bims-mitdis 2023-07-09 papers

bims-mitdis

Biomed News

on Mitochondrial disorders

Issue of 2023‒07‒09
forty-two papers selected by
Catalina Vasilescu
Helmholz Munich

Disease models of mitochondrial aminoacyl-tRNA synthetase defects.
Uncharacterized protein C17orf80: A novel interactor of human mitochondrial nucleoids.
CISD3 is required for Complex I function, mitochondrial integrity, and skeletal muscle maintenance.
Mitochondrial regulation of local supply of energy in neurons.
Yeast NDI1 reconfigures neuronal metabolism and prevents the unfolded protein response in mitochondrial complex I deficiency.
An Improved Method to Isolate Mitochondrial Contact Sites.
Ferroptosis in mitochondrial cardiomyopathy.
Mitochondria- and ER-associated actin are required for mitochondrial fusion.
Tissue specific differences in the assembly of mitochondrial complex I is revealed by a novel ENU mutation in ECSIT.
Blood-based bioenergetics: a liquid biopsy of mitochondrial dysfunction in disease.
Pyruvate transamination and NAD biosynthesis enable proliferation of succinate dehydrogenase-deficient cells by supporting aerobic glycolysis.
Novel insights into the role of mitochondria in diabetic cardiomyopathy: molecular mechanisms and potential treatments.
Phenotypic, molecular, and functional characterization of COQ7-related primary CoQ10 deficiency: Hypomorphic variants and two distinct disease entities.
Rapid degeneration of iPSC-derived motor neurons lacking Gdap1 engages a mitochondrial-sustained innate immune response.
Mitochondrial Deoxyribonucleic Acid (mtDNA), Maternal Inheritance, and Their Role in the Development of Cancers: A Scoping Review.
Oxygen consumption rate to evaluate mitochondrial dysfunction and toxicity in cardiomyocytes.
DMT1 differentially regulates mitochondrial complex activities to reduce glutathione loss and mitigate ferroptosis.
Quantifying mitochondrial redox and bilirubin content in intact primary hepatocytes of obese mice using fluorescent reporters.
Mitochondrial quality control: prime targets for antiviral therapy?
Postmortem diagnosis of very long chain acyl-CoA dehydrogenase (VLCAD) deficiency in a neonate with sudden cardiac death.
ER-mitochondria contacts and cholesterol metabolism are disrupted by disease-associated tau protein.
Docking and stability defects in mitofusin highlight the proteasome as a potential therapeutic target.
Arf1 coordinates fatty acid metabolism and mitochondrial homeostasis.
Mitochondrial MICOS complex genes, implicated in hypoplastic left heart syndrome, maintain cardiac contractility and actomyosin integrity.
The mitochondrial calcium uniporter transports Ca 2+ via a ligand-relay mechanism.
Proximity-labeling chemoproteomics defines the subcellular cysteinome and inflammation-responsive mitochondrial redoxome.
Multi-omics for better and faster rare disease diagnosis.
An Atlas of Variant Effects to understand the genome at nucleotide resolution.
Mitochondrial dysfunction in the offspring of obese mothers and it's transmission through damaged oocyte mitochondria: Integration of mechanisms.
N-acetylcysteine modulates rotenone-induced mitochondrial Complex I dysfunction in THP-1 cells.
Spatial mapping of cellular senescence: emerging challenges and opportunities.
Glutamine supplementation reverses manganese neurotoxicity by eliciting the mitochondrial unfolded protein response.
NRF1-mediated mitochondrial biogenesis antagonizes innate antiviral immunity.
Expanded vacuum-stable gels for multiplexed high-resolution spatial histopathology.
The Haves and Have-Nots: The Mitochondrial Permeability Transition Pore across Species.
Deletion of Nmnat1 in Skeletal Muscle Leads to the Reduction of NAD+ Levels but Has No Impact on Skeletal Muscle Morphology and Fiber Types.
SLC25A51 promotes tumor growth through sustaining mitochondria acetylation homeostasis and proline biogenesis.
Class 3 PI3K coactivates the circadian clock to promote rhythmic de novo purine synthesis.
Impaired mitochondrial dynamics and removal of the damaged mitochondria in diabetic retinopathy.
Predicting the Mitochondrial Toxicity of Small Molecules: Insights from Mechanistic Assays and Cell Painting Data.
Shaping mitochondria through fed-fast and circadian cycles.
Epimutation detection in the clinical context: guidelines and a use case from a new Bioconductor package.

J Inherit Metab Dis. 2023 Jul 06.

Disease models of mitochondrial aminoacyl-tRNA synthetase defects.

Henna Tyynismaa.

Mitochondrial aminoacyl-tRNA synthetases (mtARS) are enzymes critical for the first step of mitochondrial protein synthesis by charging mitochondrial tRNAs with their cognate amino acids. Pathogenic variants in all nineteen nuclear mtARS genes are now recognized as causing recessive mitochondrial diseases. Most mtARS disorders affect the nervous system, but the phenotypes range from multisystem diseases to tissue-specific manifestations. However, the mechanisms behind the tissue-specificities are poorly understood, and challenges remain in obtaining accurate disease models for developing and testing treatments. Here some of the currently existing disease models that have increased our understanding of mtARS defects are discussed. This article is protected by copyright. All rights reserved.

DOI: https://doi.org/10.1002/jimd.12652
J Cell Sci. 2023 Jul 04. pii: jcs.260822. [Epub ahead of print]

Uncharacterized protein C17orf80: A novel interactor of human mitochondrial nucleoids.

Alisa Potter, Anu Hangas, Steffi Goffart, Martijn A Huynen, Alfredo Cabrera-Orefice, Johannes N Spelbrink.

  Molecular functions of many human proteins remain unstudied, despite the demonstrated association with diseases or pivotal molecular structures, such as mitochondrial DNA (mtDNA). This small genome is crucial for proper functioning of mitochondria, the energy-converting organelles. In mammals, mtDNA is arranged into macromolecular complexes called nucleoids that serve as functional stations for its maintenance and expression. Here, we aimed to explore an uncharacterized protein C17orf80, which was previously detected close to the nucleoid components by proximity-labelling mass spectrometry. To investigate the subcellular localization and function of C17orf80, we took an advantage of immunofluorescence microscopy, interaction proteomics and several biochemical assays. We demonstrate that C17orf80 is a mitochondrial membrane-associated protein that interacts with nucleoids even when mtDNA replication is inhibited. In addition, we show that C17orf80 is not essential for mtDNA maintenance and mitochondrial gene expression in cultured human cells. These results provide a basis for uncovering the molecular function of C17orf80 and the nature of its association with nucleoids, possibly leading to new insights about mtDNA and its expression.

Keywords:  2'; 3'-dideoxycytidine; C17orf80; Mitochondria; Mitochondrial nucleoid; mtDNA

DOI:  https://doi.org/10.1242/jcs.260822
bioRxiv. 2023 Jun 04. pii: 2023.06.03.543558. [Epub ahead of print]

CISD3 is required for Complex I function, mitochondrial integrity, and skeletal muscle maintenance.

Henri-Baptiste Marjault, Ola Karmi, Linda Rowland, Thi Thao Nguyen, DeAna Grant, Camila Manrique-Acevedo, Rachel Nechushtai, Ron Mittler.

Mitochondria play a central role in muscle metabolism and function. In skeletal muscles, a unique family of iron-sulfur proteins, termed CISD proteins, support mitochondrial function. The abundance of these proteins declines with aging leading to muscle degeneration. Although the function of the outer mitochondrial proteins CISD1 and CISD2 has been defined, the role of the inner mitochondrial protein CISD3, is currently unknown. Here we show that CISD3 deficiency in mice results in muscle atrophy that shares proteomic features with Duchenne Muscular Dystrophy. We further reveal that CISD3 deficiency impairs the function and structure of skeletal muscle mitochondria, and that CISD3 interacts with, and donates its clusters to, Complex I respiratory chain subunit NDUFV2. These findings reveal that CISD3 is important for supporting the biogenesis and function of Complex I, essential for muscle maintenance and function. Interventions that target CISD3 could therefore impact muscle degeneration syndromes, aging, and related conditions.

