Genetic bases of mitochondrial respiratory chain disorders

Mitochondrial DNA: Inherent Complexities Relevant to Genetic Analyses

Mitochondrial DNA (mtDNA) exhibits distinct characteristics distinguishing it from the nuclear genome, necessitating specific analytical methods in genetic studies. This comprehensive review explores the complex role of mtDNA in a variety of genetic studies, including genome-wide, epigenome-wide, and phenome-wide association studies, with a focus on its implications for human traits and diseases. Here, we discuss the structure and gene-encoding properties of mtDNA, along with the influence of environmental factors and epigenetic modifications on its function and variability. Particularly significant are the challenges posed by mtDNA's high mutation rate, heteroplasmy, and copy number variations, and their impact on disease susceptibility and population genetic analyses. The review also highlights recent advances in methodological approaches that enhance our understanding of mtDNA associations, advocating for refined genetic research techniques that accommodate its complexities. By providing a comprehensive overview of the intricacies of mtDNA, this paper underscores the need for an integrated approach to genetic studies that considers the unique properties of mitochondrial genetics. Our findings aim to inform future research and encourage the development of innovative methodologies to better interpret the broad implications of mtDNA in human health and disease.

Arginine Supplementation in MELAS Syndrome: What Do We Know about the Mechanisms?

MELAS syndrome, characterized by mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes, represents a devastating mitochondrial disease, with the stroke-like episodes being its primary manifestation. Arginine supplementation has been used and recommended as a treatment for these acute attacks; however, insufficient evidence exists to support this treatment for MELAS. The mechanisms underlying the effect of arginine on MELAS pathophysiology remain unclear, although it is hypothesized that arginine could increase nitric oxide availability and, consequently, enhance blood supply to the brain. A more comprehensive understanding of these mechanisms is necessary to improve treatment strategies, such as dose and regimen adjustments; identify which patients could benefit the most; and establish potential markers for follow-up. This review aims to analyze the existing evidence concerning the mechanisms through which arginine supplementation impacts MELAS pathophysiology and provide the current scenario and perspectives for future investigations.

Compositional features and pattern of codon usage for mitochondrial CO genes among reptiles

The phenomenon of non-random occurrence of synonymous nucleotide triplets (codons) in the coding sequences of genes is the codon usage bias (CUB). In this study, we used bioinformatic tool kit to analyze the compositional pattern and CUB of mitogenes namely COI, COII and COIII across different orders of reptiles. Estimation of overall base composition in the protein-coding sequences of COI, COII and COIII genes of the reptilian orders revealed an uneven usage of nucleotides. The overall count of A nucleotide was found to be the highest while the overall count of G nucleotide was the least. The CO genes across the three reptilian orders were prominently AT biased. Comparison of the GC proportion at each codon position displayed that GC1 percentage ranked the highest in all the three CO genes of the reptilian orders. SCUO values indicated weaker CUB, while considerable variation of SCUO values existed in the three CO genes across the studied reptiles. Relative synonymous codon usage (RSCU) values indicated that mostly the A ending codons were preferred. Based on the parameters namely neutrality plot, mutational responsive index and translational selection, we could conclude that natural selection was the major evolutionary force in COI, COII and COIII genes in the studied reptilian orders. However, correspondence analysis, parity plot and correlation studies indicated the existence of mutation pressure as well on the CO genes.

Study of respiratory chain dysfunction in heart disease

The relentlessly beating heart has the greatest oxygen consumption of any organ in the body at rest reflecting its huge metabolic turnover and energetic demands. The vast majority of its energy is produced and cycled in form of ATP which stems mainly from oxidative phosphorylation occurring at the respiratory chain in the mitochondria. A part from energy production, the respiratory chain is also the main source of reactive oxygen species and plays a pivotal role in the regulation of oxidative stress. Dysfunction of the respiratory chain is therefore found in most common heart conditions. The pathophysiology of mitochondrial respiratory chain dysfunction in hereditary cardiac mitochondrial disease, the aging heart, in LV hypertrophy and heart failure, and in ischaemia-reperfusion injury is reviewed. We introduce the practicing clinician to the complex physiology of the respiratory chain, highlight its impact on common cardiac disorders and review translational pharmacological and non-pharmacological treatment strategies.

