Severe neonatal onset neuroregression with paroxysmal dystonia and apnoea: Expanding the phenotypic and genotypic spectrum of CARS2-related mitochondrial disease.

Disorders of mitochondrial function are a collectively common group of genetic diseases in which deficits in core mitochondrial translation machinery, including aminoacyl tRNA synthetases, are key players. Biallelic variants in the CARS2 gene (NM_024537.4), which encodes the mitochondrial aminoacyl-tRNA synthetase for cysteine (CARS2, mt-aaRScys; MIM*612800), result in childhood onset epileptic encephalopathy and complex movement disorder with combined oxidative phosphorylation deficiency (MIM#616672). Prior to this report, eight unique pathogenic variants in the CARS2 gene had been reported in seven individuals. Here, we describe a male who presented in the third week of life with apnoea. He rapidly deteriorated with paroxysmal dystonic crises and apnoea resulting in death at 16 weeks. He had no evidence of seizure activity or multisystem disease and had normal brain imaging. Skeletal muscle biopsy revealed a combined disorder of oxidative phosphorylation. Whole-exome sequencing identified biallelic variants in the CARS2 gene: one novel (c.1478T>C, p.Phe493Ser), and one previously reported (c.655G>A, p.Ala219Thr; rs727505361). Northern blot analysis of RNA isolated from the patient's fibroblasts confirmed a clear defect in aminoacylation of the mitochondrial tRNA for cysteine (mt-tRNACys). To our knowledge, this is the earliest reported case of CARS2 deficiency with severe, early onset dystonia and apnoea, without epilepsy.

Cell lineage-specific mitochondrial resilience during mammalian organogenesis.

Mitochondrial activity differs markedly between organs, but it is not known how and when this arises. Here we show that cell lineage-specific expression profiles involving essential mitochondrial genes emerge at an early stage in mouse development, including tissue-specific isoforms present before organ formation. However, the nuclear transcriptional signatures were not independent of organelle function. Genetically disrupting intra-mitochondrial protein synthesis with two different mtDNA mutations induced cell lineage-specific compensatory responses, including molecular pathways not previously implicated in organellar maintenance. We saw downregulation of genes whose expression is known to exacerbate the effects of exogenous mitochondrial toxins, indicating a transcriptional adaptation to mitochondrial dysfunction during embryonic development. The compensatory pathways were both tissue and mutation specific and under the control of transcription factors which promote organelle resilience. These are likely to contribute to the tissue specificity which characterizes human mitochondrial diseases and are potential targets for organ-directed treatments.

TEFM variants impair mitochondrial transcription causing childhood-onset neurological disease.

Mutations in the mitochondrial or nuclear genomes are associated with a diverse group of human disorders characterized by impaired mitochondrial respiration. Within this group, an increasing number of mutations have been identified in nuclear genes involved in mitochondrial RNA biology. The TEFM gene encodes the mitochondrial transcription elongation factor responsible for enhancing the processivity of mitochondrial RNA polymerase, POLRMT. We report for the first time that TEFM variants are associated with mitochondrial respiratory chain deficiency and a wide range of clinical presentations including mitochondrial myopathy with a treatable neuromuscular transmission defect. Mechanistically, we show muscle and primary fibroblasts from the affected individuals have reduced levels of promoter distal mitochondrial RNA transcripts. Finally, tefm knockdown in zebrafish embryos resulted in neuromuscular junction abnormalities and abnormal mitochondrial function, strengthening the genotype-phenotype correlation. Our study highlights that TEFM regulates mitochondrial transcription elongation and its defect results in variable, tissue-specific neurological and neuromuscular symptoms.

A library of base editors for the precise ablation of all protein-coding genes in the mouse mitochondrial genome.

The development of curative treatments for mitochondrial diseases, which are often caused by mutations in mitochondrial DNA (mtDNA) that impair energy metabolism and other aspects of cellular homoeostasis, is hindered by an incomplete understanding of the underlying biology and a scarcity of cellular and animal models. Here we report the design and application of a library of double-stranded-DNA deaminase-derived cytosine base editors optimized for the precise ablation of every mtDNA protein-coding gene in the mouse mitochondrial genome. We used the library, which we named MitoKO, to produce near-homoplasmic knockout cells in vitro and to generate a mouse knockout with high heteroplasmy levels and no off-target edits. MitoKO should facilitate systematic and comprehensive investigations of mtDNA-related pathways and their impact on organismal homoeostasis, and aid the generation of clinically meaningful in vivo models of mtDNA dysfunction.