DOI: https://doi.org/10.1101/2023.06.03.543558
Curr Opin Neurobiol. 2023 Jun 29. pii: S0959-4388(23)00072-7. [Epub ahead of print]81 102747

Mitochondrial regulation of local supply of energy in neurons.

Guillermo López-Doménech, Josef T Kittler.

Brain computation is metabolically expensive and requires the supply of significant amounts of energy. Mitochondria are highly specialized organelles whose main function is to generate cellular energy. Due to their complex morphologies, neurons are especially dependent on a set of tools necessary to regulate mitochondrial function locally in order to match energy provision with local demands. By regulating mitochondrial transport, neurons control the local availability of mitochondrial mass in response to changes in synaptic activity. Neurons also modulate mitochondrial dynamics locally to adjust metabolic efficiency with energetic demand. Additionally, neurons remove inefficient mitochondria through mitophagy. Neurons coordinate these processes through signalling pathways that couple energetic expenditure with energy availability. When these mechanisms fail, neurons can no longer support brain function giving rise to neuropathological states like metabolic syndromes or neurodegeneration.

DOI: https://doi.org/10.1016/j.conb.2023.102747
PLoS Genet. 2023 Jul 03. 19(7): e1010793

Yeast NDI1 reconfigures neuronal metabolism and prevents the unfolded protein response in mitochondrial complex I deficiency.

Lucy Granat, Debbra Y Knorr, Daniel C Ranson, Emma L Hamer, Ram Prosad Chakrabarty, Francesca Mattedi, Laura Fort-Aznar, Frank Hirth, Sean T Sweeney, Alessio Vagnoni, Navdeep S Chandel, Joseph M Bateman.

Mutations in subunits of the mitochondrial NADH dehydrogenase cause mitochondrial complex I deficiency, a group of severe neurological diseases that can result in death in infancy. The pathogenesis of complex I deficiency remain poorly understood, and as a result there are currently no available treatments. To better understand the underlying mechanisms, we modelled complex I deficiency in Drosophila using knockdown of the mitochondrial complex I subunit ND-75 (NDUFS1) specifically in neurons. Neuronal complex I deficiency causes locomotor defects, seizures and reduced lifespan. At the cellular level, complex I deficiency does not affect ATP levels but leads to mitochondrial morphology defects, reduced endoplasmic reticulum-mitochondria contacts and activation of the endoplasmic reticulum unfolded protein response (UPR) in neurons. Multi-omic analysis shows that complex I deficiency dramatically perturbs mitochondrial metabolism in the brain. We find that expression of the yeast non-proton translocating NADH dehydrogenase NDI1, which reinstates mitochondrial NADH oxidation but not ATP production, restores levels of several key metabolites in the brain in complex I deficiency. Remarkably, NDI1 expression also reinstates endoplasmic reticulum-mitochondria contacts, prevents UPR activation and rescues the behavioural and lifespan phenotypes caused by complex I deficiency. Together, these data show that metabolic disruption due to loss of neuronal NADH dehydrogenase activity cause UPR activation and drive pathogenesis in complex I deficiency.

DOI: https://doi.org/10.1371/journal.pgen.1010793
J Vis Exp. 2023 06 16.

An Improved Method to Isolate Mitochondrial Contact Sites.

Siavash Khosravi, Johanna Frickel, Max E Harner.

Mitochondria are present in virtually all eukaryotic cells and perform essential functions that go far beyond energy production, for instance, the synthesis of iron-sulfur clusters, lipids, or proteins, Ca2+ buffering, and the induction of apoptosis. Likewise, mitochondrial dysfunction results in severe human diseases such as cancer, diabetes, and neurodegeneration. In order to perform these functions, mitochondria have to communicate with the rest of the cell across their envelope, which consists of two membranes. Therefore, these two membranes have to interact constantly. Proteinaceous contact sites between the mitochondrial inner and outer membranes are essential in this respect. So far, several contact sites have been identified. In the method described here, Saccharomyces cerevisiae mitochondria are used to isolate contact sites and, thus, identify candidates that qualify for contact site proteins. We used this method to identify the mitochondrial contact site and cristae organizing system (MICOS) complex, one of the major contact site-forming complexes in the mitochondrial inner membrane, which is conserved from yeast to humans. Recently, we further improved this method to identify a novel contact site consisting of Cqd1 and the Por1-Om14 complex.

DOI: https://doi.org/10.3791/65444
Trends Cell Biol. 2023 Jul 05. pii: S0962-8924(23)00125-3. [Epub ahead of print]

Ferroptosis in mitochondrial cardiomyopathy.

Sofia Ahola, Thomas Langer.

  Ferroptosis is a form of necrotic cell death characterized by iron-dependent lipid peroxidation culminating in membrane rupture. Accumulating evidence links ferroptosis to multiple cardiac diseases and identifies mitochondria as important regulators of ferroptosis. Mitochondria are not only a major source of reactive oxygen species (ROS) but also counteract ferroptosis by preserving cellular redox balance and oxidative defense. Recent evidence has revealed that the mitochondrial integrated stress response limits oxidative stress and ferroptosis in oxidative phosphorylation (OXPHOS)-deficient cardiomyocytes and protects against mitochondrial cardiomyopathy. We summarize the multiple ways in which mitochondria modulate the susceptibility of cells to ferroptosis, and discuss the implications of ferroptosis for cardiomyopathies in mitochondrial disease.

Keywords:  Gpx4; ferroptosis; integrated stress response; mitochondrial cardiomyopathy

DOI:  https://doi.org/10.1016/j.tcb.2023.06.002
bioRxiv. 2023 Jun 13. pii: 2023.06.13.544768. [Epub ahead of print]

Mitochondria- and ER-associated actin are required for mitochondrial fusion.

Priya Gatti, Cara Schiavon, Uri Manor, Marc Germain.

Mitochondria play a crucial role in the regulation of cellular metabolism and signalling. Mitochondrial activity is modulated by the processes of mitochondrial fission and fusion, which are required to properly balance respiratory and metabolic functions, transfer material between mitochondria, and remove damaged or defective mitochondria. Mitochondrial fission occurs at sites of contact between the endoplasmic reticulum (ER) and mitochondria, and is dependent on the formation of mitochondria- and ER-associated actin filaments that drive the recruitment and activation of the fission GTPase DRP1. On the other hand, the role of mitochondria- and ER-associated actin filaments in mitochondrial fusion remains unknown. Here we show that preventing the formation of actin filaments on either mitochondria or the ER using organelle-targeted Disassembly-promoting, encodable Actin tools (DeActs) blocks both mitochondrial fission and fusion. We show that fusion but not fission is dependent on Arp2/3, and both fission and fusion are dependent on INF2 formin-dependent actin polymerization. Together, our work introduces a novel method for perturbing organelle-associated actin filaments, and demonstrates a previously unknown role for mitochondria- and ER-associated actin in mitochondrial fusion.

DOI: https://doi.org/10.1101/2023.06.13.544768
Cardiovasc Res. 2023 Jul 03. pii: cvad101. [Epub ahead of print]

Tissue specific differences in the assembly of mitochondrial complex I is revealed by a novel ENU mutation in ECSIT.

Thomas Nicol, Sara Falcone, Andrew Blease, Pratik Vikhe, Gabriele Civiletto, Saleh Salman Omairi, Carlo Viscomi, Ketan Patel, Paul K Potter.

