Janice M. Fletcher

Molecular Diagnosis of Infantile Mitochondrial Disease with Targeted Next-Generation Sequencing

Applying next-generation sequencing to 42 infants with mitochondrial disease highlights both the potential and the challenge of using this technology in clinical diagnosis. Getting to the Genetic Root of Mitochondrial Disease Next-generation DNA sequencing is being applied with great success in research settings to uncover new disease genes. Despite these successes, it is unclear how useful the technology will be for routine clinical diagnosis given the challenge of interpreting DNA variations in individual patients. In a new study, Calvo and colleagues apply next-generation sequencing to infants with mitochondrial disorders, a large collection of inherited diseases that are notoriously difficult to diagnose because of the multitude of candidate genes and the highly variable nature of the clinical presentation. First, the authors selected 42 unrelated infants with mitochondrial diseases that were refractory to standard clinical genetic testing. Then, for each child, they sequenced the DNA of the mitochondrial genome, the 100 genes previously linked to mitochondrial disease, and the ~1000 additional genes that are known to participate in mitochondrial biology. Of all the DNA differences present in the patients, the researchers prioritized those that were rare in the general population, predicted to disrupt protein function, and inherited in a recessive fashion. Such variants showed fivefold enrichment in the patients compared to that in healthy control individuals. In 10 patients (24%), firm molecular diagnoses were made in genes previously linked to mitochondrial diseases; 13 patients (31%) had prioritized recessive mutations in genes not previously linked to disease. For two of these genes, the authors were able to show that the mutations caused the mitochondrial disorder. These results suggest that next-generation sequencing may be able to provide a molecular diagnosis for ~25% of currently unsolved cases of infantile mitochondrial disease. An additional 25% of cases could be solved in the coming few years as more genes are formally proven to be linked to mitochondrial disease. The remaining 50% of patients in whom diagnosis was not possible underscores the challenge of interpreting DNA sequence data for clinical diagnosis. Nevertheless, the study by Calvo and colleagues will help to calibrate clinicians’ expectations regarding the diagnostic use of next-generation sequencing. Advances in next-generation sequencing (NGS) promise to facilitate diagnosis of inherited disorders. Although in research settings NGS has pinpointed causal alleles using segregation in large families, the key challenge for clinical diagnosis is application to single individuals. To explore its diagnostic use, we performed targeted NGS in 42 unrelated infants with clinical and biochemical evidence of mitochondrial oxidative phosphorylation disease. These devastating mitochondrial disorders are characterized by phenotypic and genetic heterogeneity, with more than 100 causal genes identified to date. We performed “MitoExome” sequencing of the mitochondrial DNA (mtDNA) and exons of ~1000 nuclear genes encoding mitochondrial proteins and prioritized rare mutations predicted to disrupt function. Because patients and healthy control individuals harbored a comparable number of such heterozygous alleles, we could not prioritize dominant-acting genes. However, patients showed a fivefold enrichment of genes with two such mutations that could underlie recessive disease. In total, 23 of 42 (55%) patients harbored such recessive genes or pathogenic mtDNA variants. Firm diagnoses were enabled in 10 patients (24%) who had mutations in genes previously linked to disease. Thirteen patients (31%) had mutations in nuclear genes not previously linked to disease. The pathogenicity of two such genes, NDUFB3 and AGK, was supported by complementation studies and evidence from multiple patients, respectively. The results underscore the potential and challenges of deploying NGS in clinical settings.

Human CIA30 is involved in the early assembly of mitochondrial complex I and mutations in its gene cause disease

In humans, complex I of the respiratory chain is composed of seven mitochondrial DNA (mtDNA)‐encoded and 38 nuclear‐encoded subunits that assemble together in a process that is poorly defined. To date, only two complex I assembly factors have been identified and how each functions is not clear. Here, we show that the human complex I assembly factor CIA30 (complex I intermediate associated protein) associates with newly translated mtDNA‐encoded complex I subunits at early stages in their assembly before dissociating at a later stage. Using antibodies we identified a CIA30‐deficient patient who presented with cardioencephalomyopathy and reduced levels and activity of complex I. Genetic analysis revealed the patient had mutations in both alleles of the NDUFAF1 gene that encodes CIA30. Complex I assembly in patient cells was defective at early stages with subunits being degraded. Complementing the deficiency in patient fibroblasts with normal CIA30 using a novel lentiviral system restored steady‐state complex I levels. Our results indicate that CIA30 is a crucial component in the early assembly of complex I and mutations in its gene can cause mitochondrial disease.

