Cross-species analysis identifies mitochondrial dysregulation as a functional consequence of the schizophrenia-associated 3q29 deletion

The 1.6Mb deletion at chromosome 3q29 (3q29Del) is the strongest identified genetic risk factor for schizophrenia, but the effects of this variant on neurodevelopment are not well understood. We interrogated the developing neural transcriptome in two experimental model systems with complementary advantages: isogenic human cortical organoids and isocortex from the 3q29Del mouse model. We profiled transcriptomes from isogenic cortical organoids that were aged for 2 months and 12 months, as well as perinatal mouse isocortex, all at single-cell resolution. Systematic pathway analysis implicated dysregulation of mitochondrial function and energy metabolism. These molecular signatures were supported by analysis of oxidative phosphorylation protein complex expression in mouse brains and assays of mitochondrial function in engineered cell lines. Together these data indicate that metabolic disruption is associated with 3q29Del and is conserved across species., Cell Culture and Genome Engineering
Whole blood samples of 5-10 mL were collected in EDTA Vacutainer test tubes and processed for the isolation of erythroid progenitor cells (EPCs) using the Erythroid Progenitor Kit (StemCell Technologies). EPCs were reprogrammed using Sendai particles (CytoTune-iPS 2.0 Reprogramming kit, Invitrogen) and plated onto Matrigel-coated six-well plates (Corning). Cultures were transitioned from erythroid expansion media to ReproTesR (StemCell Technologies) and then fed daily with ReproTesR until clones were isolated. iPSCs were maintained on Matrigel-coated tissue culture plates with mTeSR Plus (StemCell Technologies).
Cell lines were characterized for stem cell markers by RT-PCR and immunocytochemistry after at least 10 passages in culture. Total RNA was isolated from each cell line with the RNeasy Plus Kit (Qiagen) according to the manufacturer’s protocol. mRNA was reverse transcribed into cDNA using the High Capacity cDNA Synthesis Kit (Applied Biosystems..., , # Cross-species analysis identifies mitochondrial dysregulation as a functional consequence of the schizophrenia-associated 3q29 deletion

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Use the following code and input data sets to generate the figures in this paper.

Create a directory for each figure, copy the code and input files into that folder, and put all folders in a directory named \"Purcell 2023 dataset\". Place the Purcell 2023 dataset directory on the desktop for file paths in R scripts to work smoothly.

## Description of the data and file structure

### Fig. 1

Cross-species single-cell sequencing. (A) A single-cell RNA-sequencing experiment was performed in isogenic human induced pluripotent stem cell (iPSC)-derived cortical organoids at two time points (2 months and 12 months in vitro) and in postnatal day 7 mouse isocortex. An overview of the strategy to collect and filter differential gene expression data from both model systems is illustrated. (B) The human 3q29 deletion locus is nearly perfectly syntenic with ...