AIMS: Mitochondrial complex I assembly is a multi-step process which necessitates the involvement of a variety of assembly factors and chaperones to ensure the final active enzyme is correctly assembled. The role of the assembly factor ECSIT was studied across various murine tissues to determine its role in this process and how this varied between tissues of varying energetic demands. We hypothesised that many of the known functions of ECSIT were unhindered by the introduction of an ENU induced mutation, whilst it's role in complex I assembly was affected on a tissue specific basis.METHODS AND RESULTS: Here we describe a mutation in the mitochondrial complex I assembly factor ECSIT which reveals tissue specific requirements for ECSIT in complex I assembly. Mitochondrial complex I assembly is a multi-step process dependent on assembly factors that organise and arrange the individual subunits, allowing for their incorporation into the complete enzyme complex. We have identified an ENU induced mutation in ECSIT (N209I) that exhibits a profound effect on complex I component expression and assembly in heart tissue, resulting in hypertrophic cardiomyopathy in the absence of other phenotypes. The dysfunction of complex I appears to be cardiac specific, leading to a loss of mitochondrial output as measured by Seahorse extracellular flux and various biochemical assays in heart tissue, whilst mitochondria from other tissues were unaffected.
CONCLUSIONS: These data suggest that the mechanisms underlying complex I assembly and activity may have tissue specific elements tailored to the specific demands of cells and tissues. Our data suggest that tissues with high energy demands, such as the heart, may utilise assembly factors in different ways to low energy tissues in order to improve mitochondrial output. This data have implications for the diagnosis and treatment of various disorders of mitochondrial function as well as cardiac hypertrophy with no identifiable underlying genetic cause.
TRANSLATIONAL PERSPECTIVE: Mitochondrial diseases often present as multi system disorders with far reaching implications to the health and well being of patients. Diagnoses are often undertaken by characterisation of mitochondrial function from skin or muscle biopsy, with the expectation that any affect on mitochondrial function will be recognisable in all cell types. However, this study demonstrates that mitochondrial function may differ between cell types with the involvement of tissue specific proteins or isoforms, as such, current diagnostic techniques may miss diagnoses of a more specific mitochondrial dysfunction.

DOI: https://doi.org/10.1093/cvr/cvad101
Trends Endocrinol Metab. 2023 Jul 04. pii: S1043-2760(23)00115-7. [Epub ahead of print]

Blood-based bioenergetics: a liquid biopsy of mitochondrial dysfunction in disease.

Mia S Wilkinson, Kimberly J Dunham-Snary.

  Mitochondria operate as hubs of cellular metabolism that execute important regulatory functions. Damaged/dysfunctional mitochondria are recognized as major pathogenic contributors to many common human diseases. Assessment of mitochondrial function relies upon invasive tissue biopsies; peripheral blood cells, specifically platelets, have emerged as an ideal candidate for mitochondrial function assessment. Accessibility and documented pathology-related dysfunction have prompted investigation into the role of platelets in disease, the contribution of platelet mitochondria to pathophysiology, and the capacity of platelets to reflect systemic mitochondrial health. Platelet mitochondrial bioenergetics are being investigated in neurodegenerative and cardiopulmonary diseases, infection, diabetes, and other (patho)physiological states such as aging and pregnancy. Early findings support the use of platelets as a biomarker for mitochondrial functional health.

Keywords:  bioenergetics; biomarker; metabolism; mitochondria; platelet

DOI:  https://doi.org/10.1016/j.tem.2023.06.004
Cell Death Dis. 2023 Jul 06. 14(7): 403

Pyruvate transamination and NAD biosynthesis enable proliferation of succinate dehydrogenase-deficient cells by supporting aerobic glycolysis.

Luisa Ricci, Federico Uchenna Stanley, Tanja Eberhart, Francesco Mainini, David Sumpton, Simone Cardaci.

Succinate dehydrogenase (SDH) is the mitochondrial enzyme converting succinate to fumarate in the tricarboxylic acid (TCA) cycle. SDH acts as a tumor suppressor with germline loss-of-function mutations in its encoding genes predisposing to aggressive familial neuroendocrine and renal cancer syndromes. Lack of SDH activity disrupts the TCA cycle, imposes Warburg-like bioenergetic features, and commits cells to rely on pyruvate carboxylation for anabolic needs. However, the spectrum of metabolic adaptations enabling SDH-deficient tumors to cope with a dysfunctional TCA cycle remains largely unresolved. By using previously characterized Sdhb-deleted kidney mouse cells, here we found that SDH deficiency commits cells to rely on mitochondrial glutamate-pyruvate transaminase (GPT2) activity for proliferation. We showed that GPT2-dependent alanine biosynthesis is crucial to sustain reductive carboxylation of glutamine, thereby circumventing the TCA cycle truncation determined by SDH loss. By driving the reductive TCA cycle anaplerosis, GPT2 activity fuels a metabolic circuit maintaining a favorable intracellular NAD+ pool to enable glycolysis, thus meeting the energetic demands of SDH-deficient cells. As a metabolic syllogism, SDH deficiency confers sensitivity to NAD+ depletion achieved by pharmacological inhibition of nicotinamide phosphoribosyltransferase (NAMPT), the rate-limiting enzyme of the NAD+ salvage pathway. Beyond identifying an epistatic functional relationship between two metabolic genes in the control of SDH-deficient cell fitness, this study disclosed a metabolic strategy to increase the sensitivity of tumors to interventions limiting NAD availability.

DOI: https://doi.org/10.1038/s41419-023-05927-5
Cell Stress Chaperones. 2023 Jul 05.

Novel insights into the role of mitochondria in diabetic cardiomyopathy: molecular mechanisms and potential treatments.

Fumin Zhi, Qian Zhang, Li Liu, Xing Chang, Hongtao Xu.

  Diabetic cardiomyopathy describes decreased myocardial function in diabetic patients in the absence of other heart diseases such as myocardial ischemia and hypertension. Recent studies have defined numerous molecular interactions and signaling events that may account for deleterious changes in mitochondrial dynamics and functions influenced by hyperglycemic stress. A metabolic switch from glucose to fatty acid oxidation to fuel ATP synthesis, mitochondrial oxidative injury resulting from increased mitochondrial ROS production and decreased antioxidant capacity, enhanced mitochondrial fission and defective mitochondrial fusion, impaired mitophagy, and blunted mitochondrial biogenesis are major signatures of mitochondrial pathologies during diabetic cardiomyopathy. This review describes the molecular alterations underlying mitochondrial abnormalities associated with hyperglycemia and discusses their influence on cardiomyocyte viability and function. Based on basic research findings and clinical evidence, diabetic treatment standards and their impact on mitochondrial function, as well as mitochondria-targeted therapies of potential benefit for diabetic cardiomyopathy patients, are also summarized.

Keywords:  Diabetic cardiomyopathy; Mitochondria; Mitochondrial biogenesis; Mitochondrial fission/fusion; Mitochondrial metabolism; Mitochondrial oxidative stress; Mitophagy

DOI:  https://doi.org/10.1007/s12192-023-01361-w
Mol Genet Metab. 2023 Jun 22. pii: S1096-7192(23)00260-3. [Epub ahead of print]139(4): 107630

Phenotypic, molecular, and functional characterization of COQ7-related primary CoQ10 deficiency: Hypomorphic variants and two distinct disease entities.

Parith Wongkittichote, Maria Laura Duque Lasio, Martina Magistrati, Sheel Pathak, Brooke Sample, Daniel Rocha Carvalho, Adriana Banzzatto Ortega, Matheus Augusto Araújo Castro, Claudio M de Gusmao, Tomi L Toler, Emanuele Bellacchio, Cristina Dallabona, Marwan Shinawi.

  Primary coenzyme Q10 (CoQ10) deficiency is a group of inborn errors of metabolism caused by defects in CoQ10 biosynthesis. Biallelic pathogenic variants in COQ7, encoding mitochondrial 5-demethoxyubiquinone hydroxylase, have been reported in nine patients from seven families. We identified five new patients with COQ7-related primary CoQ10 deficiency, performed clinical assessment of the patients, and studied the functional effects of current and previously reported COQ7 variants and potential treatment options. The main clinical features included a neonatal-onset presentation with severe neuromuscular, cardiorespiratory and renal involvement and a late-onset disease presenting with progressive neuropathy, lower extremity weakness, abnormal gait, and variable developmental delay. Baker's yeast orthologue of COQ7, CAT5, is required for growth on oxidative carbon sources and cat5Δ strain demonstrates oxidative growth defect. Expression of wild-type CAT5 could completely rescue the defect; however, yeast CAT5 harboring equivalent human pathogenic variants could not. Interestingly, cat5Δ yeast harboring p.Arg57Gln (equivalent to human p.Arg54Gln), p.Arg112Trp (equivalent to p.Arg107Trp), p.Ile69Asn (equivalent to p.Ile66Asn) and combination of p.Lys108Met and p.Leu116Pro (equivalent to the complex allele p.[Thr103Met;Leu111Pro]) partially rescued the growth defects, indicating these variants are hypomorphic alleles. Supplementation with 2,4 dihydroxybenzoic acid (2,4-diHB) rescued the growth defect of both the leaky and severe mutants. Overexpression of COQ8 and 2,4-diHB supplementation synergistically restored oxidative growth and respiratory defect. Overall, we define two distinct disease presentations of COQ7-related disorder with emerging genotype-phenotype correlation and validate the use of the yeast model for functional studies of COQ7 variants.