De novo mutations in the mitochondrial ND3 gene as a cause of infantile mitochondrial encephalopathy and complex I deficiency

Both nuclear and mitochondrial DNA mutations can cause energy generation disorders. Respiratory chain complex I deficiency is the most common energy generation disorder and a frequent cause of infantile mitochondrial encephalopathies such as Leighs disease and lethal infantile mitochondrial disease. Most such cases have been assumed to be caused by nuclear gene defects, but recently an increasing number have been shown to be caused by mutations in the mitochondrially encoded complex I subunit genes ND4, ND5, and ND6. We report the first four cases of infantile mitochondrial encephalopathies caused by mutations in the ND3 subunit gene. Three unrelated children have the same novel heteroplasmic mutation (T10158C), only the second mutation reported in ND3, and one has the previously identified T10191C mutation. Both mutations cause disproportionately greater reductions in enzyme activity than in the amount of fully assembled complex I, suggesting the ND3 subunit plays an unknown but important role in electron transport, proton pumping, or ubiquinone binding. Three cases appear to have a de novo mutation, with no mutation detected in maternal relatives. Mitochondrial DNA disease may be considerably more prevalent in the pediatric population than currently predicted and should be considered in patients with infantile mitochondrial encephalopathies and complex I deficiency.

Outcome of neonatal screening for medium-chain acyl-CoA dehydrogenase deficiency in Australia: a cohort study

BACKGROUND Medium-chain acyl-CoA dehydrogenase (MCAD) deficiency is the disorder thought most to justify neonatal screening by tandem-mass spectrometry because, without screening, there seems to be substantial morbidity and mortality. Our aim was to assess the overall effectiveness of neonatal screening for MCAD deficiency in Australia. METHODS We identified MCAD-deficient patients from a total population of 2,495,000 Australian neonates (810,000 screened) born between April 1, 1994, and March 31, 2004. Those from a cohort of 1,995,000 (460,000 screened) were followed up for at least 4 years, and we recorded number of deaths and severe episodes, medical and neuropsychological outcome, and hospital admissions within the screened and unscreened groups. FINDINGS In cohorts aged at least 4 years there were 35 MCAD-deficient patients in those not screened (2.28 per 100,000 total population) and 24 in the screened population (5.2 per 100,000). We estimated that patients with this disorder in the unscreened cohort remained undiagnosed. Before 4 years of age, three screened patients had an episode of severe decompensation (including one neonatal death) versus 23 unscreened patients (including five deaths). At the most conservative estimate, relative risk of an adverse event was 0.44 (95% CI 0.13-1.45). In the larger cohort the relative risk (screened vs unscreened) of an adverse event by age 2 years was 0.26 (95% CI 0.07-0.97), also a conservative estimate. 38 of 52 living patients had neuropsychological testing, with no suggestions of significant differences in general cognitive outcome between the groups. INTERPRETATION Screening is effective in patients with MCAD deficiency since early diagnosis reduces deaths and severe adverse events in children up to the age of 4 years.

Expanded newborn screening: Outcome in screened and unscreened patients at age 6 years

OBJECTIVE: Tandem mass spectrometry is widely applied to routine newborn screening but there are no long-term studies of outcome. We studied the clinical outcome at six years of age in Australia. METHODS: In a cohort study, we analyzed the outcome at 6 years for patients detected by screening or by clinical diagnosis among >2 million infants born from 1994 to 1998 (1 017 800, all unscreened) and 1998 to 2002 (461 500 screened, 533 400 unscreened) recording intellectual and physical condition, school placement, other medical problems, growth, treatment, diet, and hospital admissions. Results were analyzed separately for medium-chain acyl-CoA dehydrogenase deficiency (MCADD) and other disorders, and grouped patients as those who presented clinically or died in the first 5 days of life; patients presented later or diagnosed by screening, and those with substantially benign disorders. RESULTS: Inborn errors, excluding phenylketonuria, were diagnosed in 116 of 1 551 200 unscreened infants (7.5/100 000 births) and 70 of 461 500 screened infants (15.2/100 000 births). Excluding MCADD, 21 unscreened patients with metabolic disorders diagnosed after 5 days of life died or had a significant intellectual or physical handicap (1.35/100 000 population) compared with 2 of the screened cohort (0.43/100 000; odds ratio: 3.1 [95% CI: 0.73–13.32]). Considering the likely morbidity or mortality among the expected number of never-diagnosed unscreened patients, there would be a significant difference. Growth distribution was normal in all cohorts. CONCLUSION: Screening by tandem mass spectrometry provides a better outcome for patients at 6 years of age, with fewer deaths and fewer clinically significant disabilities.