Myopathology of Adult and Paediatric Mitochondrial Diseases

Mitochondria are dynamic organelles ubiquitously present in nucleated eukaryotic cells, subserving multiple metabolic functions, including cellular ATP generation by oxidative phosphorylation (OXPHOS). The OXPHOS machinery comprises five transmembrane respiratory chain enzyme complexes (RC). Defective OXPHOS gives rise to mitochondrial diseases (mtD). The incredible phenotypic and genetic diversity of mtD can be attributed at least in part to the RC dual genetic control (nuclear DNA (nDNA) and mitochondrial DNA (mtDNA)) and the complex interaction between the two genomes. Despite the increasing use of next-generation-sequencing (NGS) and various omics platforms in unravelling novel mtD genes and pathomechanisms, current clinical practice for investigating mtD essentially involves a multipronged approach including clinical assessment, metabolic screening, imaging, pathological, biochemical and functional testing to guide molecular genetic analysis. This review addresses the broad muscle pathology landscape including genotype–phenotype correlations in adult and paediatric mtD, the role of immunodiagnostics in understanding some of the pathomechanisms underpinning the canonical features of mtD, and recent diagnostic advances in the field.

Mitochondrial disease in adults: what's old and what's new?

Ten years ago, there was an emerging view that the molecular basis for adult mitochondrial disorders was largely known and that the clinical phenotypes had been well described. Nothing could have been further from the truth. The establishment of large cohorts of patients has revealed new aspects of the clinical presentation that were not previously appreciated. Over time, this approach is starting to provide an accurate understanding of the natural history of mitochondrial disease in adults. Advances in molecular diagnostics, underpinned by next generation sequencing technology, have identified novel molecular mechanisms. Recently described mitochondrial disease phenotypes have disparate causes, and yet share common mechanistic themes. In particular, disorders of mtDNA maintenance have emerged as a major cause of mitochondrial disease in adults. Progressive mtDNA depletion and the accumulation of mtDNA mutations explain some of the clinical features, but the genetic and cellular processes responsible for the mtDNA abnormalities are not entirely clear in each instance. Unfortunately, apart from a few specific examples, treatments for adult mitochondrial disease have not been forthcoming. However, the establishment of international consortia, and the first multinational randomised controlled trial, have paved the way for major progress in the near future, underpinned by growing interest from the pharmaceutical industry. Adult mitochondrial medicine is, therefore, in its infancy, and the challenge is to harness the new understanding of its molecular and cellular basis to develop treatments of real benefit to patients.

Integrated analysis of the involvement of nitric oxide synthesis in mitochondrial proliferation, mitochondrial deficiency and apoptosis in skeletal muscle fibres

Nitric oxide (NO) is an important signaling messenger involved in different mitochondrial processes but only few studies explored the participation of NO in mitochondrial abnormalities found in patients with genetic mitochondrial deficiencies. In this study we verified whether NO synthase (NOS) activity was altered in different types of mitochondrial abnormalities and whether changes in mitochondrial function and NOS activity could be associated with the induction of apoptosis. We performed a quantitative and integrated analysis of NOS activity in individual muscle fibres of patients with mitochondrial diseases, considering mitochondrial function (cytochrome-c-oxidase activity), mitochondrial content, mitochondrial DNA mutation and presence of apoptotic nuclei. Our results indicated that sarcolemmal NOS activity was increased in muscle fibres with mitochondrial proliferation, supporting the relevance of neuronal NOS in the mitochondrial biogenesis process. Sarcoplasmic NOS activity was reduced in cytochrome-c-oxidase deficient fibres, probably as a consequence of the involvement of NO in the regulation of the respiratory chain. Alterations in NOS activity or mitochondrial abnormalities were not predisposing factors to apoptotic nuclei. Taken together, our results show that NO can be considered a potential molecular target for strategies to increase mitochondrial content and indicate that this approach may not be associated with increased apoptotic events.

Neurodegenerative disease-associated mutants of a human mitochondrial aminoacyl-tRNA synthetase present individual molecular signatures

Mutations in human mitochondrial aminoacyl-tRNA synthetases are associated with a variety of neurodegenerative disorders. The effects of these mutations on the structure and function of the enzymes remain to be established. Here, we investigate six mutants of the aspartyl-tRNA synthetase correlated with leukoencephalopathies. Our integrated strategy, combining an ensemble of biochemical and biophysical approaches, reveals that mutants are diversely affected with respect to their solubility in cellular extracts and stability in solution, but not in architecture. Mutations with mild effects on solubility occur in patients as allelic combinations whereas those with strong effects on solubility or on aminoacylation are necessarily associated with a partially functional allele. The fact that all mutations show individual molecular and cellular signatures and affect amino acids only conserved in mammals, points towards an alternative function besides aminoacylation.

