Bridging the clinical-research gap: Harnessing an electronic data capture, integration, and visualization platform to systematically assess prospective patient-reported outcomes in mitochondrial medicine.

PURPOSE: Optimizing individualized clinical care in heterogeneous rare disorders, such as primary mitochondrial disease (PMD), will require gaining more comprehensive and objective understanding of the patient experience by longitudinally tracking quantifiable patient-specific outcomes and integrating subjective data with clinical data to monitor disease progression and targeted therapeutic effects. METHODS: Electronic surveys of patient (and caregiver) reported outcome (PRO) measures were administered in REDCap within clinical domains commonly impaired in patients with PMD in the context of their ongoing routine care, including quality of life, fatigue, and functional performance. Descriptive statistics, group comparisons, and inter-measure correlations were used to evaluate system feasibility, utility of PRO results, and consistency across outcome measure domains. Real-time tracking and visualization of longitudinal individual-level and cohort-level data were facilitated by a customized data integration and visualization system, MMFP-Tableau. RESULTS: An efficient PRO electronic capture and analysis system was successfully implemented within a clinically and genetically heterogeneous rare disease clinical population spanning all ages. Preliminary data analyses demonstrated the flexibility of this approach for a range of PROs, as well as the value of selected PRO scales to objectively capture qualitative functional impairment in four key clinical domains. High inter-measure reliability and correlation were observed. Between-group analyses revealed that adults with PMD reported significantly worse quality of life and greater fatigue than did affected children, while PMD patients with nuclear gene disorders reported lower functioning relative to those with an mtDNA gene disorder in several clinical domains. CONCLUSION: Incorporation of routine electronic data collection, integration, visualization, and analysis of relevant PROs for rare disease patients seen in the clinical setting was demonstrated to be feasible, providing prospective and quantitative data on key clinical domains relevant to the patient experience. Further work is needed to validate specific PROs in diverse PMD patients and cohorts, and to formally evaluate the clinical impact and utility of harnessing integrated data systems to objectively track and integrate quantifiable PROs in the context of rare disease patient clinical care.

Advanced approach for comprehensive mtDNA genome testing in mitochondrial disease.

Mitochondrial disease diagnosis requires interrogation of both nuclear and mitochondrial (mtDNA) genomes for single-nucleotide variants (SNVs) and copy number alterations, both in the proband and often maternal relatives, together with careful phenotype correlation. We developed a comprehensive mtDNA sequencing test ('MitoGenome') using long-range PCR (LR-PCR) to amplify the full length of the mtDNA genome followed by next generation sequencing (NGS) to accurately detect SNVs and large-scale mtDNA deletions (LSMD), combined with droplet digital PCR (ddPCR) for LSMD heteroplasmy quantification. Overall, MitoGenome tests were performed on 428 samples from 394 patients with suspected or confirmed mitochondrial disease. The positive yield was 11% (43/394), including 34 patients with pathogenic or likely pathogenic SNVs (the most common being m.3243A > G in 8/34 (24%) patients), 8 patients with single LSMD, and 3 patients with multiple LSMD exceeding 10% heteroplasmy levels. Two patients with both LSMD and pathogenic SNV were detected. Overall, this LR-PCR/NGS assay provides a highly accurate and comprehensive diagnostic method for simultaneous mtDNA SNV detection at heteroplasmy levels as low as 1% and LSMD detection at heteroplasmy levels below 10%. Inclusion of maternal samples for variant classification and ddPCR to quantify LSMD heteroplasmy levels further enables accurate pathogenicity assessment and clinical correlation interpretation of mtDNA genome sequence variants and copy number alterations.

An ancestral 10-bp repeat expansion in VWA1 causes recessive hereditary motor neuropathy.

The extracellular matrix comprises a network of macromolecules such as collagens, proteoglycans and glycoproteins. VWA1 (von Willebrand factor A domain containing 1) encodes a component of the extracellular matrix that interacts with perlecan/collagen VI, appears to be involved in stabilizing extracellular matrix structures, and demonstrates high expression levels in tibial nerve. Vwa1-deficient mice manifest with abnormal peripheral nerve structure/function; however, VWA1 variants have not previously been associated with human disease. By interrogating the genome sequences of 74 180 individuals from the 100K Genomes Project in combination with international gene-matching efforts and targeted sequencing, we identified 17 individuals from 15 families with an autosomal-recessive, non-length dependent, hereditary motor neuropathy and rare biallelic variants in VWA1. A single disease-associated allele p.(G25Rfs*74), a 10-bp repeat expansion, was observed in 14/15 families and was homozygous in 10/15. Given an allele frequency in European populations approaching 1/1000, the seven unrelated homozygote individuals ascertained from the 100K Genomes Project represents a substantial enrichment above expected. Haplotype analysis identified a shared 220 kb region suggesting that this founder mutation arose >7000 years ago. A wide age-range of patients (6-83 years) helped delineate the clinical phenotype over time. The commonest disease presentation in the cohort was an early-onset (mean 2.0 ± 1.4 years) non-length-dependent axonal hereditary motor neuropathy, confirmed on electrophysiology, which will have to be differentiated from other predominantly or pure motor neuropathies and neuronopathies. Because of slow disease progression, ambulation was largely preserved. Neurophysiology, muscle histopathology, and muscle MRI findings typically revealed clear neurogenic changes with single isolated cases displaying additional myopathic process. We speculate that a few findings of myopathic changes might be secondary to chronic denervation rather than indicating an additional myopathic disease process. Duplex reverse transcription polymerase chain reaction and immunoblotting using patient fibroblasts revealed that the founder allele results in partial nonsense mediated decay and an absence of detectable protein. CRISPR and morpholino vwa1 modelling in zebrafish demonstrated reductions in motor neuron axonal growth, synaptic formation in the skeletal muscles and locomotive behaviour. In summary, we estimate that biallelic variants in VWA1 may be responsible for up to 1% of unexplained hereditary motor neuropathy cases in Europeans. The detailed clinical characterization provided here will facilitate targeted testing on suitable patient cohorts. This novel disease gene may have previously evaded detection because of high GC content, consequential low coverage and computational difficulties associated with robustly detecting repeat-expansions. Reviewing previously unsolved exomes using lower QC filters may generate further diagnoses.

