NDUFV1 mutations in complex I deficiency: Case reports and review of symptoms

Abstract Mitochondrial complex I (CI) deficiency is the most common oxidative phosphorylation disorder described. It shows a wide range of phenotypes with poor correlation within genotypes. Herein we expand the clinics and genetics of CI deficiency in the brazilian population by reporting three patients with pathogenic (c.640G>A, c.1268C>T, c.1207dupG) and likely pathogenic (c.766C>T) variants in the NDUFV1 gene. We show the mutation c.766C>T associated with a childhood onset phenotype of hypotonia, muscle weakness, psychomotor regression, lethargy, dysphagia, and strabismus. Additionally, this mutation was found to be associated with headaches and exercise intolerance in adulthood. We also review reported pathogenic variants in NDUFV1 highlighting the wide phenotypic heterogeneity in CI deficiency.


Introduction
Dysfunctions in complex I (NADH ubiquinone dehydrogenase) (CI) represents a third of all early-onset mitochondrial disorders and are genetically and clinically diverse (Hirst, 2013). They are caused by mutations in mitochondrial and nuclear genes, with clinical phenotypes ranging from severe lactic acidosis and death in infants to muscle weakness in adults. Five clinical groups were associated with CI deficiency: Leigh syndrome, progressive leukoencephalopathy, neonatal cardiomyopathy, severe infantile lactic acidosis, and a miscellaneous group of unspecified encephalomyopathies (Fassone and Rahman, 2012). Correlations between genotype and phenotype in mitochondrial diseases are not fully understood and need further exploration (Baertling et al., 2018) CI is a protein complex composed of 44 different subunits, seven of which are encoded by mitochondrial DNA (mtDNA) and the remaining by nuclear DNA (nDNA) (Hirst, 2013). CI catalyzes the oxidation of nicotinamide adenine dinucleotide (NADH) in the mitochondrial matrix, supplying electrons to complex III via reduction of coenzyme Q. The electron flux through CI sustains the translocation of four protons across the inner mitochondrial membrane, thus contributing to the mitochondrial electrochemical potential. CI is also an important source of reactive oxygen species (ROS) in mitochondria, which causes cellular oxidative stress (Murphy, 2009). CI is subdivided into three modules: the electron input (N) module, the electron output (Q) module, and the proton translocations (P) module. The N module is composed of subunits encoded by the genes NDUFV1, NDUFV2, and NDUFS1 (Brandt, 2006). The NDUFV1 gene (NG_013353.1) is located on chromosome 11 and encodes the NADHubiquinone oxidoreductase flavoprotein (NM_007103.4), a hydrophilic polypeptide of 51 kDa, which oxidizes NADH and is a major site of ROS production (Hirst, 2013;Varghese et al., 2015) In this report, we presented three patients with mutations in the NDUFV1 gene. The first patient is a compound heterozygous for a missense mutation c.640G>A (p.Glu214Lys) and a frameshift mutation c.1207dupG (p.Asp403Gly*fs), the second is homozygous for a missense mutation c.1268C>T (p.Thr423Met), and the third, combining the c.1268C>T (p.Thr423Met) and a likely pathogenic variant c.766C>T (p.Arg256Cys).

Methods
This work received the approval of the ethical standards committee of the Federal University of Paraná (CAAE: 84773818.2.0000.0102).
Total DNA was extracted from blood using the DNeasy Kit (Qiagen, Hilden, DE). Whole Exome Sequencing (WES) was carried out using Illumina ® 2000 HiSeq with Agilent SureSelect Human All Exon V7 for the first two cases, and Nextera ® Exome Capture to third, the GRCh37 reference genome and a GATK-based pipeline was used to call, filter and annotate variants (Van der Auwera et al., 2013). After identification of relevant variants, the region containing each variant was re-sequenced and family segregation was performed by Sanger sequencing.
The position of the mutations was mapped to the corresponding amino acids in the protein structures of Bos taurus (NM_174808.1) and human (PDB ID: 5XTB). The impact of the mutated amino acids on CI was investigated by visualizing the mutations in the context of the CI structures (Zhu et al., 2016) by using the PyMOL structure viewer.

