Mapping gene associations in human mitochondria using clinical disease phenotypes

Nuclear genes encode most mitochondrial proteins, and their mutations cause diverse and debilitating clinical disorders. To date, 1,200 of these mitochondrial genes have been recorded, while no standardized catalog exists of the associated clinical phenotypes. Such a catalog would be useful to develop methods to analyze human phenotypic data, to determine genotype-phenotype relations among many genes and diseases, and to support the clinical diagnosis of mitochondrial disorders. Here we establish a clinical phenotype catalog of 174 mitochondrial disease genes and study associations of diseases and genes. Phenotypic features such as clinical signs and symptoms were manually annotated from full-text medical articles and classified based on the hierarchical MeSH ontology. This classification of phenotypic features of each gene allowed for the comparison of diseases between different genes. In turn, we were then able to measure the phenotypic associations of disease genes for which we calculated a quantitative value that is based on their shared phenotypic features. The results showed that genes sharing more similar phenotypes have a stronger tendency for functional interactions, proving the usefulness of phenotype similarity values in disease gene network analysis. We then constructed a functional network of mitochondrial genes and discovered a higher connectivity for non-disease than for disease genes, and a tendency of disease genes to interact with each other. Utilizing these differences, we propose 168 candidate genes that resemble the characteristic interaction patterns of mitochondrial disease genes. Through their network associations, the candidates are further prioritized for the study of specific disorders such as optic neuropathies and Parkinson disease. Most mitochondrial disease phenotypes involve several clinical categories including neurologic, metabolic, and gastrointestinal disorders, which might indicate the effects of gene defects within the mitochondrial system. The accompanying knowledgebase (http://www.mitophenome.org/) supports the study of clinical diseases and associated genes

How Do Human Cells React to the Absence of Mitochondrial DNA?

Mitochondrial biogenesis is under the control of two different genetic systems: the nuclear genome (nDNA) and the mitochondrial genome (mtDNA). The mtDNA is a circular genome of 16.6 kb encoding 13 of the approximately 90 subunits that form the respiratory chain, the remaining ones being encoded by the nDNA. Eukaryotic cells are able to monitor and respond to changes in mitochondrial function through alterations in nuclear gene expression, a phenomenon first defined in yeast and known as retrograde regulation. To investigate how the cellular transcriptome is modified in response to the absence of mtDNA, we used Affymetrix HG-U133A GeneChip arrays to study the gene expression profile of two human cell lines, 143BTK(-) and A549, which had been entirely depleted of mtDNA (rho(o) cells), and compared it with that of corresponding undepleted parental cells (rho(+) cells).Our data indicate that absence of mtDNA is associated with: i) a down-regulation of cell cycle control genes and a reduction of cell replication rate, ii) a down-regulation of nuclear-encoded subunits of complex III of the respiratory chain and iii) a down-regulation of a gene described as the human homolog of ELAC2 of E. coli, which encodes a protein that we show to also target to the mitochondrial compartment.Our results indicate a strong correlation between mitochondrial biogenesis and cell cycle control and suggest that some proteins could have a double role: for instance in controlling both cell cycle progression and mitochondrial functions. In addition, the finding that ELAC2 and maybe other transcripts that are located into mitochondria, are down-regulated in rho(o) cells, make them good candidates for human disorders associated with defective replication and expression of mtDNA

Mutations in SLC39A14 disrupt manganese homeostasis and cause childhood-onset parkinsonism-dystonia

Although manganese is an essential trace metal, little is known about its transport and homeostatic regulation. Here we have identified a cohort of patients with a novel autosomal recessive manganese transporter defect caused by mutations in SLC39A14. Excessive accumulation of manganese in these patients results in rapidly progressive childhood-onset parkinsonism-dystonia with distinctive brain magnetic resonance imaging appearances and neurodegenerative features on post-mortem examination. We show that mutations in SLC39A14 impair manganese transport in vitro and lead to manganese dyshomeostasis and altered locomotor activity in zebrafish with CRISPR-induced slc39a14 null mutations. Chelation with disodium calcium edetate lowers blood manganese levels in patients and can lead to striking clinical improvement. Our results demonstrate that SLC39A14 functions as a pivotal manganese transporter in vertebrates

Systematic analysis of mitochondrial genes associated with hearing loss in the Japanese population: dHPLC reveals a new candidate mutation

