Individual Brain Structure Deviations and its Gene Expression Signatures in Early-Onset Schizophrenia

Abstract Background Schizophrenia is a highly heritable mental disorder associated with widespread anatomical alterations during neurodevelopment. Converging evidence suggests transcriptomic architecture underlying brain abnormalities in schizophrenia, while how individualized brain morphological deviations relate to gene expression levels remains unclear. Methods To investigate individual-level brain deviations and its transcriptomic signatures in schizophrenia, this study collected T1-weighted MRI data from 95 early-onset schizophrenia (EOS) patients and 99 typically developing (TD) controls. Normative modeling was used to measure individual deviations in cortical thickness and subcortical volume. Partial least squares regression was calculated to capture covarying patterns between structural deviations and whole-brain gene expression levels. Clustering analysis was performed on latent brain-gene covarying components, and the results were further functionally decoded through gene enrichment analyses. Results Group-level comparisons suggested patients with EOS showed consistently decreased z-scores of cortical thickness in the frontal and temporal lobe regions, while increased inter-individual variability in the lingual gyrus. Clustering analysis of z-scores with transcriptomic signatures identified two distinct brain-gene covarying subtypes. Subtype 1 showed thickening cingulate gyrus, thinning occipital pole, and atrophic subcortical nuclei. Subtype 2 exhibited widespread cortical thinning across the frontal, parietal, temporal, and limbic regions, but enlarged subcortical nuclei. Genes underlying two subtypes were both enriched for neurodevelopmental diseases. However, subtype 1 was associated with synaptic transmission, and subtype 2 was related to cytoskeletal and neuronal connectivity. Conclusion This study reveals individual-level anatomical deviations and transcriptomic heterogeneity in early-onset schizophrenia. The findings provide an individualized brain-gene coupling framework for understanding pathophysiology of schizophrenia during brain development.