bims-mitmed Biomed News
on Mitochondrial medicine
Issue of 2024–12–29
fourteen papers selected by
Dario Brunetti, Fondazione IRCCS Istituto Neurologico



  1. Nat Commun. 2024 Dec 23. 15(1): 10719
      Aberration of mitochondrial function is a shared feature of many human pathologies, characterised by changes in metabolic flux, cellular energetics, morphology, composition, and dynamics of the mitochondrial network. While some of these changes serve as compensatory mechanisms to maintain cellular homeostasis, their chronic activation can permanently affect cellular metabolism and signalling, ultimately impairing cell function. Here, we use a Drosophila melanogaster model expressing a proofreading-deficient mtDNA polymerase (POLγexo-) in a genetic screen to find genes that mitigate the harmful accumulation of mtDNA mutations. We identify critical pathways associated with nutrient sensing, insulin signalling, mitochondrial protein import, and autophagy that can rescue the lethal phenotype of the POLγexo- flies. Rescued flies, hemizygous for dilp1, atg2, tim14 or melted, normalise their autophagic flux and proteasome function and adapt their metabolism. Mutation frequencies remain high with the exception of melted-rescued flies, suggesting that melted may act early in development. Treating POLγexo- larvae with the autophagy activator rapamycin aggravates their lethal phenotype, highlighting that excessive autophagy can significantly contribute to the pathophysiology of mitochondrial diseases. Moreover, we show that the nucleation process of autophagy is a critical target for intervention.
    DOI:  https://doi.org/10.1038/s41467-024-55559-2
  2. J Cell Biol. 2025 Mar 03. pii: e202403140. [Epub ahead of print]224(3):
      While extensive work has examined the mechanisms of mitochondrial fission, it remains unclear whether internal mitochondrial proteins in metazoans play a direct role in the process. Previously, the yeast inner membrane protein Mdm33 was shown to be required for normal mitochondrial morphology and has been hypothesized to be involved in mitochondrial fission. However, it is unknown whether Mdm33 plays a direct role, and it is not thought to have a mammalian homolog. Here, we use a bioinformatic approach to identify a structural ortholog of Mdm33 in humans, CCDC51 (also called MITOK), whose depletion phenocopies loss of Mdm33. We find that knockdown of CCDC51 also leads to reduced rates of mitochondrial fission. Further, we spatially and temporally resolve Mdm33 and CCDC51 to a subset of mitochondrial fission events. Finally, we show that CCDC51 overexpression promotes its spatial association with Drp1 and induces mitochondrial fragmentation, suggesting it is a positive effector of mitochondrial fission. Together, our data reveal that Mdm33 and CCDC51 are functionally conserved and suggest that internal mitochondrial proteins are directly involved in at least a subset of mitochondrial fission events in human cells.
    DOI:  https://doi.org/10.1083/jcb.202403140
  3. RNA. 2024 Dec 24. pii: rna.080257.124. [Epub ahead of print]
      Mitochondrial tRNA (mt-tRNA) modifications play pivotal roles in decoding and sustaining tRNA stability, thereby enabling synthesis of essential respiratory complex proteins in mitochondria. Consequently, loss of human mt-tRNA modifications caused by mutations in the mitochondrial or nuclear genome can cause life-threatening mitochondrial diseases such as encephalopathy and cardiomyopathy. In this article, we first provide a comprehensive overview of the functions of mt-tRNA modifications, the responsible modification enzymes, and the diseases caused by loss of mt-tRNA modifications. We then discuss progress and potential strategies to treat these diseases, including taurine supplementation for MELAS patients, targeted deletion of mtDNA variants, and overexpression of modification-related proteins. Finally, we discuss factors that need to be overcome to cure 'mitochondrial tRNA modopathies'.
