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Introduction

Leber's hereditary optic neuropathy (LHON) is a neurodegenerative eye disorder, which is clinically characterized by rapid, painless, bilateral central visual loss, that commonly affects young adults (1–4). The majority of cases of LHON are the result of one of three primary mutations: m.11778G>A/mitochondrially encoded NADH:ubiquinone oxidoreductase core MT-ND4, m.3460G>A/MT-ND1 or m.14484T>C/MT-ND6 (5–7), whereas the remaining 5% of cases are caused by rare mitochondrial DNA (mtDNA) mutations and/or other factors. At present, ~40 mutations (www.mitomap.org/foswiki/bin/view/MITOMAP/MutationsLHON), which mainly occur in complex I, have been associated with LHON. Therefore, mtDNA mutations are considered the molecular basis for LHON disease (5,8), and they often present near or at homoplasmy. However, male bias and incomplete penetrance are typical clinical characteristics of LHON, thus indicating that LHON has a complex etiology (9,10). Therefore, mtDNA mutations are considered insufficient to result in the phenotypic expression of LHON, and other modifying determinants, including mitochondrial haplotypes and nuclear genetic backgrounds, and environmental factors, are likely to modulate the phenotypic manifestation of LHON-associated common or rare mtDNA mutations (11–14).

LHON is the first disorder that was recognized to be maternally inherited, and is the first to have been attributed to a point mutation in mtDNA (5). In previous investigations, besides the three primary mutations (m.11778G>A, m.3460G>A, m.14484T>C), we identified LHON-associated m.3394T>C/MT-ND1, m.3635G>A/MT-ND1, m.3866T>C/MT-ND1, m.11696G>A/MT-ND4, m.12238T>C/MT-ND5 and m.14502T>C/MT-ND6 mutations (15–19). In the present study, the clinical, genetic and molecular features of two Chinese families with maternally transmitted LHON were investigated; the m.5587T>C mutation in the mitochondrially encoded transfer (t)RNA alanine (MT-TA) gene was detected in the families, which lacked the three known primary mutations. To elucidate the role of other genetic factors, including mitochondrial haplotype, in the phenotypic expression of the m.5587T>C mutation, 24 overlapping fragments were used to perform polymerase chain reaction (PCR) amplification of fragments spanning the entire mitochondrial genome and a DNA sequence analysis was subsequently conducted.

Materials and methods

Subjects and ophthalmologic examinations

As shown in Fig. 1, the patients from two Han Chinese families (HZL001 and HZL002) were recruited at the School of Ophthalmology and Optometry, Wenzhou Medical University (Wenzhou, China) and at Dongfang Hospital (Beijing, China). A total of 376 control DNA samples were obtained from a panel of unaffected subjects with Han Chinese ancestry from the same region. The ophthalmic examinations of the probands and other matrilineal relatives, including visual field test, visual acuity examination, fundus photography, visual evoked potentials and determination of the degree of visual impairment, as well as other clinical evaluations, were conducted as described previously (11–13). Blood samples were also obtained from the participants. Written informed consent was obtained from the probands and other affected relatives evaluated, and the present study was approved by the Ethic Committees of Wenzhou Medical University and Zhejiang University (Hangzhou, China).

Figure 1. Two Chinese pedigrees with Leber's hereditary optic neuropathy. Vision-impaired individuals are indicated by filled symbols; females are indicated by circles; males are indicated by squares; arrows indicate the probands.

mtDNA mutational analysis

Genomic DNA was isolated from the whole blood samples of participants and controls using QIAamp DNA Blood Mini kit (cat. no. 51104; Qiagen, Inc., Valencia, CA, USA). The presence of the m.11778G>A, m.3460G>A and m.14484T>C mutations was detected as previously described (11–13). Briefly, DNA fragments of probands and affected members spanning these mtDNA mutations were amplified by PCR using oligodeoxynucleotides corresponding to mtDNA at positions 11,654 to 11,865 for the m.11778G>A mutation, 3,108 to 3,717 for the m.3460G>A mutation, and 14,260 to 14,510 for the m.14484T>C mutation (20). Each fragment was purified by PCR clean-up (cat. no. AP-PCR-50; Axygen; Corning Incorporated, Corning, NY, USA) and subsequently analyzed by direct sequencing in an ABI 3700 automated DNA sequencer (Applied Biosystems; Thermo Fisher Scientific, Inc., Waltham, MA, USA) using the Big Dye Terminator Cycle sequencing reaction kit (Thermo Fisher Scientific, Inc.). The three fragment sequence results were compared with the updated consensus Cambridge sequence (GenBank accession no. NC_012920) (13).