Development of a Mitochondrial Myopathy-Composite Assessment Tool.

BACKGROUND: 'Mitochondrial Myopathy' (MM) refers to genetically-confirmed Primary Mitochondrial Disease (PMD) that predominantly impairs skeletal muscle function. Validated outcome measures encompassing core MM domains of muscle weakness, muscle fatigue, imbalance, impaired dexterity, and exercise intolerance do not exist. The goal of this study was to validate clinically-meaningful, quantitative outcome measures specific to MM. METHODS: This was a single centre study. Objective measures evaluated included hand-held dynamometry, balance assessments, Nine Hole Peg Test (9HPT), Functional Dexterity Test (FDT), 30 second Sit to Stand (30s STS), and 6-minute walk test (6MWT). Results were assessed as z-scores, with < -2 standard deviations considered abnormal. Performance relative to the North Star Ambulatory Assessment (NSAA) of functional mobility was assessed by Pearson's correlation. RESULTS: In genetically-confirmed MM participants [n = 59, mean age 21.6 ± 13.9 (range 7 - 64.6 years), 44.1% male], with nuclear gene aetiologies, n = 18/59, or mitochondrial (mtDNA) aetiologies, n = 41/59, dynamometry measurements demonstrated both proximal [dominant elbow flexion (-2.6 ± 2.1, mean z-score ± standard deviation, SD), hip flexion (-2.5 ± 2.3), and knee flexion (-2.8 ± 1.3)] and distal muscle weakness [wrist extension (-3.4 ± 1.7), palmar pinch (-2.5 ± 2.8), and ankle dorsiflexion (-2.4 ± 2.5)]. Balance [Tandem Stance (TS) Eyes Open (-3.2 ± 8.8, n = 53) and TS Eyes Closed (-2.6 ± 2.7, n = 52)] and dexterity [FDT (-5.9 ± 6.0, n = 44) and 9HPT (-8.3 ± 11.2, n = 53)] assessments also revealed impairment. Exercise intolerance was confirmed by strength-based 30s STS test (-2.0 ± 0.8, n = 38) and mobility-based 6MWT mean z-score (-2.9 ± 1.3, n = 46) with significant decline in minute distances (slope -0.9, p = 0.03, n = 46). Muscle fatigue was quantified by dynamometry repetitions with strength decrement noted between first and sixth repetitions at dominant elbow flexors (-14.7 ± 2.2%, mean ± standard error, SEM, n = 21). All assessments were incorporated in the MM-Composite Assessment Tool (MM-COAST). MM-COAST composite score for MM participants was 1.3± 0.1(n = 53) with a higher score indicating greater MM disease severity, and correlated to NSAA (r = 0.64, p < 0.0001, n = 52) to indicate clinical meaning. Test-retest reliability of MM-COAST assessments in an MM subset (n = 14) revealed an intraclass correlation coefficient (ICC) of 0.81 (95% confidence interval: 0.59-0.92) indicating good reliability. CONCLUSIONS: We have developed and successfully validated a MM-specific Composite Assessment Tool to quantify the key domains of MM, shown to be abnormal in a Definite MM cohort. MM-COAST may hold particular utility as a meaningful outcome measure in future MM intervention trials.

Safety and efficacy of omaveloxolone in patients with mitochondrial myopathy: MOTOR trial.