Caenorhabditis elegans expressing the Saccharomyces cerevisiae NADH alternative dehydrogenase Ndi1p, as a tool to identify new genes involved in complex I related diseases

Isolated complex I deficiencies are one of the most commonly observed biochemical features in patients suffering from mitochondrial disorders. In the majority of these clinical cases the molecular bases of the diseases remain unknown suggesting the involvement of unidentified factors that are critical for complex I function. The Saccharomyces cerevisiae NDI1 gene, encoding the mitochondrial internal NADH dehydrogenase was previously shown to complement a complex I deficient strain in Caenorhabditis elegans with notable improvements in reproduction and whole organism respiration. These features indicate that Ndi1p can functionally integrate the respiratory chain, allowing complex I deficiency complementation. Taking into account the Ndi1p ability to bypass complex I, we evaluate the possibility to extend the range of defects/mutations causing complex I deficiencies that can be alleviated by NDI1 expression. We report here that NDI1 expressing animals unexpectedly exhibit a slightly shortened lifespan, a reduction in the progeny, and a depletion of the mitochondrial genome. However, Ndi1p is expressed and targeted to the mitochondria as a functional protein that confers rotenone resistance to those animals without affecting their respiration rate and ATP content. We show that the severe embryonic lethality level caused by the RNAi knockdowns of complex I structural subunit encoding genes (e.g., NDUFV1, NDUFS1, NDUFS6, NDUFS8, or GRIM-19 human orthologs) in wild type animals is significantly reduced in the Ndi1p expressing worm. All together these results open up the perspective to identify new genes involved in complex I function, assembly, or regulation by screening an RNAi library of genes leading to embryonic lethality that should be rescued by NDI1 expression.

Use of whole-exome sequencing to determine the genetic basis of multiple mitochondrial respiratory chain complex deficiencies

IMPORTANCE

Mitochondrial disorders have emerged as a common cause of inherited disease, but their diagnosis remains challenging. Multiple respiratory chain complex defects are particularly difficult to diagnose at the molecular level because of the massive number of nuclear genes potentially involved in intramitochondrial protein synthesis, with many not yet linked to human disease.

OBJECTIVE

To determine the molecular basis of multiple respiratory chain complex deficiencies.

DESIGN, SETTING, AND PARTICIPANTS

We studied 53 patients referred to 2 national centers in the United Kingdom and Germany between 2005 and 2012. All had biochemical evidence of multiple respiratory chain complex defects but no primary pathogenic mitochondrial DNA mutation. Whole-exome sequencing was performed using 62-Mb exome enrichment, followed by variant prioritization using bioinformatic prediction tools, variant validation by Sanger sequencing, and segregation of the variant with the disease phenotype in the family.

RESULTS

Presumptive causal variants were identified in 28 patients (53%; 95% CI, 39%-67%) and possible causal variants were identified in 4 (8%; 95% CI, 2%-18%). Together these accounted for 32 patients (60% 95% CI, 46%-74%) and involved 18 different genes. These included recurrent mutations in RMND1, AARS2, and MTO1, each on a haplotype background consistent with a shared founder allele, and potential novel mutations in 4 possible mitochondrial disease genes (VARS2, GARS, FLAD1, and PTCD1). Distinguishing clinical features included deafness and renal involvement associated with RMND1 and cardiomyopathy with AARS2 and MTO1. However, atypical clinical features were present in some patients, including normal liver function and Leigh syndrome (subacute necrotizing encephalomyelopathy) seen in association with TRMU mutations and no cardiomyopathy with founder SCO2 mutations. It was not possible to confidently identify the underlying genetic basis in 21 patients (40%; 95% CI, 26%-54%).

CONCLUSIONS AND RELEVANCE

Exome sequencing enhances the ability to identify potential nuclear gene mutations in patients with biochemically defined defects affecting multiple mitochondrial respiratory chain complexes. Additional study is required in independent patient populations to determine the utility of this approach in comparison with traditional diagnostic methods.

The breathing heart - mitochondrial respiratory chain dysfunction in cardiac disease

The relentlessly beating heart has the greatest oxygen consumption of any organ in the body at rest reflecting its huge metabolic turnover and energetic demands. The vast majority of its energy is produced and cycled in form of ATP which stems mainly from oxidative phosphorylation occurring at the respiratory chain in the mitochondria. Apart from energy production, the respiratory chain is also the main source of reactive oxygen species and plays a pivotal role in the regulation of oxidative stress. Dysfunction of the respiratory chain is therefore found in most common heart conditions. The pathophysiology of mitochondrial respiratory chain dysfunction in hereditary cardiac mitochondrial disease, the ageing heart, in LV hypertrophy and heart failure, and in ischaemia-reperfusion injury is reviewed. We introduce the practising clinician to the complex physiology of the respiratory chain, highlight its impact on common cardiac disorders and review translational pharmacological and non-pharmacological treatment strategies.