    Keywords:  MELAS; mitoTALEN; mitochondrial disease; tRNA modification; tRNA modopathy
    DOI:  https://doi.org/10.1261/rna.080257.124
  4. J Biol Chem. 2024 Dec 21. pii: S0021-9258(24)02626-7. [Epub ahead of print] 108124
      Human mitochondrial 12S ribosomal RNA (rRNA) 1555A>G mutation has been associated with aminoglycoside-induced and nonsyndromic deafness in many families worldwide. Our previous investigation revealed that the m.1555A>G mutation impaired mitochondrial translation and oxidative phosphorylation (OXPHOS). However, the mechanisms by which mitochondrial dysfunctions induced by m.1555A>G mutation regulate intracellular signaling for mitochondrial and cellular integrity remain poorly understood. Here, we demonstrated that the m.1555A>G mutation downregulated the expression of nuclear-encoded subunits of complexes I and IV but upregulated the expression of assemble factors for OXPHOS complexes, using cybrids derived from one hearing-impaired Chinese subject bearing the m.1555A>G mutation and from one hearing normal control lacking the mutation. These alterations resulted in the aberrant assembly, instability and reduced activities of respiratory chain enzyme complexes I, IV and V, rate of oxygen consumption, and diminished ATP production. Furthermore, the mutant cell lines carrying the m.1555A>G mutation exhibited decreased membrane potential and increased the production of reactive oxygen species. The aberrant assembly and biogenesis of OXPHOS impacted mitochondrial quality controls, including the imbalance of mitochondrial dynamics via increasing fission with abnormal mitochondrial morphology and impaired mitophagy. Strikingly, the cells bearing the m.1555A>G mutation revealed the upregulation of both ubiquitin-dependent and independent mitophagy pathways, evidenced by increasing the levels of Parkin, Pink, BNIP3L and NIX. The m.1555A>G mutation-induced deficiencies ameliorate the cell homeostasis via elevating the autophagy process and upregulating apoptotic pathways. Our findings provide new insights into pathophysiology of mitochondrial deafness arising from reshaping mitochondrial and cellular homeostasis due to 12S rRNA 1555A>G mutation.
    DOI:  https://doi.org/10.1016/j.jbc.2024.108124
  5. Muscle Nerve. 2024 Dec 23.
       INTRODUCTION AND AIMS: Mitochondrial myopathies are rare genetic disorders for which no effective treatment exists. We previously showed that the pharmacological cyclophilin inhibitor cyclosporine A (CsA) extends the lifespan of fast-twitch skeletal muscle-specific mitochondrial transcription factor A knockout (Tfam KO) mice, lacking the ability to transcribe mitochondrial DNA and displaying lethal mitochondrial myopathy. Our present aim was to assess whether the positive effect of CsA was associated with improved in vivo mitochondrial energy production.
    METHODS: Mice were treated with CsA for 4 weeks, beginning at 12 weeks (i.e., before the terminal disease phase). Hindlimb plantar flexor muscles were fatigued by 80 contractions (40 Hz, 1.5 s on, 6 s off) while measuring force and energy metabolism using phosphorus-31 magnetic resonance spectroscopy.
    RESULTS: Force decreased at similar rates in Tfam KO mice with and without the CsA treatment, reaching 50% of the baseline value after ~14 ± 1 contractions, which was faster than in control mice (25 ± 1 contractions). Phosphocreatine (PCr) decreased to ~10% of the control concentration in Tfam KO mice, independent of the treatment, which was larger than the ~20% observed in control mice. The time constant of PCr recovery was higher in untreated Tfam KO than that in control muscle (+100%) and similar in untreated and CsA-treated Tfam KO mice.
    DISCUSSION: The results do not support improved mitochondrial energy production as a mechanism underlying the prolonged lifespan of Tfam KO mitochondrial myopathy mice treated with CsA. Thus, other mechanisms must be involved, such as the previously observed CsA-mediated protection against excessive mitochondrial Ca2+ accumulation.