Testing Phylogenetic Stability with Variable Taxon Sampling.

Over the past three decades, computational capabilities have grown at such a rapid rate that they have given rise to many computationally heavy science fields such as phylogenomics. As increasingly more genomes are sequenced in the three domains of life, larger and more species-complete phylogenetic tree reconstructions are leading to a better understanding of the tree of life and the evolutionary histories in deep times. However, these large datasets pose unique challenges from a modeling and computational perspective: accurately describing the evolutionary process of thousands of species is still beyond the capability of current models, while the computational burden limits our ability to test multiple hypotheses. Thus, it is common practice to reduce the size of a dataset by selecting species to represent a clade (taxon sampling). Unfortunately, this process is subjective, and comparisons of large tree of life studies show that choice and number of species used in a dataset can alter the topology obtained. Thus, taxon sampling is, in itself, a process that needs to be fully investigated to determine its effect on phylogenetic stability. Here, we present the theory and practical application of an automated pipeline that can be easily implemented to explore the effect of taxon sampling on phylogenetic reconstructions. The application of this approach was recently discussed in a study of Terrabacteria and shows its power in investigating the accuracy of deep nodes of a phylogeny.

Genetic analysis of human RNA binding motif protein 48 (RBM48) reveals an essential role in U12-type intron splicing.

U12-type or minor introns are found in most multicellular eukaryotes and constitute ∼0.5% of all introns in species with a minor spliceosome. Although the biological significance for the evolutionary conservation of U12-type introns is debated, mutations disrupting U12 splicing cause developmental defects in both plants and animals. In human hematopoietic stem cells, U12 splicing defects disrupt proper differentiation of myeloid lineages and are associated with myelodysplastic syndrome, predisposing individuals to acute myeloid leukemia. Mutants in the maize ortholog of RNA binding motif protein 48 (RBM48) have aberrant U12-type intron splicing. Human RBM48 was recently purified biochemically as part of the minor spliceosome and shown to recognize the 5' end of the U6atac snRNA. In this report, we use CRISPR/Cas9-mediated ablation of RBM48 in human K-562 cells to show the genetic function of RBM48. RNA-seq analysis comparing wild-type and mutant K-562 genotypes found that 48% of minor intron-containing genes have significant U12-type intron retention in RBM48 mutants. Comparing these results to maize rbm48 mutants defined a subset of minor intron-containing genes disrupted in both species. Mutations in the majority of these orthologous minor intron-containing genes have been reported to cause developmental defects in both plants and animals. Our results provide genetic evidence that the primary defect of human RBM48 mutants is aberrant U12-type intron splicing, while a comparison of human and maize RNA-seq data identifies candidate genes likely to mediate mutant phenotypes of U12-type splicing defects.

A Holistic Approach to Evaluating Linear and Non-Linear Mixed Models to Predict Phosphorus Retention in Growing and Finishing Pigs.

The ability of four non-linear mixed models and one linear mixed model to describe phosphorus (P) retention as a function of dietary P intake, expressed on an available P (avP) basis, was assessed in growing and finishing pigs. Of the four non-linear models, the monomolecular and Michaelis-Menten describe diminishing returns behaviour, while the Richards and Morgan describe sigmoidal behaviour with the ability to also describe diminishing returns. Using a meta-analysis approach, models were fitted to avP intake vs. P retention data from P balance studies. Pig bodyweights (BW) ranged from 43.5 to 133 kg, P intake ranged from 0.055 to 0.468 g kg-1 BW0.75 d-1 for avP, and 0.151 to 0.806 g kg-1 BW0.75 d-1 for total P, with P retention ranging from 0.026 to 0.329 g kg-1 BW0.75 d-1. Models were evaluated using statistical measures of goodness-of-fit and inspection of residuals. The monomolecular and Michaelis-Menten best described the relationship between P retention and P intake. Endogenous P losses and P requirement for maintenance were found to be higher in finishing pigs compared to growing pigs as BW increased.

Profiling Hoarding Within the Five-Factor Model of Personality and Self-Determination Theory.