Phenotypic variability and identification of novel YARS2 mutations in YARS2 mitochondrial myopathy, lactic acidosis and sideroblastic anaemia

Background

Mutations in the mitochondrial tyrosyl-tRNA synthetase (YARS2) gene have previously been identified as a cause of the tissue specific mitochondrial respiratory chain (RC) disorder, Myopathy, Lactic Acidosis, Sideroblastic Anaemia (MLASA). In this study, a cohort of patients with a mitochondrial RC disorder for who anaemia was a feature, were screened for mutations in YARS2.

Methods

Twelve patients were screened for YARS2 mutations by Sanger sequencing. Clinical data were compared. Functional assays were performed to confirm the pathogenicity of the novel mutations and to investigate tissue specific effects.

Results

PathogenicYARS2 mutations were identified in three of twelve patients screened. Two patients were found to be homozygous for the previously reported p.Phe52Leu mutation, one severely and one mildly affected. These patients had different mtDNA haplogroups which may contribute to the observed phenotypic variability. A mildly affected patient was a compound heterozygote for two novel YARS2 mutations, p.Gly191Asp and p.Arg360X. The p.Gly191Asp mutation resulted in a 38-fold loss in YARS2 catalytic efficiency and the p.Arg360X mutation did not produce a stable protein. The p.Phe52Leu and p.Gly191Asp/p.Arg360X mutations resulted in more severe RC deficiency of complexes I, III and IV in muscle cells compared to fibroblasts, but had relatively normal YARS2 protein levels. The muscle-specific RC deficiency can be related to the increased requirement for RC complexes in muscle. There was also a failure of mtDNA proliferation upon myogenesis in patient cells which may compound the RC defect. Patient muscle had increased levels of PGC1-α and TFAM suggesting mitochondrial biogenesis was activated as a potential compensatory mechanism.

Conclusion

In this study we have identified novel YARS2 mutations and noted marked phenotypic variability among YARS2 MLASA patients, with phenotypes ranging from mild to lethal, and we suggest that the background mtDNA haplotype may be contributing to the phenotypic variability. These findings have implications for diagnosis and prognostication of the MLASA and related phenotypes.

Mitochondrial respiratory chain disease discrimination by retrospective cohort analysis of blood metabolites

Diagnosing primary mitochondrial respiratory chain (RC) dysfunction has long relied on invasive tissue biopsies, since no blood-based biomarker has been shown to have sufficiently high sensitivity and specificity across the myriad of individual clinical presentations. We sought to determine whether cohort-level evaluation of commonly obtained blood analytes might reveal consistent patterns to discriminate a heterogenous group of primary mitochondrial RC disease subjects both from control individuals and from subjects with pyruvate dehydrogenase deficiency.

METHODS

Following IRB approval, 62 biochemical analyte concentrations or ratios were retrospectively analyzed in three well-defined and intentionally heterogeneous subject cohorts reflective of clinical practice: [1] Primary mitochondrial disease (n=19); [2] pyruvate dehydrogenase deficiency (n=4); and [3] controls (n=27). Blood analyte categories included comprehensive chemistry profile, creatine kinase, lipoprotein profile, lactate, pyruvate, and plasma amino acid profile. Non-parametric analyses were used to compare the median of each analyte level between cohorts.

RESULTS

Disease cohorts differed significantly in their median levels of triglycerides, lactate, pyruvate, and multiple individual plasma amino acids. Primary mitochondrial disease was significantly discriminated at the cohort level from pyruvate dehydrogenase deficiency by greater pyruvate and alanine elevation in pyruvate dehydrogenase deficiency, as well as significantly increased branched chain amino acid (BCAA) levels and increased ratios of individual BCAAs to glutamate in mitochondrial disease. In addition, significant elevation of median blood triglyceride level was seen in the primary mitochondrial disease cohort.

CONCLUSIONS

Blood metabolite profile analysis can discriminate a heterogeneous cohort of primary mitochondrial disease both from controls and from pyruvate dehydrogenase deficiency. Elevated BCAA levels, either absolutely or when considered relative to the level of glutamate, are common metabolic sequelae of primary mitochondrial RC disease. Prospective study is needed to validate observed plasma metabolite alterations as a potential biomarker of disease both in larger cohorts and at the individual subject level.