Hyperammonemia encephalopathy: An important cause of neurological deterioration following chemotherapy

Idiopathic hyperammonemic encephalopathy is an uncommon but frequently fatal complication of chemotherapy. It is characterised by abrupt alteration in mental status with markedly elevated plasma ammonia levels in the absence of obvious liver disease or any other identifiable cause, and frequently results in intractable coma and death. It usually occurs in patients with haematologic malignancies during the period of neutropenia following cytoreductive therapy or bone marrow transplantation, and in solid organ malignancies treated with 5-fluorouracil. Although the aetiology of this syndrome is yet to be determined, it appears to be multi-factorial in nature. Optimal management remains to be formally established, and the critical step is increased awareness of the syndrome by measurement of plasma ammonium levels in patients with neurological symptoms, leading to early diagnosis and the prompt implementation of therapy.

Inhibition of Glycosaminoglycan Synthesis Using Rhodamine B in a Mouse Model of Mucopolysaccharidosis Type IIIA

Reduction of an enzyme activity required for the lysosomal degradation of glycosaminoglycan (gag) chains will result in a mucopolysaccharidosis (MPS) disorder. Substrate deprivation therapy (SDT), a potential therapy option for MPS with residual enzyme activity, aims to reduce the synthesis of gag chains, the natural substrate for the deficient enzyme. Reduced substrate levels would balance the reduced level of enzyme in patient cells, resulting in normalized gag turnover. Rhodamine B, a nonspecific inhibitor, reduced gag synthesis in a range of normal and MPS cells and also decreased lysosomal storage of gag in MPS VI (72%) and MPS IIIA (60%) cells. Body weight gain of male MPS IIIA mice treated with 1 mg/kg rhodamine B was reduced compared with untreated MPS IIIA mice and was indistinguishable from that of normal mice. Liver size, total gag content, and lysosomal gag was reduced in treated MPS IIIA animals as was urinary gag excretion. Lysosomal gag content in the brain was also reduced by treatment. The alteration in MPS IIIA clinical pathology by rhodamine B, combined with the observation that treatment had no effect on the health of normal animals, demonstrates the potential for SDT in general as a therapy for MPS disorders.

Screening for lysosomal storage disorders- : A clinical perspective

SummaryThe availability of therapies for lysosomal storage diseases (LSDs) and clear documentation from animal studies that optimal therapy depends on early diagnosis have set the scene for newborn screening for LSDs. The combined incidence of this group of conditions is approximately 1 in 7000, well within the feasible range for newborn screening programmes. The availability of multiplex technology has facilitated the technical aspects of initial screening. The scientific challenge is to predict disease severity early enough to influence choice of therapy. LSD screening is discussed from the point of view of the scientists, the families affected by these conditions, the community and clinicians.

Carbohydrate-deficient glycoprotein syndrome: Beyond the screen

We report two siblings with carbohydrate-deficient glycoprotein syndrome (CDG) type 1 (McKusick 212065) secondary to phosphomannomutase deficiency, both of whom have repeatedly normal transferrin isoform screening tests.

Quantification of Glutamine in Dried Blood Spots and Plasma by Tandem Mass Spectrometry for the Biochemical Diagnosis and Monitoring of Ornithine Transcarbamylase Deficiency

A notable deficiency in the use of tandem mass spectrometry (MS/MS) for newborn screening is the inability to screen for urea cycle defects. The most common of these, with an incidence of 1 in 14 000 births (1), is the inherited X-linked disorder ornithine transcarbamylase deficiency (OTCD). A majority (60%) of hemizygous males risk death from hyperammonemic coma during the first week of life. The remainder, including 10% of heterozygous females, exhibit lethargy, vomiting episodes, and behavioral problems during childhood. The severity of the disorder and the potential for correction of OTCD by liver transplantation and gene therapy (2) provide adequate justification for newborn screening. OTCD patients have low blood citrulline because of reduced conversion from carbamoyl phosphate. Citrulline is one of the amino acids routinely measured in MS/MS newborn-screening programs. Unfortunately, many protein-restricted newborns also have low blood citrulline (3). A more selective amino acid metabolite for OTCD is glutamine. The derivatization procedure used in many MS/MS screening programs (4), which uses butanol–hydrogen chloride, destroys glutamine. Approximately one-half of the glutamine is converted to glutamic acid dibutyl ester and is indistinguishable from that formed from endogenous glutamic acid in the blood. The surviving glutamine butyl ester is deaminated in acidic solution to a protonated form of pyroglutamic acid butyl ester in the electrospray source of the MS/MS. Again it is not possible to distinguish this pyroglutamic acid from what is already present in the blood. As a secondary consequence, the measurements of glutamic and pyroglutamic (and by analogy, aspartic) acids in blood spots after derivatization are grossly inaccurate. MS/MS newborn-screening programs that do not derivatize amino acids avoid solvolysis of glutamine and of pyroglutamic acid to glutamic acid. During electrospray ionization-MS/MS analysis, however, glutamine is again indistinguishable from pyroglutamic acid. Resolution is possible by separation with time-consuming liquid chromatography …