For detecting the m.5587T>C mutation in the MT-TA gene, PCR amplification using oligodeoxynucleotides corresponding to mtDNA at positions 5,238–6,050 was conducted. The primer pair sequences for PCR were as follows: Forward: 5′-CTAACCGGCTTTTTGCCC-3′ and reverse 5′-ACCTAGAAGGTTGCCTGGCT-3′, which were designed according to a previously described method (20). Subsequently, this fragment was purified and analyzed as aforementioned.

Haplogroup analyses and phylogenetic analysis

The mtDNA sequences of 17 different vertebrates were used to conduct an interspecific analysis as reported previously (11–13). The conservation index (CI) was calculated by comparing the human nucleotide variants with the other 16 vertebrates. The CI was used to indicate the percentage of species from the list of 16 different vertebrates that have the wild-type nucleotide at the same position.

The Asian mitochondrial haplogroup of these two probands were determined using online software (www.mitotool.org/genomeRSRS.html) or based on the nomenclature of mitochondrial haplogroups previously reported (21,22).

Results

Clinical presentation

Clinical data for the two Chinese probands are summarized in Table I. The four individuals that were affected by LHON in the two pedigrees comprised one woman and three men. Comprehensive medical histories of the probands confirmed that they suffered from no other clinical abnormalities, including hearing dysfunction, muscular diseases, diabetes and neurological diseases. In pedigree HZL001, the proband (III-5) was first examined at the age of 17 at the Ophthalmology Clinic of Wenzhou Medical University. He started to suffer from bilateral visual loss at the age of 15; he observed a dark cloud in the center of his vision and had difficulty discerning colors, which all appeared dark grey. Visual field test detected a large centrocecal scotomata in both eyes. His visual acuity was oculus dexter, 0.02; and oculus sinister, 0.05. Fundus examination demonstrated that both of his optic discs were abnormal: Vascular tortuosity of the central retinal vessels, circumpapillary telangiectatic microangiopathy and swelling of the retinal nerve fiber layer were detected. These findings indicated that the patient exhibited the typical clinical features of LHON. In addition, his uncle (II-1) and grandmother (I-2) exhibited visual loss, as presented in Table I. In family HZL002, the proband (III-1) exhibited bilateral visual loss from the age of 6. He was diagnosed with LHON by the Ophthalmology Clinic at Beijing University of Chinese Medicine and Pharmacology (Beijing, China). The visual field test detected a large centrocecal scotomata in both eyes. His visual acuity was 0.1 in both eyes. In addition, both optic discs were abnormal, as determined by fundus examination: Vascular tortuosity of the central retinal vessels, circumpapillary telangiectatic microangiopathy and swelling of the retinal nerve fiber layer were detected. These findings indicated that the patient exhibited the typical clinical features of LHON. Conversely, none of the other six matrilineal relatives in HZL001 exhibited visual loss.

Table I. Summary of clinical data for four patients with Leber's hereditary optic neuropathy from two pedigrees carrying the m.5587T>C mutation.

Table I.

Summary of clinical data for four patients with Leber's hereditary optic neuropathy from two pedigrees carrying the m.5587T>C mutation.

Subject	Sex	Age of test (years)	Age of onset (years)	Visual acuity, righta	Visual acuity, lefta	Level of visual impairment
HZL001-III-5	F	17	15	0.02	0.05	Severe
HZL001-II-1	M	42	29	0.01	CF/30 cm	Profound
HZL001-I-2	M	65	32	0.2	0.1	Mild
HZL002-III-1	M	11	6	0.1	0.1	Moderate

a According to the national standard visual acuity chart (41). F, female; M, male; CF, counting fingers.

