Prevalence of primary mutations in Leber hereditary optic neuropathy: A five-year report from a tertiary eye care center in India

• Introduction
• Results
• Discussion

Abstract

Purpose: Genetic testing for primary mutations m.3460G>A, m.11778G>A, and m.14484T>C in ND1, ND4, and ND6 genes of mitochondrial DNA is the recommended assay for Leber hereditary optic neuropathy (LHON; OMIM 535000). This report discusses the outcome of molecular genetic screening for these three primary mutations in suspected LHON cases in India.

Methods: Two hundred and seventy-eight unrelated presumed LHON patients who were seen at the neuro-ophthalmology clinic of a tertiary eye care center from 2014–2018 were analyzed. They were genotyped for the three common variants by polymerase chain reaction–based direct sequencing, and their plasmy status was also determined by restriction enzyme digestion.

Results: Eighty two of 278 patients were positive for one of the 3 common mutations with m.11778G>A in ND4 gene more frequently distributed (N=72) in homoplasmic state (N=59/82). The mean onset age of visual loss was 21.1years (SD, 9.8 years; range, 5-58 years) in patients harboring the primary mutation. The most common clinical presentation was bilateral sequential painless vision loss with central and cecocentral scotomas in the visual field due to optic disc atrophy.

Conclusions: The study subjects are a sample of a much larger number of suspected LHON cases tested for primary mutations in India. (N= 278) and 29.4% (82/278) of patients harbour one of the 3 common mutations. Screening the entire mitochondrial genome and the other nuclear genes encoding mitochondrial protein, would probably aid in identifying the other less common mtDNA mutations causing LHON in Indian population.

Leber hereditary optic neuropathy (LHON; OMIM 535000) is a blinding disorder seen predominantly in young men and characterized by selective degeneration of retinal ganglion cells (RGCs) and optic atrophy that results in maximal vision loss [1]. The clinical features include loss of visual acuity, dyschromatopsia, large central scotomas, and bilateral subacute loss of central vision due to the degenerating subset of macular RGCs that provide axons for the papillomacular bundle [2]. A method of molecular confirmation would be useful in diagnosing LHON, alongside observation of clinical features such as onset of the disease (subacute) and maternal history of visual loss (if available).

Mutations causing LHON are identified in the single subunit of mitochondrial NADH dehydrogenase genes in the complex I subunit, which upon dysfunction result in increased production of Reactive oxygen species and decreased production of ATP. The three common mutations: m.3460G>A (13%), m.11778G>A (70%) and m.14484T>C (14%) are observed in 90% of people affected by LHON. The recommended guidelines for LHON diagnosis include targeted genetic testing, primarily for the 3 common mutations [3–5], followed by sequencing of the other mitochondrial / nuclear genome based on history, evaluation history of key structural and functional visual parameters [6]. Genetic counseling of the patient and family and lifestyle changes for preventable risk factors, such as smoking, secondary smoke, alcohol consumption, and exposure to mitotoxic agents, are recommended in the management of the disease [7]. In this context, of disease management and diagnosis confirmation, screening the common mutations has proven cost effective for molecular confirmation of LHON. We report here and discuss the molecular diagnosis results for the 3 common primary mutations in suspected LHON cases referred to our genetic clinic for a period of 5 years.

Two hundred and eighty-two patients were referred for genetic counseling over a period of five years (2014–2018), of which 278 agreed to undergo genetic testing. Pedigree analysis showed a positive family history in six patients (Figure 1). Twenty-nine percent of the study cohort (82 out of 278) were positive for one of the primary mutations that were, distributed among patients in the following order: m.11778G>A (~85%; n = 70), m.14484T>C (~13%; n = 11), and m. 3460G>A (~2%; n = 1; Figure 2A–D, Figure 3A,B). PCR-based restriction enzyme digestion showed heteroplasmy (Figure 2E, Figure 3C) in 12 samples, including some m.11778G>A (n = 11) and m.14484T>C (n = 1). Appendix 2 describes the clinical details of the LHON patients’ positive results for the primary mutations. Strong family history was observed for m.11778G>A (N=5) and m.14484T>C (N=1) mutation and all the available affected family members were positive for the mutations in homoplasmy state (Table 1).

In addition to the 3 primary mutations, we identified other missense variants: m.11447G>A; (p.Val230Met) ND4 and m.3316G>A; (p.Ala4Thr), m.3644T>C; (p. Val113Ala) in the ND1 gene. The m.3316G>A (N=2) mutation were also observed in the unrelated healthy controls. Distribution of non-synonymous and synonymous coding region variants are as given in Table 2 and Appendix 3. The patients in the current study were from different geographical locations (north India (N=200), south India (N=74), Srilanka (N=2) and one each from Andaman and Nepal).

