Primary Mitochondrial Diseases

Medical Experts

Contributor

Shayota

Brian J. Shayota, MD, MPH

Assistant Professor of Pediatrics and Medical Genetics, University of Utah Health/Primary Children's Hospital

Director, Metabolic Services, and Director, ReSeq Clinic, University of Utah Health

Director, Telegenetics Consultation Services, Huntsman Cancer Institute

Contributor

Pasquali

Marzia Pasquali, PhD, FACMG

Professor of Pathology, Adjunct Professor of Pediatrics, University of Utah

Medical Director, Biochemical Genetics, ARUP Laboratories

Primary mitochondrial diseases (PMDs) are a heterogeneous group of disorders caused by genetic defects affecting the mitochondrial respiratory chain that lead to impaired oxidative phosphorylation (OXPHOS). Clinical manifestations and age of symptom onset vary widely; symptoms may present throughout the lifespan and can impact a single organ or involve multiple systems. Most commonly, there are neurologic, muscular, and metabolic abnormalities. PMDs can be caused by pathogenic variants in either nuclear DNA (nDNA), which follows classic Mendelian inheritance, or mitochondrial DNA (mtDNA), which is maternally inherited. Two unique features of mtDNA add diagnostic complexity: heteroplasmy, the coexistence of different mtDNA variants within the same cell, and the threshold effect, in which symptoms occur only when the proportion of pathogenic mtDNA variants exceeds a tissue-specific level required to impair OXPHOS. No single biomarker reliably diagnoses PMDs. Laboratory tests such as measurement of lactate and pyruvate, urine organic acids, plasma amino acids, and acylcarnitines may indicate mitochondrial dysfunction and can help inform the diagnostic evaluation, but they lack sufficient sensitivity and specificity to establish a diagnosis. Definitive diagnosis requires molecular genetic confirmation. Increasingly, comprehensive genomic sequencing is used as a first-line diagnostic approach when PMDs are suspected.

Quick Answers for Clinicians

How do mitochondrial diseases with a mitochondrial DNA vs. nuclear DNA etiology differ?

Primary mitochondrial diseases (PMDs) can arise from pathogenic variants in either mitochondrial DNA (mtDNA) or nuclear DNA (nDNA), and the two etiologies differ in important ways. The mitochondrial genome is small and maternally inherited. The nuclear genome encodes more than 1,500 mitochondrial proteins and follows classic Mendelian inheritance; therefore, it can be autosomal recessive, autosomal dominant, or X-linked. Although PMDs arising from variants from either source can have overlapping clinical features, mtDNA-related diseases are uniquely influenced by heteroplasmy, which contributes to their wide variability in symptoms. PMDs can present at any age. Although they were once thought to differ in age of onset (nDNA-related disorders in childhood and mtDNA-related disorders in later childhood or adulthood), it is now clear that both can appear across the lifespan.

How does heteroplasmy affect laboratory testing?

Most mitochondrial DNA (mtDNA) variants are heteroplasmic, meaning that more than one mtDNA variant can coexist within the same cell. However, some mtDNA variants (such as pathogenic variants associated with Leber hereditary optic neuropathy [LHON]) are homoplasmic, meaning that all mtDNA molecules within a cell carry the same variant. The proportion of pathogenic mtDNA variants can vary significantly between tissues, which impacts detection. In some cases, mtDNA variants may be undetectable in blood because the heteroplasmy level may be low or completely absent in the hematopoietic progenitor cells. Therefore, alternative sample types (most commonly skeletal muscle or urine) are often required for accurate testing and improved diagnostic sensitivity.

Are primary mitochondrial diseases identified by newborn screening?

Primary mitochondrial diseases (PMDs) are not targeted conditions on standard newborn screening panels. However, infants with MT-ATP6 pathogenic variants have been identified through the combination of low citrulline and elevated C5-OH acylcarnitine (often with C3), markers intended to detect other metabolic disorders such as proximal urea cycle disorders and organic acidemias. Notably, detection depends on state-specific reporting practices, as not all states report low citrulline levels. Additionally, citrulline cutoffs for newborn screening are not sensitive enough to detect most cases of MT-ATP6-associated mitochondrial disease, so a normal newborn screen would not reliably rule out the diagnosis. Early identification through this mechanism may enable timely interventions that could prevent neurologic symptoms.

