Microdeletion in distal PLP1 enhancers causes hereditary spastic paraplegia 2.

Xun Zhou, Yige Wang, Runcheng He, Zhenhua Liu, Qian Xu, Jifeng Guo, Xinxiang Yan, Jinchen Li, Beisha Tang, Sheng Zeng, Qiying Sun

Annals of clinical and translational neurology 2023 Sep

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Hereditary spastic paraplegia (HSP) is a genetically heterogeneous disease caused by over 70 genes, with a significant number of patients still genetically unsolved. In this study, we recruited a suspected HSP family characterized by spasticity, developmental delay, ataxia and hypomyelination, and intended to reveal its molecular etiology by whole exome sequencing (WES) and long-read sequencing (LRS) analyses. WES was performed on 13 individuals of the family to identify the causative mutations, including analyses of SNVs (single-nucleotide variants) and CNVs (copy number variants). Accurate circular consensus (CCS) long-read sequencing (LRS) was used to verify the findings of CNV analysis from WES. SNVs analysis identified a missense variant c.195G>T (p.E65D) of MORF4L2 at Xq22.2 co-segregating in this family from WES data. Further CNVs analysis revealed a microdeletion, which was adjacent to the MORF4L2 gene, also co-segregating in this family. LRS verified this microdeletion and confirmed the deletion range (chrX: 103,690,507-103,715,018, hg38) with high resolution at nucleotide level accuracy. In this study, we identified an Xq22.2 microdeletion (about 24.5 kb), which contains distal enhancers of the PLP1 gene, as a likely cause of SPG2 in this family. The lack of distal enhancers may result in transcriptional repression of PLP1 in oligodendrocytes, potentially affecting its role in the maintenance of myelin, and causing SPG2 phenotype. This study has highlighted the importance of noncoding genomic alterations in the genetic etiology of SPG2. © 2023 The Authors. Annals of Clinical and Translational Neurology published by Wiley Periodicals LLC on behalf of American Neurological Association.

Citation

Xun Zhou, Yige Wang, Runcheng He, Zhenhua Liu, Qian Xu, Jifeng Guo, Xinxiang Yan, Jinchen Li, Beisha Tang, Sheng Zeng, Qiying Sun. Microdeletion in distal PLP1 enhancers causes hereditary spastic paraplegia 2. Annals of clinical and translational neurology. 2023 Sep;10(9):1590-1602