This study investigated the dispositional profile associated with hoarding symptoms by applying a personality and motivational trait perspective. A community sample oversampling high hoarding symptoms (N = 649, ages 18-74 years) completed an online questionnaire assessing hoarding, the five-factor model of personality, and general causality orientations drawn from self-determination theory. Personality aspects (10 traits), a level of measurement intermediate to factors (5 traits) and facets (30 traits), were assessed to provide greater specificity than a factor-level approach. Hoarding was correlated with neuroticism and conscientiousness. Aspects predicting hoarding were industriousness (C), orderliness (C), withdrawal (N), and assertiveness (E). Hoarding was significantly related to impersonal and control orientations, albeit with only slight (1.4%) incremental validity for general causality orientations above personality aspects in predicting hoarding. These findings may not generalize to a clinical treatment sample, and possible configurative interactions between traits were not assessed. This study extended the existing literature by reporting aspect-level personality and general causality orientation correlates of hoarding. These data may inform preventative monitoring and intervention programs, as well as predicting meaningful personality characteristics of hoarding clients.

Journey to the other side of the brain: asymmetry in patients with chronic mild or moderate traumatic brain injury.

Aim: Patients with chronic mild or moderate traumatic brain injury have some regions of brain atrophy (including cerebral white matter) but even more regions of abnormal brain enlargement (including other cerebral regions). Hypothesis: Ipsilateral injury and atrophy cause the eventual development of contralateral compensatory hypertrophy. Materials & methods: 50 patients with mild or moderate traumatic brain injury were compared to 80 normal controls (n = 80) with respect to MRI brain volume asymmetry. Asymmetry-based correlations were used to test the primary hypothesis. Results: The group of patients had multiple regions of abnormal asymmetry. Conclusion: The correlational analyses supported the conclusion that acute injury to ipsilateral cerebral white matter regions caused atrophy, leading eventually to abnormal enlargement of contralateral regions due to compensatory hypertrophy.

Disruption of the TCA cycle reveals an ATF4-dependent integration of redox and amino acid metabolism.

The Tricarboxylic Acid (TCA) Cycle is arguably the most critical metabolic cycle in physiology and exists as an essential interface coordinating cellular metabolism, bioenergetics, and redox homeostasis. Despite decades of research, a comprehensive investigation into the consequences of TCA cycle dysfunction remains elusive. Here, we targeted two TCA cycle enzymes, fumarate hydratase (FH) and succinate dehydrogenase (SDH), and combined metabolomics, transcriptomics, and proteomics analyses to fully appraise the consequences of TCA cycle inhibition (TCAi) in murine kidney epithelial cells. Our comparative approach shows that TCAi elicits a convergent rewiring of redox and amino acid metabolism dependent on the activation of ATF4 and the integrated stress response (ISR). Furthermore, we also uncover a divergent metabolic response, whereby acute FHi, but not SDHi, can maintain asparagine levels via reductive carboxylation and maintenance of cytosolic aspartate synthesis. Our work highlights an important interplay between the TCA cycle, redox biology, and amino acid homeostasis.

Balancing of mitochondrial translation through METTL8-mediated m3C modification of mitochondrial tRNAs.

Mitochondria contain a specific translation machinery for the synthesis of mitochondria-encoded respiratory chain components. Mitochondrial tRNAs (mt-tRNAs) are also generated from the mitochondrial DNA and, similar to their cytoplasmic counterparts, are post-transcriptionally modified. Here, we find that the RNA methyltransferase METTL8 is a mitochondrial protein that facilitates 3-methyl-cytidine (m3C) methylation at position C32 of the mt-tRNASer(UCN) and mt-tRNAThr. METTL8 knockout cells show a reduction in respiratory chain activity, whereas overexpression increases activity. In pancreatic cancer, METTL8 levels are high, which correlates with lower patient survival and an enhanced respiratory chain activity. Mitochondrial ribosome profiling uncovered mitoribosome stalling on mt-tRNASer(UCN)- and mt-tRNAThr-dependent codons. Further analysis of the respiratory chain complexes using mass spectrometry revealed reduced incorporation of the mitochondrially encoded proteins ND6 and ND1 into complex I. The well-balanced translation of mt-tRNASer(UCN)- and mt-tRNAThr-dependent codons through METTL8-mediated m3C32 methylation might, therefore, facilitate the optimal composition and function of the mitochondrial respiratory chain.

YbeY is required for ribosome small subunit assembly and tRNA processing in human mitochondria.

