Sonic Hedgehog Pathway Overactivity Drives Microcephaly

During human brain development, neural stem cells must balance self-renewal and differentiation to build the cerebral cortex – the brain’s outer layer responsible for cognition and perception. If this balance is disturbed, malformations occur. “Recent advances in genome sequencing and genetic engineering are transforming our understanding of neurodevelopmental disorders”, Tuoc Tran says.

Genome screening of patients

He and his team identified de novo EXOSC10 mutations in patients with microcephaly through genomic screening of individuals with cortical malformations. To uncover how these mutations affect brain development, they generated conditional mouse models that reproduce the human mutations. In the developing mouse brain, partial loss of EXOSC10 led to premature differentiation of neural stem cells into neurons, reducing the pool of progenitors. “This reduced the stem cell population, and the cerebral cortex remained smaller – closely mirroring the patients’ phenotype”, says first author Dr. Pauline Ulmke.

Using RNA sequencing and RNA immunoprecipitation analyses, the researchers found that EXOSC10 normally degrades key transcripts of the Sonic hedgehog (Shh) signalling pathway, such as Scube1 and Scube3. When EXOSC10 function was reduced, these transcripts accumulated, leading to aberrantly high Shh activity. “Notably, reducing Shh signalling in mutant mice largely rescued cortical size, pinpointing excessive Shh activity as the main driver of microcephaly in this context”, concludes Pauline Ulmke.

Previously unknown connection

“Our study uncovers a previously unknown link between RNA decay and Sonic hedgehog signalling in brain development,” explains Tran Tuoc. “It shows that a delicate balance of RNA degradation is essential to maintain proper growth of the cerebral cortex.” Beyond identifying EXOSC10 as a novel microcephaly gene, the study provides mechanistic insight into how post-transcriptional RNA regulation controls progenitor dynamics and brain size.

The findings not only broaden the genetic landscape of primary microcephaly but also open new avenues for exploring RNA metabolism and signalling pathways in human brain malformations. This work highlights how state-of-the-art sequencing technologies and genetically engineered mouse models can reveal the molecular underpinnings of complex neurodevelopmental disorders.

Reference: Ulmke PA, Sakib MS, Nguyen DT, et al. EXOSC10 haploinsufficiency causes primary microcephaly by derepression of Sonic hedgehog signalling. Brain. 2025:awaf405. doi: 10.1093/brain/awaf405

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