent and idiopathic cognitive deficits, delusions and hallucinations. Schizophrenia has been associated with impaired nervous system development and an excitation/inhibition imbalance in the prefrontal cortex. On a molecular level, schizophrenia is moderately heritable and genetically complex. Hundreds of risk genes have been identified, spanning a heterogeneous landscape dominated by loci that confer relatively small risk. Bioinformatic analyses of genetic associations point to a limited set of neurons, mainly excitatory cortical neurons, but other analyses suggest the importance of astrocytes and microglia. To understand different cell type roles in schizophrenia and reveal novel cell-type specific aetiologically relevant perturbations in schizophrenia, our study integrated genetic analysis with single nucleus RNA-seq of 536,618 nuclei from postmortem samples of dorsal prefrontal cortex (Brodmann Area 8/9) of 43 cases with schizophrenia and 42 neurotypical controls. We found no significant difference in cell type abundance. Gene expression in excitatory layer 2-3 intra-telencephalic neurons had the greatest number of differentially expressed transcripts and, together with excitatory deep layer intra-telencephalic neurons, conferred most of the genetic risk for schizophrenia. Most differential expression of genes was found in specific cell types and was dominated by down-regulated transcripts. Down-regulated transcripts were enriched in gene sets including transmembrane transport, mitochondrial function, protein folding, and cell-cell signaling whereas up-regulated transcripts were enriched in gene sets related to RNA processing, including RNA splicing in neurons. Co-regulation network analysis identified 40 schizophrenia-relevant programs across 13 cell types. A gene program largely shared between neuronal subtypes, astrocytes, and oligodendrocytes was significantly enriched for schizophrenia risk, supporting an aetiological role for perturbed protein modification, ion transport, and mitochondrial function. These results were largely consistent with cell-type expression quantitative trait locus and transcriptome-wide association analyses. Moreover, single-cell RNA sequencing results, most prominently mitochondrial dysfunction, had multiple points of convergence with proteomic and long-read RNA sequencing results from samples from the same donors. Our study integrates genetic analysis with transcriptomics to reveal novel cell-type specific aetiologically relevant perturbations in schizophrenia. Competing Interest Statement PFS is a shareholder and consultant for Neumora Therapeutics. Funding Statement The authors gratefully acknowledge contributions of the Cuyahoga County Medical Examiner's Office and the families of the deceased. The efforts of Drs. James Overholser, George Jurjus and Herbert Y. Meltzer, and Lesa Dieter and Gouri Mahajan in the psychiatric assessments and tissue processing are also acknowledged. FACS isolation was performed with support from Biomedicum Flow Cytometry Core Facility (BFC). We acknowledge Anke A. Dijkstra and Remco V. Klaassen for technical assistance and performing mass spectrometry experiments. The authors acknowledge support from the National Genomics Infrastructure in Stockholm funded by Science for Life Laboratory, the Knut and Alice Wallenberg Foundation and the Swedish Research Council, and NAISS/Uppsala Multidisciplinary Center for Advanced Computational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure. Computational resources, data handling and support were enabled by the National Academic Infrastructure for Supercomputing in Sweden (NAISS), hosted by UPPMAX and PDC, partially funded by the Swedish Research Council through grant agreement no. 2022-06725, and by the University of North Carolina at Chapel Hill and the Research Computing group. Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Swedish Ethical Review Authority gave ethical approval for this work I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Footnotes ↵* Joint first authors Data availability The source data and processed datasets that support the findings of this study are in the process of being made available through the European Genome-Phenome Archive (EGA, https://ega-archive.org). Table files can be accessed through DOI:10.5281/zenodo.15025718. The GeneMatrix resource is available online at figshare https://figshare.com/articles/dataset/geneMatrix/13335548.