    Keywords:  force production; mitochondrial function; muscle disease; pharmacological agent; preclinical model
    DOI:  https://doi.org/10.1002/mus.28315
  6. Mol Genet Metab Rep. 2024 Dec;41 101168
       Background: Variants in NDUFAF6 have been reported to be associated with Leigh syndrome. However, further expansion of the NDUFAF6-phenotype and variants spectrum of NDUFAF6-related Leigh syndrome are still required.
    Methods: Two patients diagnosed with Leigh syndrome were recruited, and whole-exome sequencing was performed to identify the genetic variants responsible for the abnormal gait, dystonia, and bilateral basal ganglia lesions, followed by validation using Sanger sequencing. Detailed medical records of the patients were collected and reviewed. Patient-derived immortalized B lymphocytes were generalized for functional assays. The clinical manifestations of the patients in this study and previously reported studies are summarized.
    Results: Two patients developed gait dystonia followed by rapid progression to generalized dystonia and psychomotor regression. Brain magnetic resonance images showed lesions in bilateral symmetric basal ganglia. We identified that patient 1 and patient 2 had two missense changes (NM_152416 c.371 T > C, c.923 T > C and c.371 T > C, c.920 A > T) in NDUFAF6, respectively. The deficiency of mature super complex of complex I was confirmed in patient-derived immortalized B lymphocytes. Meanwhile, cellular ATP production was decreased, and mitochondrial ROS was increased. A literature review of 18 patients carrying variants in NDUFAF6 was conducted, focusing on neurological presentation.
    Conclusions: NDUFAF6-related Leigh syndrome is a relevant cause of initial symptoms with abnormal gait, dystonia, and bilateral basal ganglia lesions. Two novel genetic variants, c.923 T > C and c.920 A > T were reported, which expands NDUFAF6-related Leigh syndrome and is advantageous for genetic counseling.
    Keywords:  Complex I deficiency; Leigh syndrome; Mitochondrial disease; NDUFAF6
    DOI:  https://doi.org/10.1016/j.ymgmr.2024.101168
  7. Epilepsia Open. 2024 Dec 24.
      Neuronal ceroid lipofuscinoses (NCLs) are genetically heterogeneous neurodegenerative disorders, characterized by progressive cognitive and motor decline, epilepsy, visual impairment, and shortened life-expectancy. CLN6-related NCLs include both late-infantile and adult myoclonic form. We report a 21-year-old patient, with mild developmental delay, who developed occipital seizures at 14 years, and subsequently cognitive decline, cortical myoclonus, and photosensitivity at low and higher frequencies. Overall, the picture suited progressive myoclonus epilepsy. Electroretinogram was normal. A skin biopsy revealed a mixed storage of curvilinear and fingerprint profiles. A brain MRI showed severe cortical atrophy. Performing genetic analyses, two biallelic variants were identified in the CLN6 gene, each inherited from one of the healthy parents, one c.722T>C, p.(Met241Thr) already described in the late-infantile form and the other one c.486+28T>C, intronic and novel, causing aberrant splicing. In the patient, the expression of the allele containing c.722T>C variant was increased, in comparison with the carrier parent. The peculiar genetic pattern observed in the patient could explain a milder clinical picture when compared with late-infantile form, since CLN6 expression was partially preserved. However, the presence of a delay, and the early cognitive decline suggested a continuum phenotype connecting late-infantile and adult CLN6-related forms. PLAIN LANGUAGE SUMMARY: We report a patient with CLN6 disease who developed symptoms at an intermediate age: 9 years for mild intellectual disability and 14 years for occipital seizures and progressive myoclonus epilepsy, without visual impairment. The patient is compound heterozygous for a CLN6 missense variant c.722T>C, p.(Met241Thr) already described in the late-infantile form and for a novel intronic variant c.486+28T>C, causing aberrant splicing. In the patient, the expression of the allele containing c.722T>C variant was increased, compared with the carrier parent. The splice site variant had a milder effect. The peculiar genetic pattern may explain the continuum phenotype between late-infantile and adult forms.