Clinical and biochemical features associated with BCS1L mutation

Our study describes a novel phenotype in a series of nine Saudi patients with lactic acidosis, from four consanguineous families three of which are related. Detailed genetic studies including linkage, homozygosity mapping and targeted sequencing identified a causative mutation in the BCS1L gene. All affected members of the families have an identical mutation in this gene, mutations of which are recognized causes of Björnstad syndrome, GRACILE syndrome and a syndrome of neonatal tubulopathy, encephalopathy, and liver failure (MIM 606104) leading to isolated mitochondrial respiratory chain complex III deficiency. Here we report the appearance of a novel behavioral (five patients) and psychiatric (two patients) phenotype associated with a p.Gly129Arg BCS1L mutation, differing from the phenotype in a previously reported singleton patient with this mutation. The psychiatric symptoms emanated after childhood, initially as hypomania later evolving into intermittent psychosis. Neuroradiological findings included subtle white matter abnormalities, whilst muscle histopathology and respiratory chain studies confirmed respiratory chain dysfunction. The variable neuro-psychiatric manifestations and cortical visual dysfunction are most unusual and not reported associated with other BCS1L mutations. This report emphasizes the clinical heterogeneity associated with the mutation in BCS1L gene, even within the same family and we recommend that defects in this gene should be considered in the differential diagnosis of lactic acidosis with variable involvement of different organs.

Characterization of chemically modified oligonucleotides targeting a pathogenic mutation in human mitochondrial DNA

Defects in mitochondrial genome can cause a wide range of clinical disorders, mainly neuromuscular diseases. Most of the deleterious mitochondrial mutations are heteroplasmic, meaning that wild type and mutated forms of mtDNA coexist in the same cell. Therefore, a shift in the proportion between mutant and wild type molecules could restore mitochondrial functions. The anti-replicative strategy aims to induce such a shift in heteroplasmy by mitochondrial targeting specifically designed molecules in order to inhibit replication of mutant mtDNA. Recently, we developed mitochondrial RNA vectors that can be used to address anti-replicative oligoribonucleotides into human mitochondria and impact heteroplasmy level, however, the effect was mainly transient, probably due to a rapid degradation of RNA molecules. In the present study, we introduced various chemically modified oligonucleotides in anti-replicative RNAs. We show that the most important increase of anti-replicative molecules' lifetime can be achieved by using synthetic RNA-DNA chimerical molecules or by ribose 2'-O-methylation in nuclease-sensitive sites. The presence of inverted thymidine at 3' terminus and modifications of 2'-OH ribose group did not prevent the mitochondrial uptake of the recombinant molecules. All the modified oligonucleotides were able to anneal specifically with the mutant mtDNA fragment, but not with the wild-type one. Nevertheless, the modified oligonucleotides did not cause a significant effect on the heteroplasmy level in transfected transmitochondrial cybrid cells bearing a pathogenic mtDNA deletion, proving to be less efficient than non-modified RNA molecules.

Persistent hyperlactacidaemia: about a clinical case

Lactate is the endogenous end product of the anaerobic glycolysis, whose production is favoured in situations of hypoperfusion or mitochondrial dysfunction. Leigh syndrome is a rare, progressive encephalomyopathy that represents a spectrum of mitochondrial genetic diseases phenotypically distinct, but with neuroradiological and pathological uniform presentation. We present the case of a 7-month-old infant, with a history of prematurity, psychomotor retardation and epilepsy, admitted to the paediatric intensive care unit (PICU) due to cardio-respiratory arrest because of respiratory infection. Hyperlactacidaemia was detected and was persistent. The study of redox potential was normal but MRI with spectroscopy identified bilateral and symmetrical lesions involving thalamic and basal ganglia, with small lactate peaks at T2 flair, findings that were suggestive of Leigh syndrome. Subsequent enzymatic study identified lack of pyruvate dehydrogenase. Persistent hyperlactacidaemia, in the appropriate clinical context, should lead to the screening of mitochondrial diseases.

Complex II deficiency--a case report and review of the literature

Complex II deficiency is a rare cause of mitochondrial respiratory chain defects with a prevalence of 2-23%. It is exclusively nuclear encoded and functions in the citric acid cycle by oxidizing succinate to fumarate and in the mitochondrial electron transport chain (ETC) by transferring electrons to ubiquinone. Of the four subunits, SDHA and SDHB are catalytic and SDHC and SDHD are anchoring. Mutations in SDHA and SDHAF1 (assembly factor) have been found in patients with CII deficiency and a mitochondrial phenotype. We present a patient with CII deficiency with a previously undescribed phenotype of dilated cardiomyopathy, left ventricular noncompaction, failure to thrive, hypotonia, and developmental delay. Also, a comprehensive review of 36 cases published in the literature was undertaken. The results show that CII deficiency has a variable phenotype with no correlation with residual complex activity in muscle although the phenotype and enzyme activities are comparable within a family. For some, the condition was fatal in infancy, others had multisystem involvement and some had onset in adulthood with mild symptoms and normal cognition. Neurological involvement is most commonly observed and brain imaging commonly shows leukoencephalopathy, Leigh syndrome, or cerebellar atrophy. Mutations in SDHAF1 are associated with leukoencephalopathy. Other organ systems like heart, muscle, and eyes are only involved in about 50% of the cases but cardiomyopathy is associated with high mortality and morbidity. In some patients, riboflavin has provided clinical improvement.

