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Mitochondria and Energy Metabolism in Rare Diseases

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (30 September 2022) | Viewed by 24288

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Dr. Nadège Bellance

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INSERM U1211, Rare Diseases: Genetic and Metabolism, F-33076 Bordeaux, France
Interests: mitochondria; bioenergetics; metabolic remodeling; signaling pathways
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Rare diseases are a wide class of pathologies that can affect multiples organs of patients. Genetic mutations are responsible for these diseases. Interestingly, metabolic alterations have been reported in most of these pathologies, such as spastic paraplegias, ataxias, and other neurodegenerative diseases. Furthermore, mitochondrial dysfunctions play a role in the pathophysiological mechanisms described. In a few cases, cells adopt remodeling that induces mitochondrial upregulation or even biogenesis. On the other hand, the adaptive processes are not ubiquitous. Impairments in mitophagy have also been revealed in neurodegeneration. In this Special Issue entitled “Mitochondria and Energy Metabolism in Rare Diseases”, the various alterations in mitochondrial functions are discussed and reported. The purpose of this Special Issue focused on rare diseases is to answer the chicken-or-egg question of what came first, mitochondrial upregulation or degradation.

Dr. Nadège Bellance
Guest Editor

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Keywords

mitochondria
energy metabolism
autophagy
mitophagy
neurodegeneration
metabolic pathways
signaling pathway
traffic
reactive oxygen species
rare diseases

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Published Papers (9 papers)

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Research

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24 pages, 7632 KiB

Open AccessArticle

In Vitro Skeletal Muscle Model of PGM1 Deficiency Reveals Altered Energy Homeostasis

by Federica Conte, Angel Ashikov, Rachel Mijdam, Eline G. P. van de Ven, Monique van Scherpenzeel, Raisa Veizaj, Seyed P. Mahalleh-Yousefi, Merel A. Post, Karin Huijben, Daan M. Panneman, Richard J. T. Rodenburg, Nicol C. Voermans, Alejandro Garanto, Werner J. H. Koopman, Hans J. C. T. Wessels, Marek J. Noga and Dirk J. Lefeber

Int. J. Mol. Sci. 2023, 24(9), 8247; https://doi.org/10.3390/ijms24098247 - 4 May 2023

Cited by 3 | Viewed by 2845

Abstract

Phosphoglucomutase 1 (PGM1) is a key enzyme for the regulation of energy metabolism from glycogen and glycolysis, as it catalyzes the interconversion of glucose 1-phosphate and glucose 6-phosphate. PGM1 deficiency is an autosomal recessive disorder characterized by a highly heterogenous clinical spectrum, including hypoglycemia, cleft palate, liver dysfunction, growth delay, exercise intolerance, and dilated cardiomyopathy. Abnormal protein glycosylation has been observed in this disease. Oral supplementation with D-galactose efficiently restores protein glycosylation by replenishing the lacking pool of UDP-galactose, and rescues some symptoms, such as hypoglycemia, hepatopathy, and growth delay. However, D-galactose effects on skeletal muscle and heart symptoms remain unclear. In this study, we established an in vitro muscle model for PGM1 deficiency to investigate the role of PGM1 and the effect of D-galactose on nucleotide sugars and energy metabolism. Genome-editing of C2C12 myoblasts via CRISPR/Cas9 resulted in Pgm1 (mouse homologue of human PGM1, according to updated nomenclature) knockout clones, which showed impaired maturation to myotubes. No difference was found for steady-state levels of nucleotide sugars, while dynamic flux analysis based on ¹³C6-galactose suggested a block in the use of galactose for energy production in knockout myoblasts. Subsequent analyses revealed a lower basal respiration and mitochondrial ATP production capacity in the knockout myoblasts and myotubes, which were not restored by D-galactose. In conclusion, an in vitro mouse muscle cell model has been established to study the muscle-specific metabolic mechanisms in PGM1 deficiency, which suggested that galactose was unable to restore the reduced energy production capacity. Full article

(This article belongs to the Special Issue Mitochondria and Energy Metabolism in Rare Diseases)