Keywords:  Functional study; Hereditary neuropathy; Mitochondrial disorder; Primary CoQ10 deficiency; Yeast model

DOI:  https://doi.org/10.1016/j.ymgme.2023.107630
Cell Death Discov. 2023 Jul 01. 9(1): 217

Rapid degeneration of iPSC-derived motor neurons lacking Gdap1 engages a mitochondrial-sustained innate immune response.

Marian León, Javier Prieto, María Micaela Molina-Navarro, Francisco García-García, Manuela Barneo-Muñoz, Xavier Ponsoda, Rosana Sáez, Francesc Palau, Joaquín Dopazo, Juan Carlos Izpisua Belmonte, Josema Torres.

Charcot-Marie-Tooth disease is a chronic hereditary motor and sensory polyneuropathy targeting Schwann cells and/or motor neurons. Its multifactorial and polygenic origin portrays a complex clinical phenotype of the disease with a wide range of genetic inheritance patterns. The disease-associated gene GDAP1 encodes for a mitochondrial outer membrane protein. Mouse and insect models with mutations in Gdap1 have reproduced several traits of the human disease. However, the precise function in the cell types affected by the disease remains unknown. Here, we use induced-pluripotent stem cells derived from a Gdap1 knockout mouse model to better understand the molecular and cellular phenotypes of the disease caused by the loss-of-function of this gene. Gdap1-null motor neurons display a fragile cell phenotype prone to early degeneration showing (1) altered mitochondrial morphology, with an increase in the fragmentation of these organelles, (2) activation of autophagy and mitophagy, (3) abnormal metabolism, characterized by a downregulation of Hexokinase 2 and ATP5b proteins, (4) increased reactive oxygen species and elevated mitochondrial membrane potential, and (5) increased innate immune response and p38 MAP kinase activation. Our data reveals the existence of an underlying Redox-inflammatory axis fueled by altered mitochondrial metabolism in the absence of Gdap1. As this biochemical axis encompasses a wide variety of druggable targets, our results may have implications for developing therapies using combinatorial pharmacological approaches and improving therefore human welfare. A Redox-immune axis underlying motor neuron degeneration caused by the absence of Gdap1. Our results show that Gdap1-/- motor neurons have a fragile cellular phenotype that is prone to degeneration. Gdap1-/- iPSCs differentiated into motor neurons showed an altered metabolic state: decreased glycolysis and increased OXPHOS. These alterations may lead to hyperpolarization of mitochondria and increased ROS levels. Excessive amounts of ROS might be the cause of increased mitophagy, p38 activation and inflammation as a cellular response to oxidative stress. The p38 MAPK pathway and the immune response may, in turn, have feedback mechanisms, leading to the induction of apoptosis and senescence, respectively. CAC, citric acid cycle; ETC, electronic transport chain; Glc, glucose; Lac, lactate; Pyr, pyruvate.

DOI: https://doi.org/10.1038/s41420-023-01531-w
Cureus. 2023 Jun;15(6): e39812

Mitochondrial Deoxyribonucleic Acid (mtDNA), Maternal Inheritance, and Their Role in the Development of Cancers: A Scoping Review.

Sabitha Vadakedath, Venkataramana Kandi, Jayashankar Ca, Swapna Vijayan, Kushal C Achyut, Shivani Uppuluri, Praveen Kumar K Reddy, Monish Ramesh, P Pavan Kumar.

  Mitochondrial DNA (mtDNA) is a small, circular, double-stranded DNA inherited from the mother during fertilization. Evolutionary evidence supported by the endosymbiotic theory identifies mitochondria as an organelle that could have descended from prokaryotes. This may be the reason for the independent function and inheritance pattern shown by mtDNA. The unstable nature of mtDNA due to the lack of protective histones, and effective repair systems make it more vulnerable to mutations. The mtDNA and its mutations could be maternally inherited thereby predisposing the offspring to various cancers like breast and ovarian cancers among others. Although mitochondria are considered heteroplasmic wherein variations among the multiple mtDNA genomes are noticed, mothers can have mitochondrial populations that are homoplasmic for a given mitochondrial mutation. Homoplasmic mitochondrial mutations may be transmitted to all maternal offspring. However, due to the complex interplay between the mitochondrial and nuclear genomes, it is often difficult to predict disease outcomes, even with homoplasmic mitochondrial populations. Heteroplasmic mtDNA mutations can be maternally inherited, but the proportion of mutated alleles differs markedly between offspring within one generation. This led to the genetic bottleneck hypothesis, explaining the rapid changes in allele frequency witnessed during the transmission of mtDNA from one generation to the next. Although a physical reduction in mtDNA has been demonstrated in several species, a comprehensive understanding of the molecular mechanisms is yet to be demonstrated. Despite initially thought to be limited to the germline, there is evidence that blockages exist in different cell types during development, perhaps explaining why different tissues in the same organism contain different levels of mutated mtDNA. In this review, we comprehensively discuss the potential mechanisms through which mtDNA undergoes mutations and the maternal mode of transmission that contributes to the development of tumors, especially breast and ovarian cancers.

Keywords:  cancer; endosymbiotic theory; inheritance; mitochondrial dna; mtdna

DOI:  https://doi.org/10.7759/cureus.39812
Toxicol Res. 2023 Jul;39(3): 333-339

Oxygen consumption rate to evaluate mitochondrial dysfunction and toxicity in cardiomyocytes.

Dohee Ahn, Ryeo-Eun Go, Kyung-Chul Choi.

  The increase in the types and complexity of diseases has led to significant advances in diagnostic techniques and the availability of effective therapies. Recent studies have focused on the role of mitochondrial dysfunction in the pathogenesis of cardiovascular diseases (CVDs). Mitochondria are important organelles in cells that generate energy. Besides the production of adenosine triphosphate (ATP), the energy currency of cells, mitochondria are also involved in thermogenesis, control of intracellular calcium ions (Ca2+), apoptosis, regulation of reactive oxygen species (ROS), and inflammation. Mitochondrial dysfunction has been implicated in several diseases including cancer, diabetes, some genetic diseases, and neurogenerative and metabolic diseases. Furthermore, the cardiomyocytes of the heart are rich in mitochondria due to the large energy requirement for optimal cardiac function. One of the main causes of cardiac tissue injuries is believed to be mitochondrial dysfunction, which occurs via complicated pathways which have not yet been completely elucidated. There are various types of mitochondrial dysfunction including mitochondrial morphological change, unbalanced levels of substances to maintain mitochondria, mitochondrial damage by drugs, and mitochondrial deletion and synthesis errors. Most of mitochondrial dysfunctions are linked with symptoms and diseases, thus we focus on parts of mitochondrial dysfunction about fission and fusion in cardiomyocytes, and ways to understand the mechanism of cardiomyocyte damage by detecting oxygen consumption levels in the mitochondria.

Keywords:  Cardiomyocytes; Mitochondrial dysfunction; Mitochondrial fission; Oxygen consumption rate

DOI:  https://doi.org/10.1007/s43188-023-00183-3
Free Radic Biol Med. 2023 Jul 05. pii: S0891-5849(23)00511-7. [Epub ahead of print]

DMT1 differentially regulates mitochondrial complex activities to reduce glutathione loss and mitigate ferroptosis.

Qing Tan, Xiaoqian Zhang, Shuxiang Li, Wenbin Liu, Jiaqi Yan, Siqi Wang, Feng Cui, Dan Li, Jun Li.

  Mitochondria are vital for energy production and Redox homeostasis, yet knowledge of relevant mechanisms remains limited. Here, through a genome-wide CRISPR-Cas9 knockout screening, we have identified DMT1 as a major regulator of mitochondria membrane potential. Our findings demonstrate that DMT1 deficiency increased the activity of mitochondrial complex I and reduced that of complex III. Enhanced complex I activity leads to increased NAD+ production, which activates IDH2 by promoting its deacetylation via SIRT3, This results in higher levels of NADPH and GSH, which improve antioxidant capacity during Erastin-induced ferroptosis. Meanwhile, loss of complex III activity impairs mitochondrial biogenesis and promotes mitophagy, contributing to suppression of ferroptosis. Thus, DMT1 differentially regulates activities of mitochondrial complex I and III to cooperatly suppress Erastin-induced ferroptosis. Furthermore, NMN, an alternative method of increasing mitochondrial NAD+, exhibits similar protective effects against ferroptosis by boosting GSH in a manner similar to DMT1 deficiency, shedding a light on potential therapeutic strategy for ferroptosis-related pathologies.