Screening of mitochondrial mutations in Tunisian patients with mitochondrial disorders: an overview study

To investigate the spectrum of common mitochondrial mutations in Tunisia during the years of 2002-2012, 226 patients with mitochondrial disorders were clinically diagnosed with hearing loss, Leigh syndrome (LS), diabetes, cardiomyopathy, Kearns-Sayre syndrome (KSS), Pearson syndrome (PS), myopathy, mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes syndrome (MELAS) and Wolfram syndrome. Restriction fragment length polymorphism (PCR-RFLP), radioactive PCR, single specific primer-PCR (SSP-PCR) analysis and PCR-sequencing methods were used to identify the mutations. Two cases with m.1555A>G mutation and two families with the novel 12S rRNA m.735A>G transition were detected in patients with hearing loss. Three cases with m.8993T>G mutation, two patients with the novel m.5523T>G and m.5559A>G mutations in the tRNA(Trp) gene, and two individuals with the undescribed m.9478T>C mutation in the cytochrome c oxidase subunit III (COXIII) gene were found with LS. In addition, one case with hypertrophic cardiomyopathy and deafness presented the ND1 m.3395A>G mutation and the tRNA(Ile) m.4316A>G variation. Besides, multiple mitochondrial deletions were detected in patients with KSS, PS, and Wolfram syndrome. The m.14709T>C mutation in the tRNA(Glu) was reported in four maternally inherited diabetes and deafness patients and a novel tRNA(Val) m.1640A>G mutation was detected in a MELAS patient.

Mutation in PNPT1, which encodes a polyribonucleotide nucleotidyltransferase, impairs RNA import into mitochondria and causes respiratory-chain deficiency

Multiple-respiratory-chain deficiency represents an important cause of mitochondrial disorders. Hitherto, however, mutations in genes involved in mtDNA maintenance and translation machinery only account for a fraction of cases. Exome sequencing in two siblings, born to consanguineous parents, with severe encephalomyopathy, choreoathetotic movements, and combined respiratory-chain defects allowed us to identify a homozygous PNPT1 missense mutation (c.1160A>G) that encodes the mitochondrial polynucleotide phosphorylase (PNPase). Blue-native polyacrylamide gel electrophoresis showed that no PNPase complex could be detected in subject fibroblasts, confirming that the substitution encoded by c.1160A>G disrupts the trimerization of the protein. PNPase is predominantly localized in the mitochondrial intermembrane space and is implicated in RNA targeting to human mitochondria. Mammalian mitochondria import several small noncoding nuclear RNAs (5S rRNA, MRP RNA, some tRNAs, and miRNAs). By RNA hybridization experiments, we observed a significant decrease in 5S rRNA and MRP-related RNA import into mitochondria in fibroblasts of affected subject 1. Moreover, we found a reproducible decrease in the rate of mitochondrial translation in her fibroblasts. Finally, overexpression of the wild-type PNPT1 cDNA in fibroblasts of subject 1 induced an increase in 5S rRNA import in mitochondria and rescued the mitochondrial-translation deficiency. In conclusion, we report here abnormal RNA import into mitochondria as a cause of respiratory-chain deficiency.

Biochemical analyses of the electron transport chain complexes by spectrophotometry

In the diagnostic work-up of patients with suspected mitochondrial disease, evaluating the activity of the individual oxidative phosphorylation (OXPHOS) complexes is crucial. Here, we describe spectrophotometric assays for OXPHOS enzymology that can be applied to both tissue samples and cultured cells. These assays are designed to assess the enzymatic activity of the individual OXPHOS complexes I-V, along with the Krebs cycle enzyme citrate synthase as a mitochondrial control. As well, we include an assay for the coupled energy transfer between complexes II and III. Determining the enzymatic activities can be valuable in defining isolated or multicomplex disorders and may be relevant to the design of future molecular investigations.

Nuclear gene defects in mitochondrial disorders

Most mitochondrial cytopathies in infants are caused by mutations in nuclear genes encoding proteins targeted to the mitochondria rather than by primary mutations in the mitochondrial DNA. Over the past few years, the awareness of the number of disease-causing mutations in different nuclear genes has grown exponentially. These genes encode the various subunits of each respiratory chain complex, the ancillary proteins involved in the assembly of these subunits, proteins involved in mitochondrial DNA replication and maintenance, proteins involved in mitochondrial protein synthesis, and proteins involved in mitochondrial dynamics. This increased awareness has added a challenging dimension to the current diagnostic workup of mitochondrial cytopathies. The advent of new technologies such as next-generation sequencing should facilitate the resolution of this dilemma.