<p>Abstract</p> <p>Background</p> <p>Variants of mitochondrial DNA (mtDNA) have been evaluated for their association with hearing loss. Although ethnic background affects the spectrum of mtDNA variants, systematic mutational analysis of mtDNA in Japanese patients with hearing loss has not been reported.</p> <p>Methods</p> <p>Using denaturing high-performance liquid chromatography combined with direct sequencing and cloning-sequencing, Japanese patients with prelingual (N = 54) or postlingual (N = 80) sensorineural hearing loss not having pathogenic mutations of m.1555A > G and m.3243A > G nor <it>GJB2 </it>were subjected to mutational analysis of mtDNA genes (<it>12S rRNA</it>, <it>tRNA</it>^{<it>Leu(UUR)</it>}, <it>tRNA</it>^{<it>Ser(UCN)</it>}, <it>tRNA</it>^<it>Lys</it>, <it>tRNA</it>^<it>His</it>, <it>tRNA</it>^{<it>Ser(AGY)</it>}, and <it>tRNA</it>^<it>Glu</it>).</p> <p>Results</p> <p>We discovered 15 variants in <it>12S rRNA </it>and one homoplasmic m.7501A > G variant in <it>tRNA</it>^{<it>Ser(UCN)</it>}; no variants were detected in the other genes. Two criteria, namely the low frequency in the controls and the high conservation among animals, selected the m.904C > T and the m.1105T > C variants in <it>12S rRNA </it>as candidate pathogenic mutations. Alterations in the secondary structures of the two variant transcripts as well as that of m.7501A > G in <it>tRNA</it>^{<it>Ser(UCN) </it>}were predicted.</p> <p>Conclusions</p> <p>The m.904C > T variant was found to be a new candidate mutation associated with hearing loss. The m.1105T > C variant is unlikely to be pathogenic. The pathogenicity of the homoplasmic m.7501T > A variant awaits further study.</p

Proteome changes in platelets activated by arachidonic acid, collagen, and thrombin

<p>Abstract</p> <p>Background</p> <p>Platelets are small anucleated blood particles that play a key role in the control of bleeding. Platelets need to be activated to perform their functions and participate in hemostasis. The process of activation is accompanied by vast protein reorganization and posttranslational modifications. The goal of this study was to identify changes in proteins in platelets activated by different agonists. Platelets were activated by three different agonists - arachidonic acid, collagen, and thrombin. 2D SDS-PAGE (pI 4-7) was used to separate platelet proteins. Proteomes of activated and resting platelets were compared with each other by Progenesis SameSpots statistical software; and proteins were identified by nanoLC-MS/MS.</p> <p>Results</p> <p>190 spots were found to be significantly different. Of these, 180 spots were successfully identified and correspond to 144 different proteins. Five proteins were found that had not previously been identified in platelets: protein CDV3 homolog, protein ETHE1, protein LZIC, FGFR1 oncogene partner 2, and guanine nucleotide-binding protein subunit beta-5. Using spot expression profile analysis, we found two proteins (WD repeat-containing protein 1 and mitochondrial glycerol-3-phosphate dehydrogenase) that may be part of thrombin specific activation or signal transduction pathway(s).</p> <p>Conclusions</p> <p>Our results, characterizing the differences within proteins in both activated (by various agonists) and resting platelets, can thus contribute to the basic knowledge of platelets and to the understanding of the function and development of new antiplatelet drugs.</p

H2S biosynthesis and catabolism: new insights from molecular studies

Hydrogen sulfide (H2S) has profound biological effects within living organisms and is now increasingly being considered alongside other gaseous signalling molecules, such as nitric oxide (NO) and carbon monoxide (CO). Conventional use of pharmacological and molecular approaches has spawned a rapidly growing research field that has identified H2S as playing a functional role in cell-signalling and post-translational modifications. Recently, a number of laboratories have reported the use of siRNA methodologies and genetic mouse models to mimic the loss of function of genes involved in the biosynthesis and degradation of H2S within tissues. Studies utilising these systems are revealing new insights into the biology of H2S within the cardiovascular system, inflammatory disease, and in cell signalling. In light of this work, the current review will describe recent advances in H2S research made possible by the use of molecular approaches and genetic mouse models with perturbed capacities to generate or detoxify physiological levels of H2S gas within tissue

Epidemiology of intra-abdominal infection and sepsis in critically ill patients: “AbSeS”, a multinational observational cohort study and ESICM Trials Group Project