Keywords:  DMT1; Ferroptosis; Mitochondria NAD(+); REDOX homeostasis

DOI:  https://doi.org/10.1016/j.freeradbiomed.2023.06.023
STAR Protoc. 2023 Jul 01. pii: S2666-1667(23)00375-1. [Epub ahead of print]4(3): 102408

Quantifying mitochondrial redox and bilirubin content in intact primary hepatocytes of obese mice using fluorescent reporters.

Thomas Belmas, Marc Liesa, Michaël Shum.

  Assessing the physiological role of H2O2 requires sensitive techniques to quantify H2O2 and antioxidants in live cells. Here, we present a protocol to assess the mitochondrial redox state and unconjugated bilirubin levels in intact live primary hepatocytes from obese mice. We described steps to quantify H2O2, GSSG/GSH, and bilirubin content in the mitochondrial matrix and the cytosol using the fluorescent reporters roGFP2-ORP1, GRX1-roGFP2, and UnaG, respectively. We detail hepatocyte isolation, plating, and transduction and live-cell imaging using a high-content imaging reader. For complete details on the use and execution of this protocol, please refer to Shum et al.1.

Keywords:  Cell Biology; Metabolism; Molecular Biology

DOI:  https://doi.org/10.1016/j.xpro.2023.102408
Trends Pharmacol Sci. 2023 Jul 04. pii: S0165-6147(23)00133-5. [Epub ahead of print]

Mitochondrial quality control: prime targets for antiviral therapy?

Yijin Wang, Peicong Ji, Qiuwei Pan.

Mitochondrial quality control (MQC) plays a crucial role in maintaining mitochondrial health. Mitochondrial dynamics and mitophagy are two intricate processes of the MQC machinery acting at the organelle level to orchestrate mitochondrial homeostasis. Here, we discuss how viruses perturb these two processes to facilitate their infections and emphasize the rationale and challenges of therapeutically targeting MQC for treating viral diseases.

DOI: https://doi.org/10.1016/j.tips.2023.06.006
JIMD Rep. 2023 Jul;64(4): 261-264

Postmortem diagnosis of very long chain acyl-CoA dehydrogenase (VLCAD) deficiency in a neonate with sudden cardiac death.

Prapti Singh, Deirdre Amaro, Olugbemisola Obi, Fnu Kiran, Erin Hediger, Tomi L Toler, Patricia I Dickson, Dorothy K Grange.

  Very long chain acyl-CoA dehydrogenase (VLCAD) deficiency is an autosomal recessive long chain fatty acid β-oxidation disorder with a variable clinical spectrum, ranging from an acute neonatal presentation with cardiac and hepatic failure to childhood or adult onset of symptoms with hepatomegaly or rhabdomyolysis provoked by illness or exertion. Neonatal cardiac arrest or sudden unexpected death can be the presenting phenotype in some patients, emphasizing the importance of early clinical suspicion and intervention. We report a patient who had a cardiac arrest and died at one day of age. Following her death, the newborn screen reported biochemical evidence of VLCAD deficiency, which was confirmed with pathologic findings at autopsy and by molecular genetic testing.

Keywords:  cardiac arrest; newborn screening; very long chain acyl CoA dehydrogenase (VLCAD) deficiency

DOI:  https://doi.org/10.1002/jmd2.12365
EMBO Rep. 2023 Jul 04. e57499

ER-mitochondria contacts and cholesterol metabolism are disrupted by disease-associated tau protein.

Leonora Szabo, Nadia Cummins, Paolo Paganetti, Alex Odermatt, Andreas Papassotiropoulos, Celeste Karch, Jürgen Götz, Anne Eckert, Amandine Grimm.

  Abnormal tau protein impairs mitochondrial function, including transport, dynamics, and bioenergetics. Mitochondria interact with the endoplasmic reticulum (ER) via mitochondria-associated ER membranes (MAMs), which coordinate and modulate many cellular functions, including mitochondrial cholesterol metabolism. Here, we show that abnormal tau loosens the association between the ER and mitochondria in vivo and in vitro. Especially, ER-mitochondria interactions via vesicle-associated membrane protein-associated protein (VAPB)-protein tyrosine phosphatase-interacting protein 51 (PTPIP51) are decreased in the presence of abnormal tau. Disruption of MAMs in cells with abnormal tau alters the levels of mitochondrial cholesterol and pregnenolone, indicating that conversion of cholesterol into pregnenolone is impaired. Opposite effects are observed in the absence of tau. Besides, targeted metabolomics reveals overall alterations in cholesterol-related metabolites by tau. The inhibition of GSK3β decreases abnormal tau hyperphosphorylation and increases VAPB-PTPIP51 interactions, restoring mitochondrial cholesterol and pregnenolone levels. This study is the first to highlight a link between tau-induced impairments in the ER-mitochondria interaction and cholesterol metabolism.

Keywords:  GSK3β; cholesterol; endoplasmic reticulum; mitochondria; tau protein

DOI:  https://doi.org/10.15252/embr.202357499
iScience. 2023 Jul 21. 26(7): 107014

Docking and stability defects in mitofusin highlight the proteasome as a potential therapeutic target.

Ira Buntenbroich, Vincent Anton, Daniel Perez-Hernandez, Tânia Simões, Felix Gaedke, Astrid Schauss, Gunnar Dittmar, Jan Riemer, Mafalda Escobar-Henriques.

  Defects in mitochondrial fusion are at the base of many diseases. Mitofusins power membrane-remodeling events via self-interaction and GTP hydrolysis. However, how exactly mitofusins mediate fusion of the outer membrane is still unclear. Structural studies enable tailored design of mitofusin variants, providing valuable tools to dissect this stepwise process. Here, we found that the two cysteines conserved between yeast and mammals are required for mitochondrial fusion, revealing two novel steps of the fusion cycle. C381 is dominantly required for the formation of the trans-tethering complex, before GTP hydrolysis. C805 allows stabilizing the Fzo1 protein and the trans-tethering complex, just prior to membrane fusion. Moreover, proteasomal inhibition rescued Fzo1 C805S levels and membrane fusion, suggesting a possible application for clinically approved drugs. Together, our study provides insights into how assembly or stability defects in mitofusins might cause mitofusin-associated diseases and uncovers potential therapeutic intervention by proteasomal inhibition.

Keywords:  Biological sciences; Cell biology; Genetics; Molecular biology

DOI:  https://doi.org/10.1016/j.isci.2023.107014
Nat Cell Biol. 2023 Jul 03.

Arf1 coordinates fatty acid metabolism and mitochondrial homeostasis.

Ludovic Enkler, Viktoria Szentgyörgyi, Mirjam Pennauer, Cristina Prescianotto-Baschong, Isabelle Riezman, Aneta Wiesyk, Reut Ester Avraham, Martin Spiess, Einat Zalckvar, Roza Kucharczyk, Howard Riezman, Anne Spang.

Lipid mobilization through fatty acid β-oxidation is a central process essential for energy production during nutrient shortage. In yeast, this catabolic process starts in the peroxisome from where β-oxidation products enter mitochondria and fuel the tricarboxylic acid cycle. Little is known about the physical and metabolic cooperation between these organelles. Here we found that expression of fatty acid transporters and of the rate-limiting enzyme involved in β-oxidation is decreased in cells expressing a hyperactive mutant of the small GTPase Arf1, leading to an accumulation of fatty acids in lipid droplets. Consequently, mitochondria became fragmented and ATP synthesis decreased. Genetic and pharmacological depletion of fatty acids phenocopied the arf1 mutant mitochondrial phenotype. Although β-oxidation occurs in both mitochondria and peroxisomes in mammals, Arf1's role in fatty acid metabolism is conserved. Together, our results indicate that Arf1 integrates metabolism into energy production by regulating fatty acid storage and utilization, and presumably organelle contact sites.