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13 pages, 1709 KiB

Open AccessArticle

A Novel Mutation Associated with Neonatal Lethal Cardiomyopathy Leads to an Alternative Transcript Expression in the X-Linked Complex I NDUFB11 Gene

by Guillermo Amate-García, María Juliana Ballesta-Martínez, Pablo Serrano-Lorenzo, Rocío Garrido-Moraga, Adrián González-Quintana, Alberto Blázquez, Juan C. Rubio, Inés García-Consuegra, Joaquín Arenas, Cristina Ugalde, María Morán, Encarnación Guillén-Navarro and Miguel A. Martín

Int. J. Mol. Sci. 2023, 24(2), 1743; https://doi.org/10.3390/ijms24021743 - 16 Jan 2023

Cited by 5 | Viewed by 2296

Abstract

We report a neonatal patient with hypertrophic cardiomyopathy (HCM), lactic acidosis and isolated complex I deficiency. Using a customized next-generation sequencing panel, we identified a novel hemizygous variant c.338G>A in the X-linked NDUFB11 gene that encodes the NADH: ubiquinone oxidoreductase subunit B11 of the mitochondrial respiratory chain (MRC) complex I (CI). Molecular and functional assays performed in the proband’s target tissues—skeletal and heart muscle—showed biochemical disturbances of the MRC, suggesting a pathogenic role for this variant. In silico analyses initially predicted an amino acid missense change p.(Arg113Lys) in the NDUFB11 CI subunit. However, we showed that the molecular effect of the c.338G>A variant, which is located at the last nucleotide of exon 2 of the NDUFB11 gene in the canonical ‘short’ transcript (sized 462 bp), instead causes a splicing defect triggering the up-regulation of the expression of an alternative ‘long’ transcript (sized 492 bp) that can also be detected in the control individuals. Our results support the hypothesis that the canonical ‘short’ transcript is required for the proper NDUFB11 protein synthesis, which is essential for optimal CI assembly and activity, whereas the longer alternative transcript seems to represent a non-functional, unprocessed splicing intermediate. Our results highlight the importance of characterizing the molecular effect of new variants in the affected patient’s tissues to demonstrate their pathogenicity and association with the clinical phenotypes. Full article

(This article belongs to the Special Issue Mitochondria and Energy Metabolism in Rare Diseases)

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20 pages, 5987 KiB

Open AccessArticle

HIF-1α-Dependent Metabolic Reprogramming, Oxidative Stress, and Bioenergetic Dysfunction in SARS-CoV-2-Infected Hamsters

by Sirsendu Jana, Michael R. Heaven, Charles B. Stauft, Tony T. Wang, Matthew C. Williams, Felice D’Agnillo and Abdu I. Alayash

Int. J. Mol. Sci. 2023, 24(1), 558; https://doi.org/10.3390/ijms24010558 - 29 Dec 2022

Cited by 8 | Viewed by 2920

Abstract

The mechanistic interplay between SARS-CoV-2 infection, inflammation, and oxygen homeostasis is not well defined. Here, we show that the hypoxia-inducible factor (HIF-1α) transcriptional pathway is activated, perhaps due to a lack of oxygen or an accumulation of mitochondrial reactive oxygen species (ROS) in the lungs of adult Syrian hamsters infected with SARS-CoV-2. Prominent nuclear localization of HIF-1α and increased expression of HIF-1α target proteins, including glucose transporter 1 (Glut1), lactate dehydrogenase (LDH), and pyruvate dehydrogenase kinase-1 (PDK1), were observed in areas of lung consolidation filled with infiltrating monocytes/macrophages. Upregulation of these HIF-1α target proteins was accompanied by a rise in glycolysis as measured by extracellular acidification rate (ECAR) in lung homogenates. A concomitant reduction in mitochondrial respiration was also observed as indicated by a partial loss of oxygen consumption rates (OCR) in isolated mitochondrial fractions of SARS-CoV-2-infected hamster lungs. Proteomic analysis further revealed specific deficits in the mitochondrial ATP synthase (Atp5a1) within complex V and in the ATP/ADP translocase (Slc25a4). The activation of HIF-1α in inflammatory macrophages may also drive proinflammatory cytokine production and complement activation and oxidative stress in infected lungs. Together, these findings support a role for HIF-1α as a central mediator of the metabolic reprogramming, inflammation, and bioenergetic dysfunction associated with SARS-CoV-2 infection. Full article