Mitochondria contain their own translation apparatus which enables them to produce the polypeptides encoded in their genome. The mitochondrially-encoded RNA components of the mitochondrial ribosome require various post-transcriptional processing steps. Additional protein factors are required to facilitate the biogenesis of the functional mitoribosome. We have characterized a mitochondrially-localized protein, YbeY, which interacts with the assembling mitoribosome through the small subunit. Loss of YbeY leads to a severe reduction in mitochondrial translation and a loss of cell viability, associated with less accurate mitochondrial tRNASer(AGY) processing from the primary transcript and a defect in the maturation of the mitoribosomal small subunit. Our results suggest that YbeY performs a dual, likely independent, function in mitochondria being involved in precursor RNA processing and mitoribosome biogenesis. Issue Section: Nucleic Acid Enzymes.

Effect of solid feed level and types of roughage on passage kinetics of milk replacer, concentrate, and roughage in veal calves.

This study aimed (1) to provide estimates of total mean retention times of milk replacer (MR), concentrates, and roughage in veal calves fed a mixed diet; (2) to determine the effect of level and type of solid feed (SF) on passage kinetics of MR, concentrates, and roughages in veal calves; and (3) to compare passage kinetics in veal calves using the fecal excretion curves of indigestible markers and a noninvasive 13C tracer breath test approach to determine whether the latter technique can serve as an alternative. At the start of the trial, 48 Holstein-Friesian calves (6 wk of age; 68 ± 7.7 kg of body weight; BW) were assigned to 1 of 4 dietary treatments (for statistical analysis, only 39 calf observations were used). Three treatments contained chopped wheat straw as roughage in the SF mixture in a concentrate:roughage ratio of 90:10 (dry matter basis). The SF level was 20 g/kg of metabolic BW per day (low straw), 30 g/kg of metabolic BW per day (middle straw), or 40 g/kg of metabolic BW per day (high straw). The fourth treatment (high hay) contained long perennial ryegrass hay as roughage in the SF mixture in a concentrate:roughage ratio of 70:30 (dry matter basis, at 40 g/kg of metabolic BW per day). The quantity of MR was fixed for the high straw treatment, whereas the amount of MR for the other treatments during the adaptation period was adjusted based on a pair gain strategy (i.e., exchanging ration components but keeping similar net energy). At the end of the adaptation period, calves ranged from 12 to 15 wk of age with an average BW of 123 ± 8.6 kg. Passage kinetics of concentrates were estimated by measuring 13C enrichment excess of CO2 in breath from a pulsed-dose of [1-13C]octanoate. Passage kinetics of roughage, concentrates, and MR were also estimated using fecal excretion curves obtained after ingestion of chromium-mordanted roughage, Yb2O3, and Co-EDTA, respectively. We conclude that [1-13C]octanoate cannot serve as a measure for oro-duodenal transit of concentrates because of unrealistic estimates. Based on the fecal excretion curves, we concluded that the total mean retention time of MR (i.e., time to peak; the moment that the excretion curve reaches peak concentration) was, on average, 12.4 h, and that the passage kinetics of MR was not affected by the level or type of SF. The mean retention time of concentrates was shorter (21.4 h) than that of both straw (59.1 h) and hay (36.8 h), and was not affected by the level or type of SF. Also, the mean retention time of the slowest compartment (i.e., the rumen) was shorter for concentrates (39.6 h) than that of straw (110.0 h) and hay (59.2 h). Contrary, the passage of roughage was affected by level and type of SF. Long hay increased time to peak by 22.3 h and decreased ruminal mean retention time by 50.8 h relative to chopped straw, indicating that the passage rate of long hay is faster than that of chopped straw. We conclude that the level and type of SF only affects the passage kinetics of roughage and not that of MR and concentrates.

An Illustrative Analysis of Atypical Gas Production Profiles Obtained from In Vitro Digestibility Studies Using Fecal Inoculum.

Gas production profiles typically show a monotonically increasing monophasic pattern. However, atypical gas production profiles exist whereby at least two consecutive phases of gas production or additional extraneous features that distort the typical profile are present. Such profiles are more likely to occur with the use of a fecal inoculum and are much less well described. The presence of multiple phases or non-descript extraneous features makes it difficult to apply directly recommended modeling approaches such as standard response functions or classical growth functions. To overcome such difficulties, extensions of the Mitscherlich equation and a numerical modeling option also based on the Mitscherlich are explored. The numerical modeling option uses an estimate of relative rate obtained from the smoothed data profile and an estimate of maximum gas produced together with any lag time information drawn from the raw data to construct a simple Mitscherlich equation. In summary, this article illustrates the analysis of atypical gas production profiles obtained using a fecal inoculum and explores the methodology of numerical modeling to reconstruct equivalent typical growth-like trends.

