Cortical organoids reveal human-specific roles of METTL5 in neurodevelopment via regulation of CHCHD2

Abstract

METTL5 is a conserved methyltransferase responsible for catalyzing N6-methyladenosine (m6A) modification on 18S ribosomal RNA. Human patients with mutations in METTL5 show severe microcephaly and intellectual disability, which has not been fully recapitulated in animal models. Given its emerging role in neurodevelopment, we sought to investigate METTL5 function in a human-specific context using cortical forebrain organoids derived from human induced pluripotent stem cells. We generated METTL5 knockout organoids and observed a marked delay in neural stem cell proliferation and the timing of neuronal differentiation, suggesting a critical role for METTL5 in the temporal regulation of neurogenesis. Though METTL5 methylates rRNA near the decoding center, the mechanism of this methylation remains highly contested. In our cortical organoids, broad translational changes mirror stress response rather than transcript-specific regulation of translation. Transcriptomic analysis further revealed a significant downregulation of CHCHD2, a nuclear-encoded mitochondrial gene linked to cellular energy metabolism and neurodevelopmental processes. Overexpression of CHCHD2 rescued proliferation defects of METTL5-KO neural progenitor cells, suggesting dysregulation of CHCHD2 is heavily involved in the phenotypes of METTL5 mutant patient brains. These findings highlight a previously uncharacterized link between METTL5, ribosomal RNA modification, and cellular metabolism essential for proper human brain development.