Patient P1
Patient 1 (P1), male, 4 years old, was born by cesarean delivery at 40 weeks of gestation with 3760 g. The mother presented three previous miscarriages (8-, 8-and 12-weeks' gestation) and placenta detachment during P1 pregnancy with indication of resting. The father presented childhood seizures and no consanguinity was reported. P1 had three healthy brothers, two of whom were maternal half-brothers. P1 was 3 years old when he presented developmental delay and autistic spectrum disorder and was admitted to the hospital after episodic vomiting and dehydration associated with a cutaneous rash. After treatment P1 developed respiratory insufficiency needing orotracheal intubation. Viral encephalitis was evaluated with negative outcomes in cerebrospinal fluid (CSF), however empiric treatment with Acyclovir for 14 days showed complete recovery of neurological symptoms, with normal daily activities and no functional impairment. Brain MRI was performed after treatment and showed T2-weighted hyperintense and T1-weighted hypointense focal lesions in central portions of the upper segment of the cervical spinal cord, with additional symmetric lesions in midbrain, pons, and bulb.
One month later, P1 was admitted to the hospital with prostration, nausea, vomiting and absence seizures, developing a cutaneous rash and apnea after two days. Orotracheal intubation was performed and extubation failure occurred due to the persistency of apnea, therefore, tracheostomy and gastrostomy were performed. Arterial blood gas analysis, blood lactate, blood acylcarnitine's profile, urinary organic acids, and blood amino acid chromatography were normal. The patient continued to have recurrent apneas, but no seizures. A new MRI showed increased hyperintense lesions in T2 and hypointense lesions in T1, affecting the central portions of the upper segment of the cervical spinal cord (Figure 1, P1: A-B). Symmetric lesions also increased when compared with the first MRI, mainly affecting the mesencephalon, pons, medulla oblongata, cerebellum and upper portions of the cervical spinal cord with an elevation of lactate detected by MR spectroscopy (Figure 1, P1: C).
Based on the hypothesis of mitochondrial disease, treatment was started with coenzyme Q10 (CoQ) (300 mg/ day) and L-carnitine (100 mg/kg/day). At 4 years old, P1 presented slight clinical improvement with apnea stabilization, progressive drowsiness reduction and progress in wakefulness.

Patient P2
Patient 2 (P2), male, 11 years old, was born by cesarean delivery at 38 weeks of gestation with 2470 g, 45 cm height and 33.5 cm head circumference. Pregnancy was uneventful and no symptoms were reported in the first four months of life. The mother was 46 years old when pregnant and presented one previous miscarriage. P2 had a deceased 5 years old sister with a clinical history of seizures, and a healthy older sister. Parents were consanguineous (first degree cousins).
At 4 months old, P2 presented minor cervical hypotonia and mild right hemibody hypertonia. At 7 years of age, he started to present developmental delay, aggressive behavior, learning difficulties, and motor regression. An organic acid profile in urine showed 3-methylglutaconic aciduria. He was admitted to hospital in the same year due to lethargy alternated with irritability and needed orotracheal intubation with mechanical ventilation after apnea. Tracheostomy was performed due to the extubation failure.

Patient P3
Patient 3 (P3), female, 3 years old, the younger of two siblings from non-consanguineous parents. The mother had 4 pregnancies, with one miscarriage at 10 weeks. P3 had uneventful perinatal history, she was born at term, and had no clinical symptoms. Neurodevelopment milestones were normal up to 9 months old when she developed progressive hypotonia and somnolence, followed by a gradual loss of motor skills in the following month. Cerebrospinal fluid was NDUFV1 in Complex I deficiency negative for markers of viral infection. Her sister was healthy, however, her father presented epilepsy in infancy and frequent headaches in adulthood.
The first diagnostic hypothesis for P3 was acute disseminated encephalitis, showing normal electroencephalogram, diffuse white matter lesions by MRI and a lactate peak on spectroscopy (Figure 1, P3: A-C). Symptoms improved after treatment with methylprednisolone for three days, with an improvement of the symptoms. However, after a week, a gradual clinical decline was observed with lethargy, dysphagia and general hypotonia. After 13 months, a new MRI (not shown) showed increased white matter lesions, suggesting a mitochondrial disorder. An acylcarnitine profile in blood showed increased concentrations of 3-hydroxy-butyrylcarnitine and acetylcarnitine, amino acid chromatography showed increased alanine (656.1, normal 146 -494 mcmol/L). Lactate levels in plasma ranged from 2.7 to 7.6 (normal <2.2mmol/L) over one year. Lactic acid levels in cerebrospinal fluid were often increased, ranging from 3.5 to 5.3 (normal <0.8mmol/L). Levels of urinary organic acids were normal. Supplementation with CoQ and carnitine was started but with no significative improvement. At 3 years old, P3 lost neurodevelopmental milestones and developed hypotonia, strabismus and severe inappetence.
She was submitted to an endoscopic gastrostomy and current treatment was based on supplementation with CoQ, creatine, sodium bicarbonate, acetyl L-carnitine, riboflavin, and biotin.

