Mutation Screening of mtDNA Combined Targeted Exon Sequencing in a Cohort With Suspected Hereditary Optic Neuropathy

Jian-Kang Li, Wei Li, Feng-Juan Gao, Shou-Fang Qu, Fang-Yuan Hu, Sheng-Hai Zhang, Li-Li Li, Zi-Wei Wang, Yong Qiu, Lu-Sheng Wang, Jie Huang, Ji-Hong Wu, Fang Chen, Jian-Kang Li, Wei Li, Feng-Juan Gao, Shou-Fang Qu, Fang-Yuan Hu, Sheng-Hai Zhang, Li-Li Li, Zi-Wei Wang, Yong Qiu, Lu-Sheng Wang, Jie Huang, Ji-Hong Wu, Fang Chen

Abstract

Purpose: Leber hereditary optic neuropathy (LHON) and autosomal dominant optic atrophy (ADOA) are the two commonest forms of hereditary optic neuropathy. The aim of this study was to comprehensively investigate the incidence and spectrum of mutations in patients with suspected hereditary optic neuropathy by combining mitochondrial DNA (mtDNA) genome-wide and targeted exon sequencing.

Methods: A cohort of 1101 subjects were recruited to participate in the study, comprising 177 families (177 probands and their family members, a total of 537 subjects, including 254 patients) and 164 sporadic cases with suspected hereditary optic neuropathy, and 400 unrelated control subjects for genetic analysis: all subjects (including control subjects) underwent a comprehensive ophthalmologic examination and were subjected to sequencing analysis of mtDNA genome-wide and targeted exon. Overall, targeted exon sequencing was used to screen 792 genes associated with common hereditary eye diseases, and the mtDNA genome-wide were screened by next-generation sequencing.

Results: We found variants detected in 168 (40.2%, 168/418) of the 418 patients screened. Among these, 132 cases (78.6%, 132/168) were detected with known LHON disease-causing mtDNA variants; 40 cases (23.8%, 40/168) were detected with nuclear DNA (ntDNA) variants, which included 36 cases (21.4%, 36/168) with detected OPA1 mutations, 4 patients (2.4%, 4/168) with detected OPA3 mutations, and 2 patients (1.2%, 2/168) with detected TMEM126A homozygous mutation. Coexistence variation (mtDNA/mtDNA [n = 16], ntDNA/ntDNA [n = 4], mtDNA/ntDNA [n = 7]) was found in 27 patients (16.4%, 27/165), including mtDNA/ntDNA coexistence variation that was detected in seven patients. Among these ntDNA mutations, 38 distinct disease-causing variants, including autosomal recessive heterozygous mutations, were detected, which included 22 novel variants and two de novo variants. Total haplogroup distribution showed that 34.5% (29/84) and 28.6% (24/84) of the affected subjects with m.11778G>A belonged to haplogroup D and M, with a high frequency of subhaplogroups D4, D5, and M7.

Conclusions: The LHON-mtDNA mutations are the commonest genetic defects in this Chinese cohort, followed by the OPA1 mutations. To our knowledge, this is the first comprehensive study of LHON, ADOA, and autosomal recessive optic atrophy combined with mtDNA genome-wide and targeted exon sequencing, as well as haplogroup analysis, in a large cohort of Chinese patients with suspected hereditary optic neuropathy. Our findings provide a powerful basis for genetic counseling in patients with suspected hereditary optic neuropathy.

Translational relevance: We applied mtDNA genome-wide sequencing combined with panel-based targeted exon sequencing to explore the pathogenic variation spectrum and genetic characteristics of patients with suspected hereditary optic neuropathy, providing a comprehensive research strategy for clinical assistant diagnosis, treatment, and genetic counseling.

Keywords: Leber hereditary optic neuropathy; autosomal dominant optic atrophy; autosomal recessive optic atrophy; mtDNA; ntDNA; panel-based targeted exon sequencing.

Conflict of interest statement

Disclosure: J.-K. Li, None; W. Li, None; F.-J. Gao, None; S.-F. Qu, None; F.-Y. Hu, None; S.-H. Zhang, None; L.-L. Li, None; Z.-W. Wang, None; Y. Qiu, None; L.-S. Wang, None; J. Huang, None; J.-H. Wu, None; F. Chen, None

Copyright 2020 The Authors.

Figures

Figure 1.
Figure 1.
Basic information of clinical presentation and genetic finding of the ntDNA in the patients. (A) The age distribution of the total patients, including age ≤10 years (n = 99), 10 to 20 years (n = 86), 20 to 30 years (n = 78), 30 to 40 years (n = 67), and >40 years (n = 88). (B) The patients received a confirmed genetics diagnosis in this cohort, including mtDNA (n = 132), OPA1 (n = 36), OPA3 (n = 4), and homozygous TMEM126A (n = 2) variants. (C) Thirty-eight different pathogenic/likely pathogenic nuclear variants were detected in this cohort, including OPA1 gene (n = 30), TMEM126A gene (n = 4), RTN4IP1 gene (n = 3), and OPA3 gene (n = 1). (D) Thirty different OPA1 pathogenic/likely pathogenic variants were identified, including missense (n = 11), splicing (n = 7), nonsense (n = 5), frameshift (n = 5), and intron (n = 2) variants. (E, F) Multidimensional comparison between detection of variability in patients and age distribution.
Figure 2.
Figure 2.
Detection and evaluation of mutations in the TMEM126A gene. (A) Multiple sequence alignment of candidate missense mutations from different species to explore the conservation of these mutations. The red arrow represents variants states. (B) SWISS-MODEL was used to predict the three-dimensional structure of both the mutant and wild-type proteins. (C) Pedigrees of the families with mutations. Squares indicate men and circles women; black and white symbols represent affected and unaffected individuals, respectively. The proband is marked with an arrow, and the asterisks indicate those members enrolled in this study.

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