DOI: https://doi.org/10.1038/s41556-023-01180-2
Elife. 2023 Jul 05. pii: e83385. [Epub ahead of print]12

Mitochondrial MICOS complex genes, implicated in hypoplastic left heart syndrome, maintain cardiac contractility and actomyosin integrity.

Katja Birker, Shuchao Ge, Natalie J Kirkland, Jeanne L Theis, James Marchant, Zachary C Fogarty, Maria A Missinato, Sreehari Kalvakuri, Paul Grossfeld, Adam J Engler, Karen Ocorr, Timothy J Nelson, Alexandre R Colas, Timothy M Olson, Georg Vogler, Rolf Bodmer.

  Hypoplastic left heart syndrome (HLHS) is a severe congenital heart disease (CHD) with a likely oligogenic etiology, but our understanding of the genetic complexities and pathogenic mechanisms leading to HLHS is limited. We therefore performed whole genome sequencing (WGS) on a large cohort of HLHS patients and their families to identify candidate genes that were then tested in Drosophila heart model for functional and structural requirements. Bioinformatic analysis of WGS data from an index family comprised of a HLHS proband born to consanguineous parents and postulated to have a homozygous recessive disease etiology, prioritized 9 candidate genes with rare, predicted damaging homozygous variants. Of the candidate HLHS gene homologs tested, cardiac-specific knockdown (KD) of mitochondrial MICOS complex subunit Chchd3/6 resulted in drastically compromised heart contractility, diminished levels of sarcomeric actin and myosin, reduced cardiac ATP levels, and mitochondrial fission-fusion defects. Interestingly, these heart defects were similar to those inflicted by cardiac KD of ATP synthase subunits of the electron transport chain (ETC), consistent with the MICOS complex's role in maintaining cristae morphology and ETC complex assembly. Analysis of 183 genomes of HLHS patient-parent trios revealed five additional HLHS probands with rare, predicted damaging variants in CHCHD3 or CHCHD6. Hypothesizing an oligogenic basis for HLHS, we tested 60 additional prioritized candidate genes in these cases for genetic interactions with Chchd3/6 in sensitized fly hearts. Moderate KD of Chchd3/6 in combination with Cdk12 (activator of RNA polymerase II), RNF149 (goliath, gol, E3 ubiquitin ligase), or SPTBN1 (β Spectrin, β-Spec, scaffolding protein) caused synergistic heart defects, suggesting the potential involvement of a diverse set of pathways in HLHS. Further elucidation of novel candidate genes and genetic interactions of potentially disease-contributing pathways is expected to lead to a better understanding of HLHS and other CHDs.

Keywords:  D. melanogaster; genetics; genomics; human

DOI:  https://doi.org/10.7554/eLife.83385
bioRxiv. 2023 Jun 17. pii: 2023.06.17.545435. [Epub ahead of print]

The mitochondrial calcium uniporter transports Ca 2+ via a ligand-relay mechanism.

Connie Chan, Chen-Ching Yuan, Jason G McCoy, Patrick S Ward, Zenon Grabarek.

The mitochondrial calcium uniporter (mtCU) is a multicomponent Ca 2+ -specific channel that imparts mitochondria with the capacity to sense the cytosolic calcium signals. The metazoan mtCU comprises the pore-forming subunit MCU and the essential regulator EMRE, arranged in a tetrameric channel complex, and the Ca 2+ sensing peripheral proteins MICU1-3. The mechanism of mitochondrial Ca 2+ uptake by mtCU and its regulation is poorly understood. Our analysis of MCU structure and sequence conservation, combined with molecular dynamics simulations, mutagenesis, and functional studies, led us to conclude that the Ca 2+ conductance of MCU is driven by a ligand-relay mechanism, which depends on stochastic structural fluctuations in the conserved DxxE sequence. In the tetrameric structure of MCU, the four glutamate side chains of DxxE (the E-ring) chelate Ca 2+ directly in a high-affinity complex (site 1), which blocks the channel. The four glutamates can also switch to a hydrogen bond-mediated interaction with an incoming hydrated Ca 2+ transiently sequestered within the D-ring of DxxE (site 2), thus releasing the Ca 2+ bound at site 1. This process depends critically on the structural flexibility of DxxE imparted by the adjacent invariant Pro residue. Our results suggest that the activity of the uniporter can be regulated through the modulation of local structural dynamics. A preliminary account of this work was presented at the 67 th Annual Meeting of the Biophysical Society in San Diego, CA, February 18-22, 2023.

DOI: https://doi.org/10.1101/2023.06.17.545435
Cell Chem Biol. 2023 Jun 22. pii: S2451-9456(23)00186-1. [Epub ahead of print]

Proximity-labeling chemoproteomics defines the subcellular cysteinome and inflammation-responsive mitochondrial redoxome.

Tianyang Yan, Ashley R Julio, Miranda Villanueva, Anthony E Jones, Andréa B Ball, Lisa M Boatner, Alexandra C Turmon, Kaitlyn B Nguyễn, Stephanie L Yen, Heta S Desai, Ajit S Divakaruni, Keriann M Backus.

  Proteinaceous cysteines function as essential sensors of cellular redox state. Consequently, defining the cysteine redoxome is a key challenge for functional proteomic studies. While proteome-wide inventories of cysteine oxidation state are readily achieved using established, widely adopted proteomic methods such as OxICAT, Biotin Switch, and SP3-Rox, these methods typically assay bulk proteomes and therefore fail to capture protein localization-dependent oxidative modifications. Here we establish the local cysteine capture (Cys-LoC) and local cysteine oxidation (Cys-LOx) methods, which together yield compartment-specific cysteine capture and quantitation of cysteine oxidation state. Benchmarking of the Cys-LoC method across a panel of subcellular compartments revealed more than 3,500 cysteines not previously captured by whole-cell proteomic analysis. Application of the Cys-LOx method to LPS-stimulated immortalized murine bone marrow-derived macrophages (iBMDM), revealed previously unidentified, mitochondrially localized cysteine oxidative modifications upon pro-inflammatory activation, including those associated with oxidative mitochondrial metabolism.

Keywords:  TurboID; chemoproteomics; cysteine; cysteine oxidation; lipopolysaccharide; macrophages; mitochondria; proximity labeling

DOI:  https://doi.org/10.1016/j.chembiol.2023.06.008
Nat Med. 2023 Jul 03.

Multi-omics for better and faster rare disease diagnosis.

DOI: https://doi.org/10.1038/s41591-023-02417-1
Genome Biol. 2023 07 03. 24(1): 147

An Atlas of Variant Effects to understand the genome at nucleotide resolution.

Douglas M Fowler, David J Adams, Anna L Gloyn, William C Hahn, Debora S Marks, Lara A Muffley, James T Neal, Frederick P Roth, Alan F Rubin, Lea M Starita, Matthew E Hurles.

  Sequencing has revealed hundreds of millions of human genetic variants, and continued efforts will only add to this variant avalanche. Insufficient information exists to interpret the effects of most variants, limiting opportunities for precision medicine and comprehension of genome function. A solution lies in experimental assessment of the functional effect of variants, which can reveal their biological and clinical impact. However, variant effect assays have generally been undertaken reactively for individual variants only after and, in most cases long after, their first observation. Now, multiplexed assays of variant effect can characterise massive numbers of variants simultaneously, yielding variant effect maps that reveal the function of every possible single nucleotide change in a gene or regulatory element. Generating maps for every protein encoding gene and regulatory element in the human genome would create an 'Atlas' of variant effect maps and transform our understanding of genetics and usher in a new era of nucleotide-resolution functional knowledge of the genome. An Atlas would reveal the fundamental biology of the human genome, inform human evolution, empower the development and use of therapeutics and maximize the utility of genomics for diagnosing and treating disease. The Atlas of Variant Effects Alliance is an international collaborative group comprising hundreds of researchers, technologists and clinicians dedicated to realising an Atlas of Variant Effects to help deliver on the promise of genomics.

Keywords:  Functional genomics; Genome interpretation; Global alliance; Multiplexed assay of variant effect; Saturation mutagenesis; Variant effect

DOI:  https://doi.org/10.1186/s13059-023-02986-x
Biochim Biophys Acta Mol Basis Dis. 2023 Jul 04. pii: S0925-4439(23)00168-0. [Epub ahead of print] 166802

Mitochondrial dysfunction in the offspring of obese mothers and it's transmission through damaged oocyte mitochondria: Integration of mechanisms.