Genetic analysis
P1 revealed the heterozygous mutations c.640G>A (p.Glu214Lys) of maternal inheritance and c.1207dupG (p.Asp403Glyfs*27) from paternal inheritance in NDUFV1 gene. The allele frequency of p.Glu214Lys was not reported, whereas p.Asp403Glyfs*27 shows a frequency of 0.0008% (ExAC and gnomAD) and 0.0004 (TOPMED) in control population, the frameshift mutation causes the premature stop codon of the protein in Asp429.
The Glu214 residue was highly conserved among bilaterally symmetrical metazoans ( Figure 2A) and was positioned in the interface with the subunit NDUFS4 linked by a hydrogen-bonded ( Figure 2B). The mutation p.Glu214Lys disrupted the hydrogen bond and likely destabilized the interface with the neighboring subunit, NDUFS4.
P2 shows the c.1268C>T (p.Thr423Met) mutation in homozygosity in the NDUFV1 gene. The highest allele frequency in control population was below 0.01%. The Thr423 residue was highly conserved among bilaterally symmetrical metazoans ( Figure 2A) and faces the 4Fe-4S domain of NDUFV1 ( Figure 2B). The mutation of threonine to a larger methionine was likely to disturb the assembly of the 4Fe-4S cluster into the protein or to cause dysfunction in the assembled protein.
WES analysis of P3 identified the compound heterozygous mutations in the NDUFV1 gene, c.766C>T (p.Arg256Cys) and c.1268C>T (p.Thr423Met). Analysis of the mutations in the family members showed c.766C>T segregating from the father, and c.1268C>T from the mother ( Figure 2C). Five members of the paternal lineage were carriers for c.766C>T. The mutation c.766C>T caused the missense change p.Arg256Cys with no associated clinical conditions. Allele frequency of this variant corresponded to one heterozygous individual (0.00001648%) only and bioinformatic tools predicted this alteration as pathogenic (score 0.99 and 0.87). The amino acid arginine in this position was highly conserved in bilaterally symmetrical metazoans (Figure 2A). Arg256 was localized in the tip of the hydrophilic arm of NDUFV1 subunit and this sidechain was not resolved in the protein structure ( Figure 2B). Family carriers for p.Arg256Cys presented frequent headaches and exercise intolerance ( Figure 2C) with statistically significant (p-value 0.027) association between frequent headaches and the mutation was found.