mtDNA analysis

To explore the molecular basis of visual loss in the two pedigrees, a mutational analysis of the mitochondrial genome in the two Chinese families was conducted. Initially, three well known LHON-associated mtDNA mutations (m.11778G>A, m.3460G>A and m.14484T>C) were detected by PCR amplification and restriction enzyme digestion analysis of PCR fragments derived from each proband (data not shown). The m.11778G>A, m.3460G>A and m.14484T>C mutations were not detected. Subsequently, PCR amplification of fragments spanning the entire mitochondrial genome and a DNA sequence analysis was conducted using DNA obtained from the two probands and the affected matrilineal relatives. The homoplasmic m.5587T>C mutation was detected (Fig. 2A). The m.5587T>C mutation refers to a T to C transition at position 5,587 in the MT-TA gene, which is localized in the end of the MT-TA gene (position 73; Fig. 2B), and was detected in the two pedigrees evaluated in the present study. As shown in Table II, this point at position 73 in the MT-TA gene is highly conserved among all 17 organisms analyzed, with the exception of Hylobates lar. Notably, the m.5587T>C mutation has been reported to be associated with progressive unstable gait, dysarthria, hearing loss, muscle cramps and myalgia (23,24). Further analysis of this gene fragment sequence, demonstrated that the homoplasmic m.5587T>C mutation was detected in matrilineal relatives of the two families but not in non-matrilineal relatives (data not shown). Furthermore, none of the 376 unrelated Chinese control subjects carried the m.5587T>C mutation.

Figure 2. (A) Identification of the m.5587T>C mutation in the MT-TA gene. Partial sequence chromatograms of the MT-TA gene from two affected individuals and one Chinese control. The arrow indicates the location of the base change at position 5,587. (B) Location of the m.5587T>C mutation in the MT-TA gene. Arrow indicates the position of the m.5587T>C mutation. MT-TA, mitochondrially encoded transfer tRNA alanine.

Table II. Alignment of the MT-TA gene from 17 different species. Position 73 is the location of the m.5587T>C mutation.

Table II.

Alignment of the MT-TA gene from 17 different species. Position 73 is the location of the m.5587T>C mutation.

Species	Acc-stem, pos 1	Pos 8	D-stem, pos 10	D-loop, pos 14	D-stem, pos 22	Pos 26	Ac-stem, Pos 27	Anticd-loop, Pos 32	Ac-stem, Pos 39	V-region, Pos 44	T-stem, Pos 49	T-loop, Pos 54	T-stem, Pos 61	Acc-stem, Pos 66	CCA tail, Pos 73
Cebus albifrons	GAGGGCT	TA	GCTT	AATTA	AAGT	A	GTTGA	TTTGCGT	TCAAT	TGAT	GCAAG	GTATAG	TTTGC	AGTCCTT	A
Cercopithecus aethiops	AGGGGCT	TA	GCTT	AATTA	AAGT	G	GTTGA	TTTGCGT	TCAAT	TGAT	GCAGA	GTAGGTT	TTTGC	AGTCCTT	A
Colobus guereza	AAGGGCT	TA	GCTT	AATGA	AAGT	G	ATTGA	TTTGCGT	TCAGT	TGAT	GCAGA	GTAGAGT	TTTGC	AGTCCTT	A
Gorilla gorilla	AAGGGCT	TA	GCTT	AATTA	AAGT	G	GCTGA	TTTGCGT	TCAGT	TGAT	GCAGA	GTAGGGT	TTTGC	AGTCCTT	A
Homo sapiens	AAGGGCT	TA	GCTT	AATTA	AAGT	G	GCTGA	TTTGCGT	TCAGT	TGAT	GCAGA	GTGGGGT	TTTGC	AGTCCTT	A
Hylobates lar	AAGGGCT	TA	GCTT	AATTA	AAGT	G	ACTGA	TTTGCGT	TCGGT	TGAT	GCAAA	GTGGGC	TTTGC	AGTCCTT	G
Lemur catta	GAGGATT	TA	GCTT	AATTA	AAGT	G	ATTGA	TTTGCGT	TCAGT	TGAT	GTAAG	ATATAAT	CTTGC	AGTCCTT	A
Macaca mulatta	AAGGGCT	TA	GCTT	AATTA	AAGT	G	GTTGA	TTTGCGT	TCAAT	TGAT	GCAGA	GTAGGTG	TTTGC	AGTCCTT	A
Macaca sylvanus	AAGGGCT	TA	GCTT	AATTA	AAGT	A	GTTGA	TTTGCGT	TCAAT	TGAT	GCAGA	GCAGGTG	TTTGC	AGTCCTT	A
Nycticebus coucang	GAGGACT	TA	GCTT	AATTA	AAGT	A	ATTGA	TTTGCGT	TCAGT	TGAT	GTAGG	AGAAGT	CTTGC	AGTCCTT	A
Pan paniscus	AAGGGCT	TA	GCTT	AATTA	AAGT	G	GCTGA	TTTGCGT	TCAGT	TGAT	GCAGA	GTGGGGT	TTTGC	AGTCCTT	A
Pan troglodytes	AAGGGCT	TA	GCTT	AATTA	AAGT	G	GCTGA	TTTGCGT	TCAGT	TGAT	GCAGA	GTGGGGT	TTTGC	AGTCCTT	A
Papio hamadryas	AAGGGCT	TA	GTTT	AATTA	AAGC	G	ATTGA	TTTGCGT	TCAGT	TGAT	GCGGA	GTAGGTG	TCTGC	AGTCCTT	A
Pongo pygmaeus	GAGGGCT	TA	GCTT	AATTA	AAGT	G	GCTGA	TTTGCGC	TCAGT	TGAT	GCAAA	GTGGGGT	TTTGC	AGTCCTT	A
Pongo pygmaeus abelii	GAGGGCT	TA	GCTT	AATTA	AAGT	G	GCTGG	TTTGCGT	TCAGT	TGAT	GCAGA	GCGGGGC	TTTGC	AGTCCTT	A
Tarsius bancanus	GAGGACT	TA	GCTT	AAGTTA	AAGT	A	GCTAA	TTTGCAG	TTAGT	TGAT	GTAGA	GTGAGTC	TTTGC	AGTCCTT	A
Trachypithecus bscurus	AAGGGCT	TA	GCTT	AATTA	AAGT	A	ACTGG	TTTGCGT	TCAGT	TGAT	GCAGA	ATGAGAT	TCTGT	AGTCCTT	A