How are mitochondrial diseases treated?

Given the diversity of potential symptoms and organ systems involved, a multidisciplinary team of specialists is often involved in the care of a patient with a primary mitochondrial disease (PMD). The majority of PMDs do not have targeted therapies, although there may still be ways to help alleviate symptoms and/or slow the progression of the disease. In these cases, it is best to consult with a provider who specializes in PMDs or clinical biochemical genetics.

Indications for Testing

Clinical and Biochemical Indicators

Clinical Features

PMDs lack a single pathognomonic feature; clinical recognition is usually prompted by a combination of features that affect multiple, apparently unrelated organs.

Clinical features of PMDs include stroke-like episodes, acquired ptosis and/or ophthalmoplegia, optic atrophy, pigmentary retinopathy, sideroblastic anemia, epilepsia partialis continua, proximal myopathy, exercise intolerance, cardiomyopathy, sensorineural deafness, and diabetes mellitus.^,

Biochemical Indicators

In some cases, biochemical abnormalities may be the first diagnostic indication of a PMD. Abnormalities may include elevations in blood or cerebrospinal fluid (CSF) lactate, plasma alanine, and urinary 3-methylglutaconic acid (3-MGA).

Laboratory Testing

Diagnostic testing for PMDs requires a combination of biochemical and genetic testing. Clinical features or family history may occasionally point to a specific syndrome, which would make targeted testing appropriate. However, because PMDs often overlap with other disorders, broad testing is often the preferred approach.

Biochemical Testing

Initial blood testing for PMDs may include a CBC, plasma amino acids, acylcarnitine profile, creatine phosphokinases, transaminase, albumin, lactate, and pyruvate.

Urine organic acids should also be ordered, along with quantitative 3-MGA in urine and plasma if possible.

For patients with muscular symptoms and suspected PMD, creatine phosphokinases and uric acid labs are particularly useful.

For patients with neurologic symptoms and suspected PMD, evaluation of CSF for lactate, pyruvate, amino acids, and 5-methyltetrahydrofolate is recommended. Imaging studies in these patients, such as magnetic resonance imaging (MRI) or magnetic resonance spectroscopy (MRS), may also provide some clues to suggest a PMD.

Growth differentiation factor 15 (GDF-15) and fibroblast growth factor 21 (FGF-21) are hormones associated with mitochondrial stress and can be used as supportive diagnostic markers, but notably, these hormones can also be elevated in a number of other nongenetic disease processes.

Genetic Testing

Genetic testing is used to confirm a diagnosis of PMD and establish a molecular etiology that can inform prognosis, management, and familial recurrence risk.

Two main diagnostic testing strategies are recommended:

Targeted testing: Targeted testing of common pathogenic variants in mtDNA and nDNA may be appropriate when the clinical phenotype or family history is strongly suggestive of a specific genetic etiology or when comprehensive genomic testing is not immediately feasible. If targeted testing is nondiagnostic, comprehensive genomic analysis should be pursued.
Comprehensive genomic sequencing: Comprehensive sequencing of mtDNA and nDNA, using whole genome sequencing (WGS) that includes mtDNA, is appropriate for all referral indications and is particularly recommended for individuals with complex or multisystem phenotypes. When feasible, trio testing (analysis of the affected individual and both biological parents) is strongly recommended to improve nDNA variant interpretation and pathogenicity assessment. When available, comprehensive sequencing of both mtDNA and nDNA is generally preferred over targeted testing.^,

Detection of mtDNA variants and heteroplasmy levels are highly tissue dependent. Pathogenic mtDNA variants may not be detectable in blood. Therefore, if initial testing using blood is nondiagnostic, analysis using alternative sample types such as urine should be considered. For select cases in which noninvasive testing is nondiagnostic, muscle biopsy may be required for genetic and/or biochemical evaluation.