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A Strategy to Identify de Novo Mutations in Common Disorders such as Autism and Schizophrenia

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Developmentally dynamic, non-convergent transcriptomic profiles in CNV models for schizophrenia risk.

Hayley French¹, Shuyang Yao^1,2, Lisa Bast^1,3

¹Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.

Molecular Psychiatry

|June 18, 2026

Summary

Rare genetic variations (copy number variations or CNVs) linked to schizophrenia impact distinct molecular pathways differently across development. These distinct pathways, not a shared mechanism, contribute to schizophrenia

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Area of Science:

Neuroscience
Genetics
Psychiatry

Background:

Schizophrenia exhibits significant genetic and clinical heterogeneity.
Numerous rare copy number variations (CNVs) are associated with high schizophrenia risk but lack overlapping gene content or function.

Purpose of the Study:

To investigate whether downstream effects of schizophrenia-associated CNVs converge on shared molecular pathways.
To analyze age- and cell type-specific molecular alterations in response to distinct CNVs.

Main Methods:

Single-cell RNA sequencing was employed on prefrontal cortex tissue from five schizophrenia-associated CNV mouse models (15q13.3del, 3q29del, 1q21.1del, 22q11.2del, and 16p11.2dup).
Transcriptomes were analyzed across adolescent and adult developmental stages.
Differential gene expression and pathway perturbations were identified in over 292,000 single-cell transcriptomes.

Main Results:

Each CNV model displayed unique, age- and cell type-specific patterns of gene expression and pathway alterations.
No convergence on a shared molecular mechanism was observed; instead, CNVs affected distinct cellular pathways dynamically throughout development.
Genes dysregulated in specific neuronal populations (15q13.3del, 16p11.2dup, and 22q11.2del models) were enriched for schizophrenia single nucleotide polymorphism (SNP) heritability.

Conclusions:

Rare CNVs contribute to schizophrenia genetic risk through distinct, developmentally dynamic molecular pathways, rather than a single shared mechanism.
This finding refines our understanding of the complex genetic architecture of schizophrenia.