A L Elías-López, O Vázquez-Mena, A N Sferruzzi-Perri.

  In vivo and in vitro studies demonstrate that mitochondria in the oocyte, are susceptible to damage by suboptimal pre/pregnancy conditions, such as obesity. These suboptimal conditions have been shown to induce mitochondrial dysfunction (MD) in multiple tissues of the offspring, suggesting that mitochondria of oocytes that pass from mother to offspring, can carry information that can programme mitochondrial and metabolic dysfunction of the next generation. They also suggest that transmission of MD could increase the risk of obesity and other metabolic diseases in the population inter- and trans-generationally. In this review, we examined whether MD observed in offspring tissues of high energetic demand, is the result of the transmission of damaged mitochondria from obese mothers' oocytes to the offspring. The contribution of genome-independent mechanisms (namely mitophagy) in this transmission were also explored. Finally, potential interventions aimed at improving oocyte/embryo health were investigated, to see if they may provide an opportunity to halter the generational effects of MD.

Keywords:  Downregulated mitophagy; Maternal obesity; Metabolic dysfunction; Milpa diet; Mitochondrial metabolic dysfunction; Mitophagy; Offspring mitochondrial dysfunction; Oocyte mitochondria; Preconceptional interventions; Traditional diet

DOI:  https://doi.org/10.1016/j.bbadis.2023.166802
Mitochondrion. 2023 Jul 05. pii: S1567-7249(23)00056-9. [Epub ahead of print]

N-acetylcysteine modulates rotenone-induced mitochondrial Complex I dysfunction in THP-1 cells.

Winston Tse-Hou Kwok, Haejin Angela Kwak, Ana Cristina Andreazza.

  Mitochondrial Complex I dysfunction and oxidative stress have been part of the pathophysiology of several diseases ranging from mitochondrial disease to chronic diseases such as diabetes, mood disorders and Parkinson's Disease. Nonetheless, to investigate the potential of mitochondria-targeted therapeutic strategies for these conditions, there is a need further our understanding on how cells respond and adapt in the presence of Complex I dysfunction. In this study, we used low doses of rotenone, a classical inhibitor of mitochondrial complex I, to mimic peripheral mitochondrial dysfunction in THP-1 cells, a human monocytic cell line, and explored the effects of N-acetylcysteine on preventing this rotenone-induced mitochondrial dysfunction. Our results show that in THP-1 cells, rotenone exposure led to increases in mitochondrial superoxide, levels of cell-free mitochondrial DNA, and protein levels of the NDUFS7 subunit. N-acetylcysteine (NAC) pre-treatment ameliorated the rotenone-induced increase of cell-free mitochondrial DNA and NDUFS7 protein levels, but not mitochondrial superoxide. Furthermore, rotenone exposure did not affect protein levels of the NDUFV1 subunit but induced NDUFV1 glutathionylation. In summary, NAC may help to mitigate the effects of rotenone on Complex I and preserve the normal function of mitochondria in THP-1 cells.

Keywords:  Cell model; Complex I; Mitochondrial; N-acetylcysteine; Reactive oxygen species; Rotenone

DOI:  https://doi.org/10.1016/j.mito.2023.07.001
Nat Aging. 2023 Jul 03.

Spatial mapping of cellular senescence: emerging challenges and opportunities.

Aditi U Gurkar, Akos A Gerencser, Ana L Mora, Andrew C Nelson, Anru R Zhang, Anthony B Lagnado, Archibald Enninful, Christopher Benz, David Furman, Delphine Beaulieu, Diana Jurk, Elizabeth L Thompson, Fei Wu, Fernanda Rodriguez, Grant Barthel, Hao Chen, Hemali Phatnani, Indra Heckenbach, Jeffrey H Chuang, Jeremy Horrell, Joana Petrescu, Jonathan K Alder, Jun Hee Lee, Laura J Niedernhofer, Manoj Kumar, Melanie Königshoff, Marta Bueno, Miiko Sokka, Morten Scheibye-Knudsen, Nicola Neretti, Oliver Eickelberg, Peter D Adams, Qianjiang Hu, Quan Zhu, Rebecca A Porritt, Runze Dong, Samuel Peters, Stella Victorelli, Thomas Pengo, Timur Khaliullin, Vidyani Suryadevara, Xiaonan Fu, Ziv Bar-Joseph, Zhicheng Ji, João F Passos.

Cellular senescence is a well-established driver of aging and age-related diseases. There are many challenges to mapping senescent cells in tissues such as the absence of specific markers and their relatively low abundance and vast heterogeneity. Single-cell technologies have allowed unprecedented characterization of senescence; however, many methodologies fail to provide spatial insights. The spatial component is essential, as senescent cells communicate with neighboring cells, impacting their function and the composition of extracellular space. The Cellular Senescence Network (SenNet), a National Institutes of Health (NIH) Common Fund initiative, aims to map senescent cells across the lifespan of humans and mice. Here, we provide a comprehensive review of the existing and emerging methodologies for spatial imaging and their application toward mapping senescent cells. Moreover, we discuss the limitations and challenges inherent to each technology. We argue that the development of spatially resolved methods is essential toward the goal of attaining an atlas of senescent cells.

DOI: https://doi.org/10.1038/s43587-023-00446-6
iScience. 2023 Jul 21. 26(7): 107136

Glutamine supplementation reverses manganese neurotoxicity by eliciting the mitochondrial unfolded protein response.

Shixuan Zhang, Junrou Zhang, Luli Wu, Li Chen, Piye Niu, Jie Li.

  Excessive exposure to manganese (Mn) can cause neurological abnormalities, but the mechanism of Mn neurotoxicity remains unclear. Previous studies have shown that abnormal mitochondrial metabolism is a crucial mechanism underlying Mn neurotoxicity. Therefore, improving neurometabolic in neuronal mitochondria may be a potential therapy for Mn neurotoxicity. Here, single-cell sequencing revealed that Mn affected mitochondrial neurometabolic pathways and unfolded protein response in zebrafish dopaminergic neurons. Metabolomic analysis indicated that Mn inhibited the glutathione metabolic pathway in human neuroblastoma (SH-SY5Y) cells. Mechanistically, Mn exposure inhibited glutathione (GSH) and mitochondrial unfolded protein response (UPRmt). Furthermore, supplementation with glutamine (Gln) can effectively increase the concentration of GSH and triggered UPRmt which can alleviate mitochondrial dysfunction and counteract the neurotoxicity of Mn. Our findings highlight that UPRmt is involved in Mn-induced neurotoxicity and glutathione metabolic pathway affects UPRmt to reverse Mn neurotoxicity. In addition, Gln supplementation may have potential therapeutic benefits for Mn-related neurological disorders.

Keywords:  Biochemistry; Cell biology; Metabolomics; Toxicology; Transcriptomics

DOI:  https://doi.org/10.1016/j.isci.2023.107136
EMBO J. 2023 Jul 06. e113258

NRF1-mediated mitochondrial biogenesis antagonizes innate antiviral immunity.

Tian Zhao, Jiaojiao Zhang, Hong Lei, Yuanyuan Meng, Hongcheng Cheng, Yanping Zhao, Guangfeng Geng, Chenglong Mu, Linbo Chen, Qiangqiang Liu, Qian Luo, Chuanmei Zhang, Yijia Long, Jingyi Su, Yinhao Wang, Zhuoya Li, Jiaxing Sun, Guo Chen, Yanjun Li, Xudong Liao, Yingli Shang, Gang Hu, Quan Chen, Yushan Zhu.