Purpose: To describe the epidemiology of intra-abdominal infection in an international cohort of ICU patients according to a new system that classifies cases according to setting of infection acquisition (community-acquired, early onset hospital-acquired, and late-onset hospital-acquired), anatomical disruption (absent or present with localized or diffuse peritonitis), and severity of disease expression (infection, sepsis, and septic shock). Methods: We performed a multicenter (n = 309), observational, epidemiological study including adult ICU patients diagnosed with intra-abdominal infection. Risk factors for mortality were assessed by logistic regression analysis. Results: The cohort included 2621 patients. Setting of infection acquisition was community-acquired in 31.6%, early onset hospital-acquired in 25%, and late-onset hospital-acquired in 43.4% of patients. Overall prevalence of antimicrobial resistance was 26.3% and difficult-to-treat resistant Gram-negative bacteria 4.3%, with great variation according to geographic region. No difference in prevalence of antimicrobial resistance was observed according to setting of infection acquisition. Overall mortality was 29.1%. Independent risk factors for mortality included late-onset hospital-acquired infection, diffuse peritonitis, sepsis, septic shock, older age, malnutrition, liver failure, congestive heart failure, antimicrobial resistance (either methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci, extended-spectrum beta-lactamase-producing Gram-negative bacteria, or carbapenem-resistant Gram-negative bacteria) and source control failure evidenced by either the need for surgical revision or persistent inflammation. Conclusion: This multinational, heterogeneous cohort of ICU patients with intra-abdominal infection revealed that setting of infection acquisition, anatomical disruption, and severity of disease expression are disease-specific phenotypic characteristics associated with outcome, irrespective of the type of infection. Antimicrobial resistance is equally common in community-acquired as in hospital-acquired infection

Dinámica de infección de Mycoplasma hyopneumoniae en granjas con diferentes esquemas de vacunación

Control of swine enzootic pneumonia (EP), a disease caused by Mycoplasma hyopneumoniae, is mainly through vaccination. Three herds with different vaccination schedules against this agent were studied in order to determine the infection dynamics. A group of 250 pigs from each herd were followed over time from weaning to slaughter, measuring daily weight gain and percentage of cough (at the end of weaning and finishing stages). Thirty pigs were sampled from each group at 9, 15 and 23 weeks of age to determine the percentage of seropositives. In addition, 30 pigs from the different groups were sacrificed at 6 and 12 weeks of age, respectively, to detect the presence of the agent by PCR in nasal swab (NS) and broncho-alveolar lavage (BAL) samples and for macroscopic and microscopic lung lesions evaluation. In each group, the lungs of the remaining animals were inspected at slaughter for the same purpose. Lung affected area and proportion of PCR positives were significantly higher (p <0.05) at slaughter. Proportion of PCR positives was significantly higher (p <0.05) in BAL vs HN samples. Different serological profiles were found on each herd. It was concluded that the dynamics of infection in each farm should be evaluated before M. hyopneumoniae vaccination.Fil: Bautista, S. Universidad Nacional de Río Cuarto. Facultad de Agronomía y Veterinaria. Departamento Patología Animal. Cátedra de Enfermedades Transmisibles y Tóxicas de los Porcinos. Córdoba, ArgentinaFil: Tiranti, K. Universidad Nacional de Río Cuarto. Facultad de Agronomía y Veterinaria. Departamento Patología Animal. Córdoba, ArgentinaFil: Ferrero, S. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas, Fisico-químicas y Naturales. Departamento de Matemática. Córdoba, ArgentinaFil: Ambrogi, A.Universidad Nacional de Río Cuarto. Facultad de Agronomía y Veterinaria. Departamento Patología Animal. Córdoba, ArgentinaFil: Tamiozzo P.J. Universidad Nacional de Río Cuarto. Facultad de Agronomía y Veterinaria. Departamento Patología Animal. Córdoba, ArgentinaFil: Tamiozzo P.J. CONICET. Córdoba, ArgentinaUna de las maneras de controlar la Neumonía enzoótica porcina (NEP), enfermedad causada por Mycoplasma hyopneumoniae, es la vacunación. Se trabajó en 3 granjas similares con distintos esquemas de vacunación contra NEP con el objetivo de analizar la dinámica de la infección. Un grupo de 250 cerdos de cada granja fueron seguidos en el tiempo desde el destete hasta el frigorífico midiendo ganancia diaria de peso y porcentaje de tos (al final de las etapas de recría y terminación). De cada grupo fueron muestreados 30 cerdos a las 9, 15 y 23 semanas de edad para determinar el porcentaje de seropositivos. Además, de esos grupos, 30 cerdos fueron sacrificados a las 6 y 12 semanas de edad, respectivamente, para determinar la presencia del agente mediante PCR en muestras de hisopado nasal (HN) y lavado bronquio-alveolar (LBA) y para la evaluación de lesiones pulmonares macroscópicas y microscópicas. De cada grupo, los pulmones de los animales remanentes fueron inspeccionados en frigorífico con el mismo fin. El área pulmonar afectada y la proporción de PCR positivos fue significativamente mayor (p<0,05) en el muestreo de frigorífico respecto a los otros muestreos. La proporción de PCR positivos fue significativamente mayor (p<0,05) en muestras de LBA vs HN. Se encontraron distintos perfiles serológicos en cada granja. Se concluyó que la dinámica de infección en cada granja debería ser evaluada antes de vacunar