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Prefrontal co-expression of schizophrenia risk genes is associated with treatment response in patients

By Giulio Pergola, Pasquale Di Carlo, Andrew E. Jaffe, Marco Papalino, Qiang Chen, Thomas M. Hyde, Joel E Kleinman, Joo Heon Shin, Antonio Rampino, Giuseppe Blasi, Daniel R Weinberger, Alessandro Bertolino

Posted 16 May 2018
bioRxiv DOI: 10.1101/323428 (published DOI: 10.1016/j.biopsych.2019.03.981)

Gene co-expression networks are relevant to functional and clinical translation of schizophrenia (SCZ) risk genes. We hypothesized that SCZ risk genes may converge into co-expression pathways which may be associated with gene regulation mechanisms and with response to treatment in patients with SCZ. We identified gene co-expression networks in two prefrontal cortex post-mortem RNA sequencing datasets (total N=688) and replicated them in four more datasets (total N=227). We identified and replicated (all p-values<.001) a single module enriched for SCZ risk loci (13 risk genes in 10 loci). In silico screening of potential regulators of the SCZ risk module via bioinformatic analyses identified two transcription factors and three miRNAs associated with the risk module. To translate post-mortem information into clinical phenotypes, we identified polymorphisms predicting co-expression and combined them to obtain an index approximating module co-expression (Polygenic Co-expression Index: PCI). The PCI-co-expression association was successfully replicated in two independent brain transcriptome datasets (total N=131; all p-values<.05). Finally, we tested the association between the PCI and short-term treatment response in two independent samples of patients with SCZ treated with olanzapine (total N=167). The PCI was associated with treatment response in the positive symptom domain in both clinical cohorts (all p-values<.05). In summary, our findings in a large sample of human post-mortem prefrontal cortex show that co-expression of a set of genes enriched for schizophrenia risk genes is relevant to treatment response. This co-expression pathway may be co-regulated by transcription factors and miRNA associated with it.

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