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

METTL5 catalyzes N6-methyladenosine (m6A) modification on 18S rRNA. In humans, loss-of-function mutations in METTL5 cause severe microcephaly and intellectual disability, whereas Mettl5 knockout (KO) animal models display inconsistent and incomplete microcephaly phenotypes. To better model human disease, we generated METTL5-KO human induced pluripotent stem cell (hiPSC)-derived cortical organoids, which exhibited impaired neural progenitor cell (NPC) proliferation and differentiation, leading to reduced ventricle-like structures and more faithful recapitulation of patient phenotypes. Mechanistically, Ribo-seq analysis revealed broad translational changes in METTL5-KO NPCs consistent with cellular stress responses rather than transcript-specific translational changes. Single-cell RNA-seq identified downregulation of CHCHD2, a mitochondrial regulator of oxidative metabolism. Reintroduction of CHCHD2 in METTL5-KO NPCs rescued proliferation and partially rescued oxidative metabolism defects. This suggests dysregulation of CHCHD2 is a driver of METTL5-mediated regulation of neurogenesis. These findings highlight a previously uncharacterized link between METTL5, CHCHD2, and cellular metabolism as essential for proper human brain development.