(This article belongs to the Special Issue Mitochondria and Energy Metabolism in Rare Diseases)

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14 pages, 2557 KiB

Open AccessArticle

Evidence for a Conserved Function of Eukaryotic Pantothenate Kinases in the Regulation of Mitochondrial Homeostasis and Oxidative Stress

by Camilla Ceccatelli Berti, Shalev Gihaz, Sonia Figuccia, Jae-Yeon Choi, Anasuya C. Pal, Paola Goffrini and Choukri Ben Mamoun

Int. J. Mol. Sci. 2023, 24(1), 435; https://doi.org/10.3390/ijms24010435 - 27 Dec 2022

Cited by 3 | Viewed by 2706

Abstract

Human PANK1, PANK2, and PANK3 genes encode several pantothenate kinase isoforms that catalyze the phosphorylation of vitamin B5 (pantothenic acid) to phosphopantothenate, a critical step in the biosynthesis of the major cellular cofactor, Coenzyme A (CoA). Mutations in the PANK2 gene, which encodes the mitochondrial pantothenate kinase (PanK) isoform, have been linked to pantothenate-kinase associated neurodegeneration (PKAN), a debilitating and often fatal progressive neurodegeneration of children and young adults. While the biochemical properties of these enzymes have been well-characterized in vitro, their expression in a model organism such as yeast in order to probe their function under cellular conditions have never been achieved. Here we used three yeast mutants carrying missense mutations in the yeast PanK gene, CAB1, which are associated with defective growth at high temperature and iron, mitochondrial dysfunction, increased iron content, and oxidative stress, to assess the cellular function of human PANK genes and functional conservation of the CoA-controlled processes between humans and yeast. Overexpression of human PANK1 and PANK3 in these mutants restored normal cellular activity whereas complementation with PANK2 was partial and could only be achieved with an isoform, PanK2^mtmΔ, lacking the mitochondrial transit peptide. These data, which demonstrate functional conservation of PanK activity between humans and yeast, set the stage for the use of yeast as a model system to investigate the impact of PKAN-associated mutations on the metabolic pathways altered in this disease. Full article

(This article belongs to the Special Issue Mitochondria and Energy Metabolism in Rare Diseases)

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14 pages, 4890 KiB

Open AccessArticle

The Consequences of Mitochondrial T10432C Mutation in Cika Cattle: A “Potential” Model for Leber’s Hereditary Optic Neuropathy

by Dinko Novosel, Vladimir Brajković, Mojca Simčič, Minja Zorc, Tanja Svara, Karmen Branovic Cakanic, Andreja Jungić, Betka Logar, Vlatka Cubric-Curik, Peter Dovc and Ino Curik

Int. J. Mol. Sci. 2022, 23(11), 6335; https://doi.org/10.3390/ijms23116335 - 6 Jun 2022

Cited by 2 | Viewed by 2059

Abstract

While mitogenome mutations leading to pathological manifestations are rare, more than 200 such mutations have been described in humans. In contrast, pathogenic mitogenome mutations are rare in domestic animals and have not been described at all in cattle. In the small local Slovenian cattle breed Cika, we identified (next-generation sequencing) two cows with the T10432C mitogenome mutation in the ND4L gene, which corresponds to the human T10663C mutation known to cause Leber’s hereditary optic neuropathy (LHON). Pedigree analysis revealed that the cows in which the mutation was identified belong to two different maternal lineages with 217 individual cows born between 1997 and 2020. The identified mutation and its maternal inheritance were confirmed by Sanger sequencing across multiple generations, whereas no single analysis revealed evidence of heteroplasmy. A closer clinical examination of one cow with the T10432C mutation revealed exophthalmos, whereas histopathological examination revealed retinal ablations, subretinal oedema, and haemorrhage. The results of these analyses confirm the presence of mitochondrial mutation T10432C with homoplasmic maternal inheritance as well as clinical and histopathological signs similar to LHON in humans. Live animals with the mutation could be used as a suitable animal model that can improve our understanding of the pathogenesis of LHON and other mitochondriopathies. Full article