Geographical Differences in Cardiovascular Comorbidities and Outcomes of COVID-19 Hospitalized Patients in the USA.

INTRODUCTION: Cardiovascular comorbidities may predispose to adverse outcomes in hospitalized patients with coronavirus disease 2019 (COVID-19). However, across the USA, the burden of cardiovascular comorbidities varies significantly. Whether clinical outcomes of hospitalized patients with COVID-19 differ between regions has not yet been studied systematically. Here, we report differences in underlying cardiovascular comorbidities and clinical outcomes of patients hospitalized with COVID-19 in Texas and in New York state. METHODS: We established a multicenter retrospective registry including patients hospitalized with COVID-19 between March 15 and July 12, 2020. Demographic and clinical data were manually retrieved from electronic medical records. We focused on the following outcomes: mortality, need for pharmacologic circulatory support, need for mechanical ventilation, and need for hemodialysis. Univariate and multivariate logistic regression analyses were performed. RESULTS: Patients in the Texas cohort (n = 296) were younger (57 vs. 63 years, p value <0.001), they had a higher BMI (30.3 kg/m2 vs. 28.5 kg/m2, p = 0.015), and they had higher rates of diabetes mellitus (41 vs. 30%; p = 0.014). In contrast, patients in the New York state cohort (n = 218) had higher rates of coronary artery disease (19 vs. 10%, p = 0.005) and atrial fibrillation (11 vs. 5%, p = 0.012). Pharmacologic circulatory support, mechanical ventilation, and hemodialysis were more frequent in the Texas cohort (21 vs. 13%, p = 0.020; 30 vs. 12%, p < 0.001; and 11 vs. 5%, p = 0.009, respectively). In-hospital mortality was similar between the 2 cohorts (16 vs. 18%, p = 0.469). After adjusting for differences in underlying comorbidities, only the use of mechanical ventilation remained significantly higher in the participating Texas hospitals (odds ratios [95% CI]: 3.88 [1.23, 12.24]). Median time to pharmacologic circulatory support was 8 days (interquartile range: 2, 13.8) in the Texas cohort compared to 1 day (0, 3) in the New York state cohort, while median time to in-hospital mortality was 16 days (10, 25.5) and 7 days (4, 14), respectively (both p < 0.001). In-hospital mortality was higher in the late versus the early study phase in the New York state cohort (24 vs. 14%, p = 0.050), while it was similar between the 2 phases in the Texas cohort (16 vs. 15%, p = 0.741). CONCLUSIONS: Geographical differences, including practice pattern variations and the impact of disease burden on provision of health care, are important for the evaluation of COVID-19 outcomes. Unadjusted data may cause bias affecting future regulatory policies and proper allocation of resources.

Reconstruction of the Proximal Scaphoid With a Medial Femoral Trochlea Osteochondral Graft: Minimum 2-Year Results.

PURPOSE: To report the clinical and radiological outcomes after medial femoral trochlear (MFT) osteochondral graft for the salvage of proximal scaphoid fractures with a minimum 2-year follow-up. METHODS: A retrospective review was performed of patients with comminuted fractures of the proximal scaphoid treated by excision of the proximal pole and replacement with free vascularized MFT osteochondral graft. Demographic data, objective and radiographic measurements, and patient-reported outcome measures of the upper limb and knee were collected. Pain was assessed by completion of a visual analog scale (VAS). RESULTS: Between February 2014 and May 2015, 12 MFT osteochondral grafts were performed. Eight patients were available for follow-up at a mean of 34 months (range, 28-39 months). The mean range of wrist flexion was 31° (range, 15°-60°), extension was 34° (range, 5°-60°), radial deviation was 9° (range, 0°-20°), ulnar deviation was 28° (range, 10°-45°) and grip strength was 42 kg (range, 25-53 kg). The median wrist pain, as measured by VAS, was 0.7 (mean, 1.3; range, 0-6). The average follow-up scapholunate, radiolunate, and radioscaphoid angles were 58.9° (range, 44°-93°), 12.9° (range, 0°-30°), and 46.0° (range, 35°-63°), respectively. The mean Disabilities of the Arm, Shoulder, and Hand (DASH) score was 13.9 (range, 3-43) and Patient Rated Wrist Evaluation (PRWE) score was 22.4 (range, 2-68). The mean postoperative Oxford Knee Score was 42 (range, 14-48). One patient suffered notable knee pain at 37-month follow-up. One patient suffered notable pain on the radial side of the wrist and underwent scaphoid excision and 4-corner arthrodesis. CONCLUSIONS: Replacement of the fragmented proximal scaphoid by MFT graft is an alternative to other salvage options and most patients can expect pain relief and acceptable wrist motion. These results need to be balanced against the potential for donor-site morbidity. TYPE OF STUDY/LEVEL OF EVIDENCE: Therapeutic V.