Protein localization as a principal feature of the etiology and comorbidity of genetic diseases

Proteins localized within the same subcellular compartment tend to be functionally associated. This study shows that subcellular localization and network distance between disease-associated proteins provide complementary information explaining patterns of disease comorbidity.

A positive correlation was found between subcellular localization of disease-associated protein pairs and measures of comorbidity.

A higher comorbidity tendency was found for disease-associated protein pairs that are positioned within a shorter distance in the protein interaction network.

The integration of subcellular localization information with protein interaction network sheds light onto the potential molecular connections underlying comorbidity patterns and will help to understand the mechanisms of human disease.

It was shown that the emergence of phenotypically similar diseases are triggered as a result of molecular connections between disease-causing genes (Oti and Brunner, 2007; Zaghloul and Katsanis, 2010). From a genetics, perspective diseases are associated with certain genes (Goh et al, 2007; Feldman et al, 2008), whereas from a proteomics perspective phenotypically similar diseases are connected via biological modules such as protein–protein interactions (PPIs) or molecular pathways (Lage et al, 2007; Jiang et al, 2008; Wu et al, 2008; Linghu et al, 2009; Suthram et al, 2010). These molecular connections between diseases were observed on the population level as well: diseases connected through molecular connections such as shared genes, PPIs, and metabolic pathways tend to show elevated comorbidity (Rzhetsky et al, 2007; Lee et al, 2008; Zhernakova et al, 2009; Park et al, 2009a, 2009b). While these findings constitute a step toward improving our understanding of the mechanism of disease progression, there are still many more molecule-level connections between disease pairs that need to be explored in order to establish a firmer comorbidity association.

Subcellular localization provides spatial information of proteins in the cell; proteins target subcellular localizations to interact with appropriate partners and form functional complexes in signaling pathways and metabolic processes (Au et al, 2007). Abnormal protein localizations are known to lead to the loss of functional effects in diseases (Luheshi et al, 2008; Laurila and Vihinen, 2009). For example, mis-localizations of nuclear/cytoplasmic transport have been detected in many types of carcinoma cells (Kau et al, 2004). A proper identification of protein subcellular localization can hence be useful in discovering disease-associated proteins (Giallourakis et al, 2005; Calvo and Mootha, 2010). With this understanding, we postulate that disease-associated proteins connected by subcellular localizations could also explain the phenotypic similarities between diseases. Furthermore, such connections may also couple to disease progressions that contribute to multiple disease manifestation, that is, comorbidity.

Protein subcellular localization has been extensively studied through various methods to determine a variety of protein functions. To the best of our knowledge, the connection between diseases and subcellular localizations are yet to be studied systematically. To resolve this we constructed, for the first time, a human Disease-associated Protein and subcellular Localization (DPL) matrix (top panel in Box 1). Our DPL matrix provides the ‘cellular localization map of diseases' that represents the spatial index of diseases in the cell. We found that each disease shows unique characteristics of subcellular localization profile in the DPL matrix. We were interested in determining whether subsets of 1284 human diseases exhibit distinct enrichment profiles across subcellular localizations. We calculated pairwise correlations and performed a hierarchical clustering of the enrichments of the 1284 diseases across 10 different subcellular localizations.

Our DPL matrix revealed that 778 diseases (∼62%, P=1.40 × 10⁻³) are enriched in a single localization and 273 diseases (∼21%, P=3.45 × 10⁻³) are enriched in dual localizations. In the DPL matrix, certain disease-associated proteins are likely to be found in membrane-bounded organelles such as mitochondria, lysosome, and peroxisome, indicating that the mutations of proteins localized to these compartments are connected to the pathophysiological conditions of those organelles. Meanwhile, certain disease-associated proteins in the DPL matrix are enriched in dual localizations, such as extracellular/plasma membrane or endoplasmic reticulum/Golgi. Although these two pairs of subcellular localizations appear to be distinct compartments at first, they are functionally related compartments in close proximity during protein translocation process in the cell, and thus are likely to share interacting protein partners (Gandhi et al, 2006).

Comorbidity represents the co-occurrence of multiple diseases in the same individual (Lee et al, 2008; Hidalgo et al, 2009; Park et al, 2009a). Many comorbid disease pairs have been shown to share common genes in the human disease network. For example, Diabetes and Alzheimer's disease share a risk factor in angiotensin I converting enzyme, and frequently occur together in an individual. In such instances, comorbidity can be partially attributed to the disease connections on the molecular level. To explore the impact of protein subcellular localization on comorbidity, we hypothesized that certain disease pairs could also be connected via subcellular localization by the molecular connections between the disease-associated proteins (bottom panel in Box 1).