(This article belongs to the Special Issue Mitochondria and Energy Metabolism in Rare Diseases)

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17 pages, 25591 KiB

Open AccessArticle

Novel Purine Derivative ITH15004 Facilitates Exocytosis through a Mitochondrial Calcium-Mediated Mechanism

by Ricardo de Pascual, Francesco Calzaferri, Paula C. Gonzalo, Rubén Serrano-Nieto, Cristóbal de los Ríos, Antonio G. García and Luis Gandía

Int. J. Mol. Sci. 2022, 23(1), 440; https://doi.org/10.3390/ijms23010440 - 31 Dec 2021

Cited by 1 | Viewed by 1914

Abstract

Upon depolarization of chromaffin cells (CCs), a prompt release of catecholamines occurs. This event is triggered by a subplasmalemmal high-Ca²⁺ microdomain (HCMD) generated by Ca²⁺ entry through nearby voltage-activated calcium channels. HCMD is efficiently cleared by local mitochondria that avidly take up Ca²⁺ through their uniporter (MICU), then released back to the cytosol through mitochondrial Na⁺/Ca²⁺ exchanger (MNCX). We found that newly synthesized derivative ITH15004 facilitated the release of catecholamines triggered from high K⁺-depolarized bovine CCs. Such effect seemed to be due to regulation of mitochondrial Ca²⁺ circulation because: (i) FCCP-potentiated secretory responses decay was prevented by ITH15004; (ii) combination of FCCP and ITH15004 exerted additive secretion potentiation; (iii) such additive potentiation was dissipated by the MICU blocker ruthenium red (RR) or the MNCX blocker CGP37157 (CGP); (iv) combination of FCCP and ITH15004 produced both additive augmentation of cytosolic Ca²⁺ concentrations ([Ca²⁺]_c) K⁺-challenged BCCs, and (v) non-inactivated [Ca²⁺]_c transient when exposed to RR or CGP. On pharmacological grounds, data suggest that ITH15004 facilitates exocytosis by acting on mitochondria-controlled Ca²⁺ handling during K⁺ depolarization. These observations clearly show that ITH15004 is a novel pharmacological tool to study the role of mitochondria in the regulation of the bioenergetics and exocytosis in excitable cells. Full article

(This article belongs to the Special Issue Mitochondria and Energy Metabolism in Rare Diseases)

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15 pages, 2785 KiB

Open AccessArticle

Swim Training Ameliorates Hyperlocomotion of ALS Mice and Increases Glutathione Peroxidase Activity in the Spinal Cord

by Katarzyna Patrycja Dzik, Damian Józef Flis, Zofia Kinga Bytowska, Mateusz Jakub Karnia, Wieslaw Ziolkowski and Jan Jacek Kaczor

Int. J. Mol. Sci. 2021, 22(21), 11614; https://doi.org/10.3390/ijms222111614 - 27 Oct 2021

Cited by 5 | Viewed by 2513

Abstract

(1) Background: Amyotrophic lateral sclerosis (ALS) is an incurable, neurodegenerative disease. In some cases, ALS causes behavioral disturbances and cognitive dysfunction. Swimming has revealed a neuroprotective influence on the motor neurons in ALS. (2) Methods: In the present study, a SOD1-G93A mice model of ALS were used, with wild-type B6SJL mice as controls. ALS mice were analyzed before ALS onset (10th week of life), at ALS 1 onset (first symptoms of the disease, ALS 1 onset, and ALS 1 onset SWIM), and at terminal ALS (last stage of the disease, ALS TER, and ALS TER SWIM), and compared with wild-type mice. Swim training was applied 5 times per week for 30 min. All mice underwent behavioral tests. The spinal cord was analyzed for the enzyme activities and oxidative stress markers. (3) Results: Pre-symptomatic ALS mice showed increased locomotor activity versus control mice; the swim training reduced these symptoms. The metabolic changes in the spinal cord were present at the pre-symptomatic stage of the disease with a shift towards glycolytic processes at the terminal stage of ALS. Swim training caused an adaptation, resulting in higher glutathione peroxidase (GPx) and protection against oxidative stress. (4) Conclusion: Therapeutic aquatic activity might slow down the progression of ALS. Full article