OBJECTIVE: To investigate the safety and efficacy of escalating doses of the semi-synthetic triterpenoid omaveloxolone in patients with mitochondrial myopathy. METHODS: In cohorts of 8-13, 53 participants were randomized double-blind to 12 weeks of treatment with omaveloxolone 5, 10, 20, 40, 80, or 160 mg, or placebo. Outcome measures were change in peak cycling exercise workload (primary), in 6-minute walk test (6MWT) distance (secondary), and in submaximal exercise heart rate and plasma lactate (exploratory). RESULTS: No differences in peak workload or 6MWT were observed at week 12 with omaveloxolone treatment vs placebo for all omaveloxolone dose groups. In contrast, omaveloxolone 160 mg reduced heart rate at week 12 by 12.0 ± 4.6 bpm (SE) during submaximal exercise vs placebo, p = 0.01, and by 8.7 ± 3.5 bpm (SE) vs baseline, p = 0.02. Similarly, blood lactate was 1.4 ± 0.7 mM (SE) lower vs placebo, p = 0.04, and 1.6 ± 0.5 mM (SE) lower vs baseline at week 12, p = 0.003, with omaveloxolone 160 mg treatment. Adverse events were generally mild and infrequent. CONCLUSIONS: Omaveloxolone 160 mg was well-tolerated, and did not lead to change in the primary outcome measure, but improved exploratory endpoints lowering heart rate and lactate production during submaximal exercise, consistent with improved mitochondrial function and submaximal exercise tolerance. Therefore, omaveloxolone potentially benefits patients with mitochondrial myopathy, which encourages further investigations of omaveloxolone in this patient group. CLINICALTRIALSGOV IDENTIFIER: NCT02255422. CLASSIFICATION OF EVIDENCE: This study provides Class II evidence that, for patients with mitochondrial myopathy, omaveloxolone compared to placebo did not significantly change peak exercise workload.

Mitochondrial Genomics: A complex field now coming of age.

PURPOSE OF REVIEW: The groundwork for mitochondrial medicine was laid 30 years ago with identification of the first disease-causing mitochondrial DNA (mtDNA) mutations in 1988. Three decades later, mutations in nearly 300 genes involving every possible mode of inheritance within both nuclear and mitochondrial genomes are now recognized to collectively comprise the largest class of inherited metabolic disease affecting at least 1 in 4,300 individuals across all ages. Significant progress has been made in recent years to improve understanding of mitochondrial biology and disease pathophysiology. RECENT FINDINGS: Markedly improved understanding of the highly diverse molecular etiologies of multi-systemic phenotypes in primary mitochondrial disease has resulted from massively parallel genomic sequencing technologies and improved bioinformatic resources that enable identification in individual patients of their disease's precise genetic etiology. Key informatics resources of particular utility to the mitochondrial disease genomics community have been developed, including: (1) Mitocarta 2.0 repository of 1200+ verified mitochondria-localized proteins, (2) MITOMAP Web resource of curated mtDNA genome variants, and (3) Mitochondrial Disease Sequence Data Resource (MSeqDR) that centralizes Web curation and annotation of mitochondrial disease genes and variants in both genomes, ontology-defined phenotypes, and access to many analytic tools to support genomic data mining and interpretation. Gene and mutation-based disease categorization has proven particularly useful to identify the full clinical spectrum of disease that may affect a given individual. SUMMARY: Extensive genomic advances, both in technologic platforms and bioinformatics resources, have facilitated dramatic improvement in the accurate recognition and understanding of primary mitochondrial disease.

Mitochondrial Disease: Advances in clinical diagnosis, management, therapeutic development, and preventative strategies.

PURPOSE OF REVIEW: Primary mitochondrial disease encompasses an impressive range of inherited energy deficiency disorders having highly variable molecular etiologies as well as clinical onset, severity, progression, and response to therapies of multi-system manifestations. Significant progress has been made in primary mitochondrial disease diagnostic approaches, clinical management, therapeutic options, and preventative strategies that are tailored to major mitochondrial disease phenotypes and subclasses. RECENT FINDINGS: The extensive phenotypic pleiotropy of individual mitochondrial diseases from an organ-based perspective is reviewed. Improved consensus on standards for mitochondrial disease patient care are being complemented by emerging therapies that target specific molecular subtypes of mitochondrial disease. Reproductive counseling options now include preimplantation genetic diagnosis at the time of in vitro fertilization for familial mutations in nuclear genes and some mtDNA disorders. Mitochondrial replacement technologies have promise for some mtDNA disorders, although practical and societal challenges remain to allow their further research analyses and clinical utilization. SUMMARY: A dramatic increase has occurred in recent years in the recognition, understanding, treatment options, and preventative strategies for primary mitochondrial disease.

Loss-of-Function Mutations in FRRS1L Lead to an Epileptic-Dyskinetic Encephalopathy.

Glutamatergic neurotransmission governs excitatory signaling in the mammalian brain, and abnormalities of glutamate signaling have been shown to contribute to both epilepsy and hyperkinetic movement disorders. The etiology of many severe childhood movement disorders and epilepsies remains uncharacterized. We describe a neurological disorder with epilepsy and prominent choreoathetosis caused by biallelic pathogenic variants in FRRS1L, which encodes an AMPA receptor outer-core protein. Loss of FRRS1L function attenuates AMPA-mediated currents, implicating chronic abnormalities of glutamatergic neurotransmission in this monogenic neurological disease of childhood.