Long‑Range Gene Networks Uncover 641 New Schizophrenia‑Associated Genes
Schizophrenia’s genetic landscape just expanded dramatically. A new study in Nature Genetics identifies 641 previously unrecognized genes associated with schizophrenia, thanks to a modeling framework that captures how distant genetic variants regulate gene expression through co‑expression networks. The work reframes schizophrenia not as a collection of isolated genetic hits, but as a disorder shaped by long‑range regulatory relationships across the brain. The study is titled, “Co‑expression‑based models improve eQTL predictions for transcriptome‑wide association studies and highlight new schizophrenia‑associated genes.”
The research team, led by Giulio Pergola, PhD, at the Lieber Institute for Brain Development (LIBD), developed two trans‑aware predictive models—INGENE and MODULE—that quantify how variants far from a gene influence its expression through co‑regulated partners. Traditional transcriptome‑wide association studies (TWAS) focus almost exclusively on cis‑expression quantitative trait loci (cis–eQTLs), variants within ±1 Mb of a gene. But as the paper noted, “Most transcriptome‑wide association approaches primarily model local (cis) genetic effects, leaving much of gene regulation unexplained.” By contrast, the new models incorporate distal (trans) regulatory effects, capturing regulatory relationships that behave more like social networks than neighborhood blocks.
Using RNA‑seq data from six human post‑mortem brain regions and genetic data from more than 102,000 individuals, the team integrated cis‑based predictors (CIS, EpiXcan) with their new trans‑based frameworks. The combined approach improved gene‑expression prediction for 18,744 genes, and when applied to Psychiatric Genomics Consortium (PGC3) datasets, it identified 766 schizophrenia‑associated genes, including 641 not previously detected by TWAS.
Pergola said the field has been “looking for the light under the lamppost, focusing only on genes close to disease‑associated DNA variants.” By illuminating long‑range interactions, he explained, “we’ve essentially turned on lights across the entire neighborhood, revealing how distant genetic variants coordinate to build the genetic basis of schizophrenia.”
The findings converge on pathways involved in glutamate signaling, neuronal communication, immune processes, and neurodevelopment—biological systems repeatedly implicated in psychiatric risk. MODULE‑derived trans‑single nucleotide polymorphisms (SNPs) showed particularly strong enrichment for schizophrenia‑associated variants, and many overlapped with cis‑eQTLs for transcription factors such as GATAD2A, RERE, IRF3, and SP4, all previously prioritized in schizophrenia GWAS.
Daniel Weinberger, MD, CEO and director of LIBD, emphasized the shift in perspective: “Schizophrenia risk isn’t just about individual genes acting one after another—it’s about how networks of genes work together. Understanding these coordinated genetic programs brings us closer to precision psychiatry.”
By demonstrating that trans‑regulatory architecture is both detectable and biologically meaningful, the study provides a roadmap for expanding TWAS beyond local effects. It also underscores the importance of integrating multi‑region brain transcriptomics with large‑scale genetic cohorts to reveal disease‑relevant regulatory relationships.
