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MEG3 Enhances Survival of Developing Human Neurons with CLCN4-Linked Autophagy Impairment

Kim, D.; Koh, Y.; Jeong, H. S.; Kim, J.; Do, H.; Son, G.; Kim, Y.; Kim, D.; Lim, H.-H.; Park, J.-E.; Han, J.

2025-07-19 neuroscience
10.1101/2025.07.16.665078 bioRxiv
Show abstract

Genetic variations in CLCN4, encoding the H+/Cl- exchanger CLC-4, are associated with human neurodevelopmental disorders with highly variable phenotypes. A lack of physiologically relevant models has hampered molecular understanding of pathogenic mechanisms. We now establish engineered brain organoid and neuronal cell systems to examine impacts of patient-relevant CLCN4 genetic variations. We find that CLCN4 variants reduced excitatory neuron numbers due to early-stage cell death, accompanied by altered endo-lysosomal dynamics and disrupted autophagic flux. Transcriptomic profiling showed significant downregulation of long non-coding RNA MEG3 in CLCN4-variant neurons. Restoring MEG3 expression is sufficient to rescue cellular defects and improve survival of CLCN4-variant neurons. These findings link CLCN4 dysfunction with impaired autophagy and neuronal cell death, highlighting MEG3 as a potential therapeutic target for neurodevelopmental disorders involving autophagic dysfunction.

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