We found a positive correlation between subcellular localization similarity and relative risk (Figure 3B, Pearson's correlation coefficient between relative risk and subcellular localization similarity=0.81, P=2.96 × 10⁻⁵). The subcellular localization similarity represents the correlation of subcellular localization profiles between disease pairs. To our surprise, when we compared the relative risk of disease pairs linked via various molecular connections, we found that disease pairs connected by subcellular localization showed a near three-fold higher comorbidity tendency (with link distances equal to 2 or 3) when compared with random pairs (Figure 3E).

We then assessed quantitatively the impact of network distances and subcellular localizations on the comorbidity tendency of disease pairs. We expected the proteins associated with comorbid disease pairs to be located closely in the protein interaction network via fewer links compared with random disease pairs. Indeed, a higher comorbidity tendency was found when two disease-associated proteins were positioned within a shorter distance (gray plots in Figure 3F). Moreover, when subcellular localization information was combined with small network distances, the comorbidity tendency increased dramatically (orange plots in Figure 3F). It suggests that subcellular localization and close network distances, two conceptually distinct molecular connections, contributed synergistically to the comorbidity tendency.

Disease progression is not restricted to the mutation of disease-causing genes, but also affected by molecular connections in ‘disease modules,' resulting in comorbidity (Fraser, 2006; Lee et al, 2008). In this study, for the first time we applied subcellular localization information to elucidate the molecular connections between comorbid diseases. We believe that, based on our finding, our approach helps to define the boundaries of ‘disease modules.' Taken together, integration of diverse molecular connections should improve the molecular level understanding of hitherto unexplained comorbid disease pairs and help us in expanding the scope of our knowledge of the mechanism of human disease progression.

Proteins targeting the same subcellular localization tend to participate in mutual protein–protein interactions (PPIs) and are often functionally associated. Here, we investigated the relationship between disease-associated proteins and their subcellular localizations, based on the assumption that protein pairs associated with phenotypically similar diseases are more likely to be connected via subcellular localization. The spatial constraints from subcellular localization significantly strengthened the disease associations of the proteins connected by subcellular localizations. In particular, certain disease types were more prevalent in specific subcellular localizations. We analyzed the enrichment of disease phenotypes within subcellular localizations, and found that there exists a significant correlation between disease classes and subcellular localizations. Furthermore, we found that two diseases displayed high comorbidity when disease-associated proteins were connected via subcellular localization. We newly explained 7584 disease pairs by using the context of protein subcellular localization, which had not been identified using shared genes or PPIs only. Our result establishes a direct correlation between protein subcellular localization and disease association, and helps to understand the mechanism of human disease progression.

The use of individual patient's fibroblasts in the search for personalized treatment of nuclear encoded OXPHOS diseases

Mitochondrial diseases, are a prevalent but diverse group of inherited disorders affecting the oxidative phosphorylation (OXPHOS) system. Vast amount of information with respect to pathomechanism and the assembly of the various OXPHOS complexes has been accumulated by studying the different variants of these diseases. Conversely, the investigation of therapeutic strategies has been hampered by this extreme variability. Individual patient's fibroblast may therefore provide a suitable platform in the search for personalized treatments, of nuclear encoded defects, when the phenotype is expressed in multiple tissues. Examples and different approaches in the search for treatment options, while using fibroblasts from patients with nuclear encoded OXPHOS defects as model systems, are summarized and discussed.

Transduction of human recombinant proteins into mitochondria as a protein therapeutic approach for mitochondrial disorders

Protein therapy is considered an alternative approach to gene therapy for treatment of genetic-metabolic disorders. Human protein therapeutics (PTs), developed via recombinant DNA technology and used for the treatment of these illnesses, act upon membrane-bound receptors to achieve their pharmacological response. On the contrary, proteins that normally act inside the cells cannot be developed as PTs in the conventional way, since they are not able to "cross" the plasma membrane. Furthermore, in mitochondrial disorders, attributed either to depleted or malfunctioned mitochondrial proteins, PTs should also have to reach the subcellular mitochondria to exert their therapeutic potential. Nowadays, there is no effective therapy for mitochondrial disorders. The development of PTs, however, via the Protein Transduction Domain (PTD) technology offered new opportunities for the deliberate delivery of human recombinant proteins inside eukaryotic subcellular organelles. To this end, mitochondrial disorders could be clinically encountered with the delivery of human mitochondrial proteins (engineered via recombinant DNA and PTD technologies) at specific intramitochondrial sites to exert their function. Overall, PTD-mediated Protein Replacement Therapy emerges as a suitable model system for the therapeutic approach for mitochondrial disorders.