[i] Pos, position.

As presented in Tables II and III, in addition to the m.5587T>C mutation, which exhibited evolutionary conservation among 17 organisms, there are many mtDNA polymorphic loci in the two families investigated in the present study. Of the other identified nucleotide alterations in these two mitochondrial genomes, there were 15 known variants in the D-loop, two known variants in the 12S ribosomal (r)RNA gene, one known variant in the 16S rRNA gene, 23 silent variants (one novel) in protein-encoding genes, and seven missense mutations in protein-encoding genes. The missense mutations were as follows: m.8860A>G(p.T112A) in the mitochondrially encoded ATP synthase 6 gene, m.10609T>C(p.M47T) in the MT-ND4 L gene, m.12406G>A(p.V24I) and m.13928G>C(p.S531T) in the MT-ND5 gene, m.14766C>T(p.T7I), m.15024G>A (p.C93H) and m.15326A>G(p.T194A) in the mitochondrially encoded cytochrome B (MT-CYB) gene. Subsequently, these RNA and polypeptide variants were further assessed by phylogenetic analysis of these variants and sequences from other organisms, including mice (25), cows (26) and Xenopus laevis (27). The mtDNA variant m.15024G>A(p.C93H) in the MT-CYB gene exhibited evolutionary conservation among the four organisms. However, none of the other variants exhibited evolutionary conservation, suggesting that these variants may not be functionally significant. Based on the nomenclature of mitochondrial haplogroups, the mtDNA sequence variations among two Chinese probands were used to establish the haplogroup affiliation of each mtDNA (23,24). In the present study, the mtDNAs of the two pedigrees belonged to haplogroup F1.

Table III. mtDNA variants in two Chinese families with Leber's hereditary optic neuropathy.

Table III.

mtDNA variants in two Chinese families with Leber's hereditary optic neuropathy.