Outcomes of rotational atherectomy in complex lesions of the superficial femoral artery.

BACKGROUND: The effectiveness of rotational atherectomy in the treatment of complex superficial femoral artery (SFA) lesions remains poorly defined. Outcomes of SFA lesions treated with rotational atherectomy were analyzed. METHODS: This retrospective review assessed all patients who underwent rotational atherectomy of the SFA at a single institution between 2015 and 2018. The data of all patients were deidentified, and the study was approved by the Institutional Review Board. Informed consent was not obtained for this retrospective analysis. Main outcomes were Kaplan-Meier primary patency rate, freedom from major amputation, and 2-year survival rate. The effect of drug-coated balloon angioplasty (DCBA) on patency and time to death was investigated with univariate regression. The safety profile for atherectomy and DCBA was assessed by the 30-day incidence of major amputation and all-cause mortality. RESULTS: Fifty-three patients (mean age, 70.2 ± 9.8 years; 73% male; 65% critical limb-threatening ischemia; 47 [90%] current or former smokers; seven [13%] with prior failed ipsilateral endovascular intervention) underwent rotational atherectomy (Jetstream; Boston Scientific, Marlborough, Mass) with mean follow-up of 543 days. Forty-six (87%) patients underwent DCBA (Lutonix; BD Bard, Covington, Ga) after atherectomy. Mean lesion length was 13.2 ± 9.0 cm. Thirty-one (58%) lesions were TransAtlantic Inter-Society Consensus C or D class. At 1-month follow-up, 39 of 45 (87%) patients experienced improvement in symptoms and Rutherford class. An improvement in ankle-brachial index was also noted in 13% of patients without improvement of symptoms, with no patients progressing to surgical bypass or major amputation. Mean ankle-brachial index increased from 0.54 ± 0.035 to 0.90 ± 0.031 at 1 month after intervention (P < .001) and remained constant out to 18 months. Mean toe pressure increased from 36 ± 3.8 mm Hg to 67 ± 4.5 mm Hg at 1 month after intervention (P < .001) and remained constant out to 18 months. Kaplan-Meier primary patency rate was 75% (95% confidence interval, 61%-85%) at 12 months and 65% (51%-77%) at 24 months. There was a trend toward improved primary patency after adjunctive DCBA compared with plain balloon angioplasty at 1 year (75% vs 43%; P = .1082). There was no significant difference in mortality between adjunctive DCBA and plain balloon angioplasty at 2 years (11% vs 0%). The 2-year incidence of major amputation in critical limb-threatening ischemia patients was 3.9% (1.2%-6.5%). One patient died and none underwent amputation within 30 days. CONCLUSIONS: Rotational atherectomy with adjunctive DCBA of long SFA lesions has excellent long-term patency. Two-year major amputation and mortality rates are low, and the technique has an exceptional safety profile.

Metabolic shift underlies recovery in reversible infantile respiratory chain deficiency.

Reversible infantile respiratory chain deficiency (RIRCD) is a rare mitochondrial myopathy leading to severe metabolic disturbances in infants, which recover spontaneously after 6-months of age. RIRCD is associated with the homoplasmic m.14674T>C mitochondrial DNA mutation; however, only ~ 1/100 carriers develop the disease. We studied 27 affected and 15 unaffected individuals from 19 families and found additional heterozygous mutations in nuclear genes interacting with mt-tRNAGlu including EARS2 and TRMU in the majority of affected individuals, but not in healthy carriers of m.14674T>C, supporting a digenic inheritance. Our transcriptomic and proteomic analysis of patient muscle suggests a stepwise mechanism where first, the integrated stress response associated with increased FGF21 and GDF15 expression enhances the metabolism modulated by serine biosynthesis, one carbon metabolism, TCA lipid oxidation and amino acid availability, while in the second step mTOR activation leads to increased mitochondrial biogenesis. Our data suggest that the spontaneous recovery in infants with digenic mutations may be modulated by the above described changes. Similar mechanisms may explain the variable penetrance and tissue specificity of other mtDNA mutations and highlight the potential role of amino acids in improving mitochondrial disease.