Two hundred and seventy eight LHON suspects were referred for genetic testing and further proceeded for PCR based direct sequencing and restriction enzyme digestion after their informed consented for the test. History of smoking and alcohol consumption was noted only in 2 patients. The mean onset age of visual loss was 21.1years (SD, 9.8 years; range, 5-58 years) in patients harboring any one of the primary mutations and 22.5 years (SD,12.4 years; range, 1-70 years) for the patients without primary mutations. We did not observe any association with history of smoking and alcohol consumption in those patients positive for primary mutations (Appendix 2). Comparison of the clinical features among the patients did not show any significant correlation with primary mutations (Appendix 2). There weren’t any significant differences in age of onset, plasmy status and visual prognosis (between and within homoplasmic and heteroplasmic individuals). Male predominance observed in our study (89.9% (250/278)) is similar to that reported in other population [10–12]. LHON is described as maternally inherited [13]; however pedigree analysis of the samples (96%) in the current study did not show such typical inheritance pattern. However six families showed family history of LHON with more than one affected member as described in Table 1. There wasn’t any difference in the plasmy state and clinical features between the affected family members harboring the primary mutations.

Genetic testing of the other unaffected family members is further suggested to better understand the level of penetrance in this cohort.

Case reports and cohort based studies in LHON patients from India, has shown that frequency distribution of primary mutation ranges from 15% - 27.5% in North India [14–16] and 12%–43% in South India [17–19]; our results are comparable with the reported frequencies. In the current study, 29.4% (82/278) of the study cohort had the primary mutations. Screening 40 LHON patients (within the age group of 10-50) for primary mutation, Mishra et al reported a frequency of 27.5% for m.G11778A mutation in North Indian families [16]. Screening 55 with LHON patients from south India, in a span of 5 years, Gowri et al reports a high frequency of (43.6%) primary mutations [19]. Screening 2 LHON families, Verma et al reports G3460A and G11778A mutation in 2 families [14].

Characterization of 8 unrelated probands with m.14484T>C mutation, has shown an overall penetrance of 19.75% (16/81) but was not associated with any specific haplogroup within the Indian population. Similarly the m.11778G>A mutation was also reported to coexist with different haplogroup Background with variable penetrance. [20,21].

The current study results also suggest the putative involvement of other mitochondrial mutations / nuclear genome / Copy number variations (CNVs) in our population similar to other studies. The prevalence (29.4%: 82/278) of primary mutations observed in this study is similar to the reported from the Chinese population (29.3%: 89/304) [22] and in the majority of worldwide reports (95%) [23].

In addition to primary mutations, we have also identified other mutations (m.3644 T>C and m.11696G>A) in the current study. The m.3644T>C [N=1] variation in ND1 gene was earlier reported in patients with bipolar disease and correlated with increased risk of bipolar disease with syndromic comorbidity [24,25]; however, the index case in this study did not report any such history in the study subjects.

The other mutation, m.11696G>A [N=1] was observed in LHON patient with additional features of dystonia, hypertension and muscle weakness [26], which are observed in patients diagnosed with Leber optic neuropathy and dystonia (LDYT).

Whole mitochondrial genome sequencing and phylogenetic analysis in 75 LHON patients and 40 healthy controls from south India showed the M group as the most commonly observed haplogroup in LHON patients among the 12 different haplogroups (M, R, U, HV, H, N, C, P, L, D, K and W) [17]. In our earlier studies we did not observe significant association with haplogroup or clinical penetrance in LHON patients with m.14484T>C and m.11778G>A mutation [20,21]. However, we are unable to make any correlation with specific mutations and haplogroup.

Heteroplasmy (males: ~30–50%; females: ~10–15%) was associated with incomplete penetrance in LHON [13]. In this study, we observed heteroplasmy in 16% and 9% of the patients with the m.11778G>A and m.14484T>C mutations, respectively, as compared to other Indian studies (20% for m.11778G>A [21] and nil for m.14484T<C [20]). Interestingly, homoplasmy was observed in the family members of the index cases harboring the m.11778G>A (n = 5) and m.14484T>C (n = 1) mutations. The m.11778G>A mutation was associated with 0.39 fold lesser risk of poor vision prognosis in heteroplasmy when compared to homplasmy status [21]. In our study we did not find any significant association with the risk of visual failure. The role of other risk factors like alcohol consumption, tobacco usage and drug toxicity [like anti-tubercular treatment (ATT) – ethambutol] in addition to the mitochondrial variations makes the patients more susceptible for the disease [27]. We did not screen the other family members to assess the role of incomplete penetrance in this study cohort. The current study represents large LHON cohort (N=258) from a single ophthalmic center (both north and south India) for primary mutation screening when compared to the other reports from India (sample size N<100). In addition to the larger sample size, the study reports the plasmy status by polymerase chain reaction - restriction enzyme (PCR-RE) method which is not mentioned in other studies from India.