(This article belongs to the Special Issue Mitochondria and Energy Metabolism in Rare Diseases)

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Review

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16 pages, 1127 KiB

Open AccessReview

Mitochondrial Dysfunction and Oxidative Stress in Hereditary Ectopic Calcification Diseases

by Lukas L. Nollet and Olivier M. Vanakker

Int. J. Mol. Sci. 2022, 23(23), 15288; https://doi.org/10.3390/ijms232315288 - 4 Dec 2022

Cited by 4 | Viewed by 2492

Abstract

Ectopic calcification (EC) is characterized by an abnormal deposition of calcium phosphate crystals in soft tissues such as blood vessels, skin, and brain parenchyma. EC contributes to significant morbidity and mortality and is considered a major health problem for which no effective treatments currently exist. In recent years, growing emphasis has been placed on the role of mitochondrial dysfunction and oxidative stress in the pathogenesis of EC. Impaired mitochondrial respiration and increased levels of reactive oxygen species can be directly linked to key molecular pathways involved in EC such as adenosine triphosphate homeostasis, DNA damage signaling, and apoptosis. While EC is mainly encountered in common diseases such as diabetes mellitus and chronic kidney disease, studies in rare hereditary EC disorders such as pseudoxanthoma elasticum or Hutchinson–Gilford progeria syndrome have been instrumental in identifying the precise etiopathogenetic mechanisms leading to EC. In this narrative review, we describe the current state of the art regarding the role of mitochondrial dysfunction and oxidative stress in hereditary EC diseases. In-depth knowledge of aberrant mitochondrial metabolism and its local and systemic consequences will benefit the research into novel therapies for both rare and common EC disorders. Full article

(This article belongs to the Special Issue Mitochondria and Energy Metabolism in Rare Diseases)

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21 pages, 3625 KiB

Open AccessCase Report

Biallelic Variants in PYROXD2 Cause a Severe Infantile Metabolic Disorder Affecting Mitochondrial Function

by Nicole J. Van Bergen, Daniella H. Hock, Lucy Spencer, Sean Massey, Tegan Stait, Zornitza Stark, Sebastian Lunke, Ain Roesley, Heidi Peters, Joy Yaplito Lee, Anna Le Fevre, Oliver Heath, Cristina Mignone, Joseph Yuan-Mou Yang, Monique M. Ryan, Colleen D’Arcy, Margot Nash, Sile Smith, Nikeisha J. Caruana, David R. Thorburn, David A. Stroud, Susan M. White, John Christodoulou and Natasha J. Brown Show full author list Hide full author list

Int. J. Mol. Sci. 2022, 23(2), 986; https://doi.org/10.3390/ijms23020986 - 17 Jan 2022

Cited by 4 | Viewed by 3497

Abstract

Pyridine Nucleotide-Disulfide Oxidoreductase Domain 2 (PYROXD2; previously called YueF) is a mitochondrial inner membrane/matrix-residing protein and is reported to regulate mitochondrial function. The clinical importance of PYROXD2 has been unclear, and little is known of the protein’s precise biological function. In the present paper, we report biallelic variants in PYROXD2 identified by genome sequencing in a patient with suspected mitochondrial disease. The child presented with acute neurological deterioration, unresponsive episodes, and extreme metabolic acidosis, and received rapid genomic testing. He died shortly after. Magnetic resonance imaging (MRI) brain imaging showed changes resembling Leigh syndrome, one of the more common childhood mitochondrial neurological diseases. Functional studies in patient fibroblasts showed a heightened sensitivity to mitochondrial metabolic stress and increased mitochondrial superoxide levels. Quantitative proteomic analysis demonstrated decreased levels of subunits of the mitochondrial respiratory chain complex I, and both the small and large subunits of the mitochondrial ribosome, suggesting a mitoribosomal defect. Our findings support the critical role of PYROXD2 in human cells, and suggest that the biallelic PYROXD2 variants are associated with mitochondrial dysfunction, and can plausibly explain the child’s clinical presentation. Full article

(This article belongs to the Special Issue Mitochondria and Energy Metabolism in Rare Diseases)

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