CETN3 deficiency induces microcephaly by disrupting neural stem/progenitor cell fate through impaired centrosome assembly and RNA splicing

Xu, Jing; Mao, Xiao; Liu, Zhen; Jiang, Na; Wong, Xin E; Liu, Deng; Wang, Yuan; Zhan, Huaizhe; Liu, Shiyi; Yu, Jiayao; Yuan, Ruiying; Bai, Qingran; Bai, Xianshu; Huang, Wenhui; Xie, Ruoxiao; Krenn, Veronica; Kirchhoff, Frank; Wang, Hua; Guo, Zhenming; Bian, Shan

doi:10.1038/s44321-025-00302-7

Article / Essay Fri Oct 10 2025 CC BY 4.0

published

CETN3 deficiency induces microcephaly by disrupting neural stem/progenitor cell fate through impaired centrosome assembly and RNA splicing

Xu, Jing ; Mao, Xiao ; Liu, Zhen ; Jiang, Na ; Wong, Xin E ; Liu, Deng ; Wang, Yuan ; Zhan, Huaizhe ; Liu, Shiyi ; Yu, Jiayao ; Yuan, Ruiying ; Bai, Qingran ; Bai, Xianshu ; Huang, Wenhui ; Xie, Ruoxiao ; Krenn, Veronica ; Kirchhoff, Frank ; Wang, Hua ; Guo, Zhenming ; Bian, Shan

Abstract Primary microcephaly, a rare congenital condition characterized by reduced brain size, occurs due to impaired neurogenesis during brain development. Through whole-exome sequencing, we identified compound heterozygous loss-of-function mutations in CENTRIN 3 ( CETN3 ) in a 5-year-old patient with primary microcephaly. As CETN3 has not been previously linked to microcephaly, we investigated its potential function in neurodevelopment in human pluripotent stem cell-derived cerebral organoids. We showed that CETN3 -knockout (KO) organoids successfully recapitulated the microcephaly phenotype of reduced size compared to the control organoids. Through transcriptomic, histological, and protein analyses, we found that CETN3 deficiency directly interferes with neuronal differentiation and reduces proliferative capacity in neural stem/progenitor cells by impairing centrosome assembly required in cell cycle progression, consequently activating apoptosis. Furthermore, our data uncovered previously undocumented indirect effects of CETN3 through interaction with RNA splicing machinery involved in brain development. These findings expand the scope of known regulatory mechanisms of CETN3 in brain development and its etiological roles in human brain malformation.

Synopsis CETN3 loss-of-function mutations were identified in a primary microcephaly patient. Mechanistic studies revealed that CETN3 knockout results in impaired centrosome assembly, disrupted neurogenesis, and defective neural stem/progenitor cell (NS/PC) proliferation. CETN3 knockout in human cerebral organoids recapitulated microcephaly. The orientation of mitotic spindles in NS/PCs is altered by CETN3 deficiency, resulting in a bias toward differentiation rather than proliferation. Cell cycle progression is disrupted by CETN3 deficiency, thereby diminishing the proliferative capacity of NS/PCs. Centrosome overduplication is induced by CETN3 deficiency, which contributes to increased NS/PC apoptosis. The expression of genes involved in centriole biogenesis, ciliogenesis, and cell cycle regulation is modulated by CETN3 deficiency through altered RNA splicing.

CETN3 loss-of-function mutations were identified in a primary microcephaly patient. Mechanistic studies revealed that CETN3 knockout results in impaired centrosome assembly, disrupted neurogenesis, and defective NS/PC proliferation.