Gene	Position	Replacement	Conservation (H/B/M/X)	CRS	HZL001	HZL002	Previously reporteda
D-loop	73	A-G		A	G	G	Yes
	150	C-T		C		T	Yes
	195	T-C		T		C	Yes
	204	T-C		T	C		Yes
	207	G-A		G	A		Yes
	215	A-G		A	G		Yes
	249	delA		A	del	del	Yes
	263	A-G		A	G	G	Yes
	310	T-CTC		T	CTC	CTC	Yes
	522	Del C		C	Del		Yes
	523	Del A		A	Del		Yes
	16,183	A-C		A	C		Yes
	16,189	T-C		T	C		Yes
	16,304	T-C		T	C	C	Yes
	16,519	T-C		T	C	C	Yes
MT-RNR1	750	A-G	A/A/A/-	A	G	G	Yes
	1,438	A-G	A/A/A/G	A	G	G	Yes
MT-RNR2	2,706	A-G	A/G/A/A	A	G	G	Yes
MT-ND1	3,970	C-T		C	T	T	Yes
MT-ND2	4,769	A-G		A	G	G	Yes
	5,201	T-C		T	C		Yes
MT-TA	5,587	T-C	T/T/-/T	T	C	C	Yes
MT-CO1	6,182	G-A		G		A	Yes
	6,392	T-C		T	C	C	Yes
	6,962	G-A		G	A	A	Yes
	7,028	C-T		C	T	T	Yes
MT-CO2	8,149	A-G		A		G	Yes
	8,152	G-A		G	A		Yes
MT-ATP6	8,860	A-G(Thr-Ala)	T/A/A/T	A	G	G	Yes
	9,165	T-C		T		C	Yes
MT-CO3	10,310	G-A		G	A	A	Yes
MT-ND4L	10,490	T-C		T	C		Yes
	10,609	T-C(Met-Thr)	M/T/T/T	T	C	C	Yes
MT-ND4	11,471	C-T		C		T	Yes
	11,719	G-A		G	A	A	Yes
MT-ND5	12,406	G-A(Val-Ile)	V/F/S/F	G	A	A	Yes
	12,882	C-T		C	T	T	Yes
	13,707	G-A		G	A		Yes
	13,928	G-C(Ser-Thr)	S/T/S/T	G	C	C	Yes
MT-CYB	14,766	C-T(Thr-Ile)	T/S/T/S	C	T	T	Yes
	15,024	G-A(Cys-His)	C/C/C/C	G	A	A	No
	15,326	A-G(Thr-Ala)	T/M/I/I	A	G	G	Yes

{ label (or @symbol) needed for fn[@id='tfn3-mmr-16-06-8997'] } Conservation of amino acids in polypeptides or nucleotides in RNA in humans (H), cows (B), mice (M) and Xenopus laevis (X). CRS, Cambridge reference sequence.

a As presented in online mitochondrial genome databases: www.mitomap.org and www.genpat.uu.se/mtDB.

Discussion

In the present study, the genetic, clinical and molecular features of two Chinese pedigrees with LHON were reported. The primary characteristic of LHON is bilateral visual loss, which was only present in the maternal lineage of the pedigrees evaluated, thus suggesting that mtDNA mutations are the molecular basis for this disorder. Sequence analysis of the complete mitochondrial genomes of these pedigrees demonstrated that the three primary mutations associated with LHON were not present; however, distinct mtDNA polymorphisms and the m.5587T>C mutation in the MT-TA gene were detected in both pedigrees. Notably, this homoplasmic mutation was only present in the maternal lineage of the pedigrees, but not in the other members of these families. Position 73 is evolutionarily conserved in the MT-TA gene. This mutation may influence the 3′ end sequences of the amino acid arm of tRNA; amino acids linked affect the tRNA structure and infer structural changes. Therefore, this mutation may affect the efficiency of amino acid translation, hinder protein synthesis and induce mitochondrial dysfunction; in particular it may affect encoding of the compound enzyme that initiates mitochondrial oxidative phosphorylation required for respiratory chain and enzyme activity. In response to abnormal oxidative phosphorylation, a series of pathological alterations may be induced, including production of oxygen free radicals and a reduction in the use of nitric oxide. In addition, this mutation may have a potential modifying role in deafness by worsening m.7505T>C mutation-induced mitochondrial dysfunction (23). Furthermore, in a previous study, a 28-year-old woman that carried this mutation presented with a 16-year history of progressive unstable gait, dysarthria, hearing loss, muscle cramps and myalgia (24). Notably, in the present study, the presence of the m.5587T>C mutation in the two genetically different pedigrees, both influenced by visual loss, indicated that this mutation may be associated with the pathogenesis of visual loss.

