MEG3 Prevents Cell Death by Restoring Autophagic Flux in Developing Neurons with CLCN4 Variants

To investigate their impact, we introduced patient-relevant CLCN4 variants into human pluripotent stem cells via genome editing and differentiated them into neurons and brain organoids. CLCN4 variants led to a reduction in excitatory neurons due to early-stage neurodegeneration, altering vesicular dynamics in the endo-lysosomal system, disrupting autophagic flux, and increasing neuronal vulnerability.

Transcriptomic profiling identified MEG3, a significantly downregulated long non-coding RNA in CLCN4-variant neurons. Restoring MEG3 expression rescued autophagic flux, mitigated lysosomal dysfunction, and improved survival of CLCN4-variant neurons. These findings establish a link between CLCN4 dysfunction, impaired autophagy, and neurodegeneration, highlighting MEG3 as a potential therapeutic target for neurodevelopmental disorders involving autophagy dysfunction.