    Keywords:  Kufs' disease; neuronal ceroidlipofuscinosis; occipital seizures; photoparoxysmal response; progressive myoclonus epilepsy
    DOI:  https://doi.org/10.1002/epi4.13119
  8. Orphanet J Rare Dis. 2024 Dec 24. 19(1): 487
       BACKGROUND AND OBJECTIVES: Mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes (MELAS) syndrome is a maternally inherited mitochondrial disorder that mostly affects the central nervous system and skeletal muscle. This study provides a comprehensive summary of the clinical symptoms, multisystemic pathogenesis, and genetic characteristics of MELAS syndrome. The aim was to improve comprehension of clinical practice and gain a deeper understanding of the latest pathophysiological theories.
    METHODS: The present investigation involved a cohort of patients diagnosed with MELAS at Nanjing Drum Tower Hospital between January 2014 and December 2022. Multisystem symptoms, magnetic resonance imaging/spectroscopy (MRI/MRS), muscle biopsy, and mitochondrial DNA (mtDNA) data were summarized and subsequently analysed.
    RESULTS: This retrospective study included a cohort of 29 MELAS patients who predominantly presented symptoms such as stroke-like episodes, proximal muscle weakness, and exercise intolerance. MRI scans revealed very small infarcts beneath the deep cortex during stroke-like episodes, indicating nonvascular brain damage. Pathology analyses of the brain also showed neuronal degeneration and glial cell proliferation in the cerebral parenchyma. Proton magnetic resonance spectroscopy (1H-MRS) analysis revealed an increase in the lactate peak and a reduction in the N-acetylaspartate (NAA) level. Similarly, the phosphorus magnetic resonance spectroscopy (31P-MRS) analysis revealed an abnormal ratio of inorganic phosphate (Pi) to phosphocreatine (PCr). Muscle biopsy revealed the presence of ragged red fibres (RRFs) and cytochrome c oxidase (COX) enzyme-defective cells. These abnormalities indicate structural abnormalities in the mitochondria and deficiencies in oxidative phosphorylation, respectively. In addition to the common m.3243A > G variant, other prevalent variants, including m.5628 T > C, m.6352-13952del, and a 9-bp small deletion combined with m.3243A > G, exist.
    CONCLUSIONS: MELAS is a rare mitochondrial syndrome characterized by clinical heterogeneity and genetic heteroplasmy. Abnormalities in mitochondrial metabolic function and impairments in enzyme activity are the pathogenic processes underlying MELAS. Mitochondrial vasculopathy and mitochondrial neuropathy may provide a partial explanation for the unique aetiology of stroke-like episodes.
    Keywords:  COX enzyme defects; MELAS; MRS; RRFs; Stroke-like episodes
    DOI:  https://doi.org/10.1186/s13023-024-03511-4
  9. Elife. 2024 Dec 27. pii: RP96536. [Epub ahead of print]13
      Mitochondrial biogenesis requires the expression of genes encoded by both the nuclear and mitochondrial genomes. However, aside from a handful transcription factors regulating specific subsets of mitochondrial genes, the overall architecture of the transcriptional control of mitochondrial biogenesis remains to be elucidated. The mechanisms coordinating these two genomes are largely unknown. We performed a targeted RNAi screen in developing eyes with reduced mitochondrial DNA content, anticipating a synergistic disruption of tissue development due to impaired mitochondrial biogenesis and mitochondrial DNA (mtDNA) deficiency. Among 638 transcription factors annotated in the Drosophila genome, 77 were identified as potential regulators of mitochondrial biogenesis. Utilizing published ChIP-seq data of positive hits, we constructed a regulatory network revealing the logic of the transcription regulation of mitochondrial biogenesis. Multiple transcription factors in core layers had extensive connections, collectively governing the expression of nearly all mitochondrial genes, whereas factors sitting on the top layer may respond to cellular cues to modulate mitochondrial biogenesis through the underlying network. CG1603, a core component of the network, was found to be indispensable for the expression of most nuclear mitochondrial genes, including those required for mtDNA maintenance and gene expression, thus coordinating nuclear genome and mtDNA activities in mitochondrial biogenesis. Additional genetic analyses validated YL-1, a transcription factor upstream of CG1603 in the network, as a regulator controlling CG1603 expression and mitochondrial biogenesis.