In these two families, the age of onset for visual impairment ranged between 6 and 32 years old (average, 20.5 years old). Previous studies confirmed that the age of onset for visual impairment in the two pedigrees harboring the m.5587T>C mutation was similar to that in other Chinese families with LHON carrying the m.11778G>A mutation (28–32). In contrast, a number of Chinese subjects carrying the m.11778G>A mutation, which exhibited profound visual loss, the affected subjects carrying the m.5587T>C mutation suffered from mild to profound visual impairment, similar to that exhibited in patients carrying m.3394T>C, m.3635G>A, m.3866T>C, m.11696G>A, m.12238T>C and m.14502T>C mutations (15–19,33). Furthermore, there is a high penetrance of visual loss in some Chinese subjects harboring the m.11778G>A mutation (28,29,31–34); however, the penetrance of visual impairment was very low in the two Chinese pedigrees carrying the m.5587T>C mutation. In addition, the m.5587T>C mutation was not detected in the 376 Chinese control subjects. Similar to the three common mutations, and m.3394T>C, m.33635G>A, m.3866T>C, m.11696G>A, m.12238T>C and m.14502T>C mutations (15–19), the incomplete penetrance of visual loss associated with the m.5587T>C mutation, and the lack of the mutation in any of the 376 control subjects, indicated that the m.5587T>C mutation is itself insufficient to result in the clinical phenotype. These findings suggested that other modifying factors, including mitochondrial haplotype, environmental factors and nuclear background are required for the phenotypic manifestation of the m.5587T>C mutation. In particular, mitochondrial haplotypes have been reported to influence the penetrance and expressivity of visual loss associated with primary mtDNA mutations. Therefore, secondary LHON mutations, such as m.4216T>C and m.13708G>A, have been implicated to increase the penetrance of LHON-associated primary m.11778G>A or m.14484T>C mutations (35). In addition, in a large cohort of subjects with European ancestry, the mitochondrial haplogroup J was able to affect the phenotypic manifestation of LHON-associated m.11778G>A and m.14484T>C mutations (36,37). Furthermore, the m.11696G>A, m.14502T>C, m.15951A>G and m.4435A>G mutations have been reported to increase LHON penetrance in Chinese subjects (28,31,38). In the two pedigrees evaluated in the present study, the mtDNA variants p.C93H in the MT-CYB gene exhibited evolutionary conservation; however, other known mutations were not detected in the LHON pedigrees. This mtDNA variant may have a potential modifying role in the development of visual impairment associated with the m.5587T>C mutation in these two pedigrees.

It has been suggested that mitochondrial haplotypes may affect the penetrance and expressivity of LHON associated with the three primary mutations (m.11778G>A, m.3460G>A and m.14484T>C). In European pedigrees, mitochondrial haplogroup J may raise the risk of LHON-associated m.11778G>A or m.14484T>C mutations (14,39), whereas haplogroup K may aggrandize the penetrance of primary LHON-associated m.3460G>A mutation (14). Conversely, haplogroup H may reduce the risk of LHON-associated m.11778G>A mutation (14). In addition, the haplogroup M7b1′2 significantly increases the occurrence of LHON, whereas the haplogroup M8a has a protective effect in Chinese pedigrees (40). In the two families analyzed in the present study, the mitochondrial genomes of the HZL001 and HZL002 pedigrees belonged to the Eastern Asian haplogroup F1. However, since data from only two families were analyzed, and due to the lack of a large data analysis, the role the mitochondrial haplotype serves in the two families cannot be fully explained. In addition, nuclear modifier genes, including the tyrosyl-tRNA synthetase 2 gene in Chinese families (11), or environmental factors, may have an important role in the phenotypic expression of the LHON-associated m.5587T>C mutation in the two Chinese pedigrees. Thus, the results of the present study may provide novel insights into the understanding of clinical diagnosis and valuable information on the management of LHON.

Acknowledgements

The present study was supported by grants from the Natural Science Foundation of China (grant nos. 31471191, 81400434 and 31601025); the College Students' Science and Technology Innovation (Xinmiao Talents Program) in Zhejiang province (grant no. 2015R401217); and a general financial grant from China Postdoctoral Science Foundation (grant no. 2016M591986).

References