(W1332) Identification and mitigation of major confounders in psychiatric disease models: clonal, batch-to batch, operator- and material-based variability

Abstract: While iPSC-based models provide a powerful tool for studying psychiatric disorders, even small variabilities related to interclonal homogeneity, robustness of differentiation protocols, and standardization of supplies can compromise reproducibility and data interpretation. Using risk-stratified patient-derived iPSCs and a genome editing-based candidate gene approach, we scrutinized key obstacles impacting iPSC-based modeling of depression-associated neurodevelopmental disorders. Using a cohort of patients and healthy donors, we generated cortical neural progenitors stratified by polygenic risk scores for bipolar disorder (BD1) and assessed neurodevelopmental phenotypes. We also employed a genome editing approach to study GPM6A, a gene linked to depression, schizophrenia, and BD1. Confounders including clonal variability, donor blood mosaicism, and culture conditions were systematically evaluated. In the BD1 model, clonal variability largely impacted reproducibility. Neurodevelopmental phenotypes were further highly dependent on iPSC handling and subtle differences in differentiation dynamics.
Furthermore, network activity in GPM6A-deficient cortical neurons was biased by cell density and clone-specific culture composition. After addressing these confounders, only few of the previously reported pathophenotypes related to BD1 and GPM6A could be confirmed. However, we identified several new interesting BD1-associated candidates, including NBPF3, a gene involved in the regulation of vitamin B6 clearance and previously linked to symptom severity in schizophrenia. Our findings underscore the critical need for improved standardization in iPSC-based models, especially for polygenic disease models and candidate genes with small effect sizes. Patient-derived models require extended cohorts, optimized donor selection, and advanced standardized protocols incorporating genetic and environmental risk factors. In isogenic models, expanded genetic backgrounds and robust culture systems are essential. Both lines of research depend on careful PSC clone selection, a standardized supply of high-end materials, and operator consistency. Such advancements are also vital for enhancing the reliability of iPSC models in therapy development and compound testing.

Funding Source: This project was supported by a grant of the German Research Foundation and Swiss National Science Foundation (grant no. GZ: BR 1337/4-1, project no. 412637376)

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