    Keywords:  ChIP-seq; D. melanogaster; RNA-seq; SDHA; TFAM; genetics; genomics; mitochondrial biogenesis; transcription factors
    DOI:  https://doi.org/10.7554/eLife.96536
  10. Orphanet J Rare Dis. 2024 Dec 23. 19(1): 486
      Mitochondrial transcription factor A (TFAM) deficiency may cause mtDNA depletion syndrome, which manifests as neonatal liver failure or primary ovarian insufficiency, hearing loss, seizures, and intellectual disability. Treatment focusing on symptomatic management, and the clinical prognosis remains poor. Here, we describe a novel case of TFAM mutation presenting with progressive neonatal cholestasis, hypoglycemia and abnormal amino acid profiling. The patient progressed to liver failure at 6 months of age but did not exhibit neurological involvement. No morphologic abnormalities were observed in muscle biopsy, while mtDNA copy number was reduced in comparison to age- and tissue-matched controls. After liver transplantation, liver biochemistries and blood amino acid profiling normalized three weeks later. Moreover, the boy was doing well post-transplant without any clinical concerns, and his development and neurological examination remain normal 33 months after liver transplantation. Our report suggests that liver transplantation appears to have a favorable profile in such patients.
    Keywords:  Liver transplantation; MtDNA depletion syndrome; Neonatal liver failure; TFAM
    DOI:  https://doi.org/10.1186/s13023-024-03487-1
  11. Clin Genet. 2024 Dec 23.
      An in-depth analysis of susceptibility factors modifying the penetrance of rare Leber hereditary optic neuropathy-causing mutations in respiratory complex I genes encoded in mitochondrial deoxyribonucleic acid has not been performed. To bridge this gap, we conducted a review of the literature on rare mutations associated with LHON, selected those with substantial evidence of pathogenicity, and performed an in-depth analysis of the various pedigrees. Examining the influences that modify the penetrance of the classical mutations associated with this disease may offer insights into susceptibility factors in individuals carrying the rare mutations.
    Keywords:  Leber hereditary optic neuropathy; incomplete penetrance; mitochondrial deoxyribonucleic acid; rare mutation; respiratory complex I genes
    DOI:  https://doi.org/10.1111/cge.14683
  12. Aging Cell. 2024 Dec 25. e14446
      Mesenchymal stem cells (MSCs) are promising candidates for regenerative therapies due to their self-renewal and differentiation capabilities. Pathological microenvironments expose MSCs to senescence-inducing factors such as reactive oxygen species (ROS), resulting in MSC functional decline and loss of stemness. Oxidative stress leads to mitochondrial dysfunction, a hallmark of senescence, and is prevalent in aging tissues characterized by elevated ROS levels. We hypothesized that overexpression of nuclear respiratory factor-1 (NRF1), a driver of mitochondrial biogenesis, could metabolically potentiate MSCs and prevent MSC senescence. Single-cell RNA sequencing (scRNA-Seq) revealed that MSCs transfected with NRF1 messenger RNA (mRNA) exhibited upregulated expression of genes associated with oxidative phosphorylation (OXPHOS), decreased glycolytic markers, and suppression of senescence-related pathways. To test whether NRF1 induction could mitigate stress-induced premature senescence, we exposed MSCs to hydrogen peroxide (H2O2) and validated our findings in a replicative senescence model. NRF1 mRNA transfection significantly increased mitochondrial mass and improved aberrant mitochondrial processes associated with senescence, including reduced mitochondrial and intracellular total ROS production. Mitochondrial health and dynamics were preserved, and respiratory function was restored, as evidenced by enhanced OXPHOS, reduced glycolysis, and increased ATP production. Notably, NRF1 overexpression led to decreased senescence-associated β-galactosidase (SA-β-gal) activity and reduced expression of senescence markers p53, p21, and p16. Our findings demonstrate that NRF1 induction attenuates MSC senescence by enhancing mitochondrial function, suggesting potential translational applications for MSC-based therapies and senescence-targeted interventions.
