KMT2D deficiency leads to cellular developmental disorders and enhancer dysregulation in neural-crest-containing brain organoids

• Published in: Science bulletin (Beijing) Vol. 69; no. 22; pp. 3533 - 3546
• Main Authors: Shan, Ziyun, Zhao, Yingying, Chen, Xiuyu, Zhan, Guodong, Huang, Junju, Yang, Xuejie, Xu, Chongshen, Guo, Ning, Xiong, Zhi, Wu, Fang, Liu, Yujian, Liu, He, Chen, Biyuan, Chen, Bingqiu, Sun, Jiaoyang, He, Jiangping, Guo, Yiping, Cao, Shangtao, Wu, Kaixin, Mao, Rui, Wu, Guangming, Lin, Lihui, Zou, Xiaobing, Wang, Jie, Chen, Jiekai
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 30-11-2024
• Subjects: Cerebral organoids; Enhancer; KMT2D; Niche; Single-cell multiome; KMT2D; Niche; Enhancer; Cerebral organoids; Single-cell multiome
• ISSN: 2095-9273
• DOI: 10.1016/j.scib.2024.09.004

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KMT2D, a H3K4me1 methyltransferase primarily regulating enhancers, is a leading cause of KABUKI syndrome. This multisystem disorder leads to craniofacial and cognitive abnormalities, possibly through neural crest and neuronal lineages. However, the impacted cell-of-origin and molecular mechanism of KMT2D during the development of KABUKI disease remains unknown. Here we have optimized a brain organoid model to investigate neural crest and neuronal differentiation. To pinpoint KMT2D’s enhancer target, we developed a genome-wide cis-regulatory element explorer (GREE) based on single-cell multiomic integration. Single cell RNA-seq revealed that KMT2D-knockout (KO) and patient-derived organoids exhibited neural crest deformities and GABAergic overproduction. Mechanistically, GREE identified that KMT2D targets a roof-plate-like niche cell and activates the niche cell-specific WNT3A enhancer, providing the microenvironment for neural crest and neuronal development. Interestingly, KMT2D-mutated mice displayed decreased WNT3A expression in the diencephalon roof plate, indicating impaired niche cell function. Deleting the WNT3A enhancer in the organoids presented phenotypic similarities to KMT2D-depletion, emphasizing the WNT3A enhancer as the predominant target of KMT2D. Conversely, reactivating WNT signaling in KMT2D-KO rescued the lineage defects by restoring the microenvironment. Overall, our discovery of KMT2D’s primary target provides insights for reconciling complex phenotypes of KABUKI syndrome and establishes a new paradigm for dissecting the mechanisms of genetic disorders from genotype to phenotype.