Literature review
Several studies described mutations in the NDUFV1 gene associated with CI deficiency (Table 1). In this review we found 24 patients with mutations in the NDUFV1 gene, of which 8 were homozygous and 15 were compound heterozygous. The most frequent mutations were c.1268C>T (p.Thr423Met) and c.1156C>T (p.Arg386Cys).
The most common features in MRI were hyperintense lesions in T2 affecting several regions of the brain, white matter changes, brain atrophy, and presence of lactate peak in MR spectroscopy.  Schuelke et al., 1999 Discussion This work presents three patients with clinical presentation of mitochondrial disease with mutations in the NDUFV1 gene ( Table 2). The mutation p.Asp403Glyfs*27 was found in trans with p.Glu214Lys in P1, and the combination of p.Arg256Cys with p.Thr423Met was observed in P3. Both p.Glu214Lys and p.Thr423Met were described as pathogenic and cause CI deficiency (Baertling et al., 2018;Incecik et al., 2018;Srivastava et al., 2018;Wadhwa et al., 2018). The homozygous mutation p.Thr423Met in NDUFV1 gene was found in P2.
The mutation p.Asp403Glyfs*27 leads to a truncated protein with likely functional consequences due to a stop codon preceding the 4Fe-4S domain (Hirst, 2013), and was not previously associated with mitochondrial disease. Despite this, the frameshift variant should be classified as pathogenic following the ACMG guideline. The variant p.Glu214Lys was previously described as likely pathogenic in a patient with seizures, cerebellar ataxia, and psychomotor regression presenting CI deficiency (Incecik et al., 2018). The phenotype described was different from P1, which presented a mitochondrial disease phenotype characterized by developmental delay, autistic spectrum disorder, respiratory insufficiency, T1weighted hypointense, symmetric lesions in white matter and presence of lactate peak at spectroscopy. The recurrent apneas, prostation and vomiting led P1 to hospitalization several times, making artificial respiration necessary, despite this, metabolic and laboratory profiles were normal.
p.Glu214Lys changed a medium-sized acid residue to a large basic amino acid and may prevent hydrogen bonds, thus destabilizing the interface with the subunit NDUFS4. Mutations in this position probably reduce electron transfer through the redox Fe-S centers of CI (Incecik et al., 2018). Modeling of the reported mutation in NDUFV1 suggested a disturbance of the assembly or function of the 4Fe-4S cluster (Fang et al., 2017) P2 was identified as homozygous for c.1268C>T (p.Thr423Met) mutation in NUDFV1. This mutation was described leading to myopathy, depression, fatigue, strabismus, progressive muscular hypotonia, myoclonic epilepsy and psychomotor regression. Another case of homozygosity for c.1268C>T was described leading to horizontal nystagmus, dysarthria, bilateral dysmetria and intention tremor, dysdiadochokinesia, and gait ataxia (Wadhwa et al., 2018), a different presentation from P2, which presented hypotonia, developmental delay, learning difficulties and motor regression, nevertheless presenting a typical mitochondrial disease phenotype with presence of lactate peak in spectroscopy and 3-methylglutaconic aciduria.
P3 presented two compound heterozygous missense mutations, c.1268C>T (p.Thr423Met), also found in P2, and c.766C>T (p.Arg256Cys) segregating from the father with a clinical history of infant seizures and exercise intolerance with frequent headaches in adulthood. An association of headaches and exercise intolerance was found for the paternal family carriers of c.766C>T, which was statistically significant. Arg256 residue was highly conserved in bilaterally symmetrical metazoans and was localized in the tip of the hydrophilic arm of NDUFV1 subunit, which unfortunately, was not structurally elucidated and further studies are needed for its functional characterization. Despite that c.766C>T (p.Arg256Cys) is found described in ClinVar as likely pathogenic and, the Arg257 residue, neighboring Arg256, was associated with CI deficiency (Nafisinia et al., 2016). This residue was shown to be essential for protein function and predicted to be post-translationally modified to a N-methylarginine by similarity with the mouse protein (Fang et al., 2017). The variant c.766C>T (p.Arg256Cys) was predicted as pathogenic (score 0.99 and 0.87) and we propose that in combination with c.1268C>T (p.Thr423Met), they might be responsible for P3 phenotype, characterized by a childhood-onset development of hypotonia, muscle weakness, physical exercise intolerance, psychomotor regression, lethargy, dysphagia, and strabismus. The same phenotype was commonly associated with mild CI deficiency (Fassone and Rahman, 2012;Hirst, 2013;Baertling et al., 2018). This phenotype could be explained by a dominant-negative effect of the post-translational modification in the affected region, masking the effect of the wild-type version of the protein.

Conclusion
CI deficiency was associated with many nuclear and mitochondrial genes, and the understanding of the genetics of this mitochondrial disease has expanded significantly in recent years. Here we described three cases of mutations in the NDUFV1 subunit, associated with mitochondrial disease and possibly CI deficiency. The case reports and the review of NDUFV1 mutations showed heterogeneous phenotypes