    Keywords:  mesenchymal stem cells; mitochondrial biogenesis; mitochondrial dysfunction; nuclear respiratory factor‐1 (NRF1); oxidative stress; senescence
    DOI:  https://doi.org/10.1111/acel.14446
  13. Exp Neurol. 2024 Dec 20. pii: S0014-4886(24)00449-7. [Epub ahead of print]385 115123
      Swallowing, both nutritive and non-nutritive, is highly dysfunctional in children with Leigh Syndrome (LS) and contributes to the need for both gastrostomy and tracheostomy tube placement. Without these interventions aspiration of food, liquid, and mucus occur resulting in repeated bouts of respiratory infection. No study has investigated whether mouse models of LS, a neurometabolic disorder, exhibit dysfunctions in neuromuscular activity of swallow and breathing integration. We used a genetic mouse model of LS in which the NDUFS4 gene is knocked out (KO) specifically in Vglut2 or Gad2 neurons. We found increased variability of the swallow motor pattern, disruption in breathing regeneration post swallow, and water-induced apneas only in Vglut2 KO mice. These physiological changes likely contribute to weight loss and premature death seen in this mouse model. Following chronic hypoxia (CH) exposure, there was no difference in swallow motor pattern, breathing regeneration, weight, and life expectancy in the Vglut2-Ndufs4-KO CH mice compared to control CH, indicating a phenotypic rescue or prevention. These findings show that like patients with LS, Ndufs4 mouse models of LS exhibit swallow impairments as well as swallow-breathing discoordination alongside the other phenotypic traits described in previous studies. Understanding this aspect of LS will open roads for the development of future more efficacious therapeutic intervention for this illness.
    Keywords:  Airway protection; Dysphagia; Hypoxia; Mitochondrial disease
    DOI:  https://doi.org/10.1016/j.expneurol.2024.115123
  14. Front Cell Dev Biol. 2024 ;12 1496244
       Background and objectives: Friedreich's Ataxia (FRDA) is a genetic disease that affects a variety of different tissues. The disease is caused by a mutation in the frataxin gene (FXN) which is important for the synthesis of iron-sulfur clusters. The primary pathologies of FRDA are loss of motor control and cardiomyopathy. These occur due to the accumulation of reactive oxygen species (ROS) in the brain and the heart due to their high metabolic rates. Our research aims to understand how developmental processes and the kidney are impacted by a deficiency of FXN.
    Methods: We utilized an antisense oligomer, or morpholino, to knockdown the frataxin gene (fxn) in zebrafish embryos. Knockdown was confirmed via RT-PCR, gel electrophoresis, and Sanger sequencing. To investigate phenotypes, we utilized several staining techniques including whole mount in situ hybridization, Alcian blue, and acridine orange, as well as dextran-FITC clearance assays.
    Results: fxn deficient animals displayed otolith malformations, edema, and reduced survival. Alcian blue staining revealed craniofacial defects in fxn deficient animals, and gene expression studies showed that the pronephros, or embryonic kidney, had several morphological defects. We investigated the function of the pronephros through clearance assays and found that the renal function is disrupted in fxn deficient animals in addition to proximal tubule endocytosis. Utilizing acridine orange staining, we found that cell death is a partial contributor to these phenotypes.
    Discussion and conclusion: This work provides new insights about how fxn deficiency impacts development and kidney morphogenesis. Additionally, this work establishes an additional model system to study FRDA.
    Keywords:  development; frataxin; kidney; metabolism; nephron; zebrafish
    DOI:  https://doi.org/10.3389/fcell.2024.1496244