  Mitochondrial biogenesis is the process of generating new mitochondria to maintain cellular homeostasis. Here, we report that viruses exploit mitochondrial biogenesis to antagonize innate antiviral immunity. We found that nuclear respiratory factor-1 (NRF1), a vital transcriptional factor involved in nuclear-mitochondrial interactions, is essential for RNA (VSV) or DNA (HSV-1) virus-induced mitochondrial biogenesis. NRF1 deficiency resulted in enhanced innate immunity, a diminished viral load, and morbidity in mice. Mechanistically, the inhibition of NRF1-mediated mitochondrial biogenesis aggravated virus-induced mitochondrial damage, promoted the release of mitochondrial DNA (mtDNA), increased the production of mitochondrial reactive oxygen species (mtROS), and activated the innate immune response. Notably, virus-activated kinase TBK1 phosphorylated NRF1 at Ser318 and thereby triggered the inactivation of the NRF1-TFAM axis during HSV-1 infection. A knock-in (KI) strategy that mimicked TBK1-NRF1 signaling revealed that interrupting the TBK1-NRF1 connection ablated mtDNA release and thereby attenuated the HSV-1-induced innate antiviral response. Our study reveals a previously unidentified antiviral mechanism that utilizes a NRF1-mediated negative feedback loop to modulate mitochondrial biogenesis and antagonize innate immune response.

Keywords:  NRF1; TBK1; innate immunity; mitochondrial biogenesis

DOI:  https://doi.org/10.15252/embj.2022113258
Nat Commun. 2023 Jul 07. 14(1): 4013

Expanded vacuum-stable gels for multiplexed high-resolution spatial histopathology.

Yunhao Bai, Bokai Zhu, John-Paul Oliveria, Bryan J Cannon, Dorien Feyaerts, Marc Bosse, Kausalia Vijayaragavan, Noah F Greenwald, Darci Phillips, Christian M Schürch, Samuel M Naik, Edward A Ganio, Brice Gaudilliere, Scott J Rodig, Michael B Miller, Michael Angelo, Sean C Bendall, Xavier Rovira-Clavé, Garry P Nolan, Sizun Jiang.

Cellular organization and functions encompass multiple scales in vivo. Emerging high-plex imaging technologies are limited in resolving subcellular biomolecular features. Expansion Microscopy (ExM) and related techniques physically expand samples for enhanced spatial resolution, but are challenging to be combined with high-plex imaging technologies to enable integrative multiscaled tissue biology insights. Here, we introduce Expand and comPRESS hydrOgels (ExPRESSO), an ExM framework that allows high-plex protein staining, physical expansion, and removal of water, while retaining the lateral tissue expansion. We demonstrate ExPRESSO imaging of archival clinical tissue samples on Multiplexed Ion Beam Imaging and Imaging Mass Cytometry platforms, with detection capabilities of > 40 markers. Application of ExPRESSO on archival human lymphoid and brain tissues resolved tissue architecture at the subcellular level, particularly that of the blood-brain barrier. ExPRESSO hence provides a platform for extending the analysis compatibility of hydrogel-expanded biospecimens to mass spectrometry, with minimal modifications to protocols and instrumentation.

DOI: https://doi.org/10.1038/s41467-023-39616-w
Cells. 2023 May 17. pii: 1409. [Epub ahead of print]12(10):

The Haves and Have-Nots: The Mitochondrial Permeability Transition Pore across Species.

Elena Frigo, Ludovica Tommasin, Giovanna Lippe, Michela Carraro, Paolo Bernardi.

  The demonstration that F1FO (F)-ATP synthase and adenine nucleotide translocase (ANT) can form Ca2+-activated, high-conductance channels in the inner membrane of mitochondria from a variety of eukaryotes led to renewed interest in the permeability transition (PT), a permeability increase mediated by the PT pore (PTP). The PT is a Ca2+-dependent permeability increase in the inner mitochondrial membrane whose function and underlying molecular mechanisms have challenged scientists for the last 70 years. Although most of our knowledge about the PTP comes from studies in mammals, recent data obtained in other species highlighted substantial differences that could be perhaps attributed to specific features of F-ATP synthase and/or ANT. Strikingly, the anoxia and salt-tolerant brine shrimp Artemia franciscana does not undergo a PT in spite of its ability to take up and store Ca2+ in mitochondria, and the anoxia-resistant Drosophila melanogaster displays a low-conductance, selective Ca2+-induced Ca2+ release channel rather than a PTP. In mammals, the PT provides a mechanism for the release of cytochrome c and other proapoptotic proteins and mediates various forms of cell death. In this review, we cover the features of the PT (or lack thereof) in mammals, yeast, Drosophila melanogaster, Artemia franciscana and Caenorhabditis elegans, and we discuss the presence of the intrinsic pathway of apoptosis and of other forms of cell death. We hope that this exercise may help elucidate the function(s) of the PT and its possible role in evolution and inspire further tests to define its molecular nature.

Keywords:  ATP synthase; adenine nucleotide translocase; calcium signaling; cell death; channels; mitochondria; permeability transition

DOI:  https://doi.org/10.3390/cells12101409
J Nutr Sci Vitaminol (Tokyo). 2023 ;69(3): 184-189

Deletion of Nmnat1 in Skeletal Muscle Leads to the Reduction of NAD+ Levels but Has No Impact on Skeletal Muscle Morphology and Fiber Types.

Mariam Karim, Tooba Iqbal, Allah Nawaz, Keisuke Yaku, Takashi Nakagawa.

  Nicotinamide adenine dinucleotide (NAD+) is a coenzyme that mediates many redox reactions in energy metabolism. NAD+ is also a substrate for ADP-ribosylation and deacetylation by poly (ADP-ribose) polymerase and sirtuin, respectively. Nicotinamide mononucleotide adenylyltransferase 1 (Nmnat1) is a NAD+ biosynthesizing enzyme found in the nucleus. Recent research has shown that the maintaining NAD+ levels is critical for sustaining muscle functions both in physiological and pathological conditions. However, the role of Nmnat1 in skeletal muscle remains unexplored. In this study, we generated skeletal muscle-specific Nmnat1 knockout (M-Nmnat1 KO) mice and investigated its role in skeletal muscle. We found that NAD+ levels were significantly lower in the skeletal muscle of M-Nmnat1 KO mice than in control mice. M-Nmnat1 KO mice, in contrast, had similar body weight and normal muscle histology. Furthermore, the distribution of muscle fiber size and gene expressions of muscle fiber type gene expression were comparable in M-Nmnat1 KO and control mice. Finally, we investigated the role of Nmnat1 in muscle regeneration using cardiotoxin-induced muscle injury model, but muscle regeneration appeared almost normal in M-Nmnat1 KO mice. These findings imply that Nmnat1 has a redundancy in the pathophysiology of skeletal muscle.

Keywords:  NAD+; Nmnat1; fiber type; muscle injury; skeletal muscle

DOI:  https://doi.org/10.3177/jnsv.69.184
Cell Death Differ. 2023 Jul 07.

SLC25A51 promotes tumor growth through sustaining mitochondria acetylation homeostasis and proline biogenesis.

Yutong Li, Juntao Bie, Long Zhao, Chen Song, Tianzhuo Zhang, Meiting Li, Changjiang Yang, Jianyuan Luo.

Solute carrier family 25 member 51 (SLC25A51) was recently identified as the mammalian mitochondrial NAD+ transporter essential for mitochondria functions. However, the role of SLC25A51 in human disease, such as cancer, remains undefined. Here, we report that SLC25A51 is upregulated in multiple cancers, which promotes cancer cells proliferation. Loss of SLC25A51 elevates the mitochondrial proteins acetylation levels due to SIRT3 dysfunctions, leading to the impairment of P5CS enzymatic activity, which is the key enzyme in proline biogenesis, and the reduction in proline contents. Notably, we find fludarabine phosphate, an FDA-approved drug, is able to bind with and inhibit SLC25A51 functions, causing mitochondrial NAD+ decrease and proteins hyperacetylation, which could further synergize with aspirin to reinforce the anti-tumor efficacy. Our study reveals that SLC25A51 is an attractive anti-cancer target, and provides a novel drug combination of fludarabine phosphate with aspirin as a potential cancer therapy strategy.

DOI: https://doi.org/10.1038/s41418-023-01185-2
Nat Cell Biol. 2023 Jul 06.

Class 3 PI3K coactivates the circadian clock to promote rhythmic de novo purine synthesis.

Chantal Alkhoury, Nathaniel F Henneman, Volodymyr Petrenko, Yui Shibayama, Arianna Segaloni, Alexis Gadault, Ivan Nemazanyy, Edouard Le Guillou, Amare Desalegn Wolide, Konstantina Antoniadou, Xin Tong, Teruya Tamaru, Takeaki Ozawa, Muriel Girard, Karim Hnia, Dominik Lutter, Charna Dibner, Ganna Panasyuk.

Metabolic demands fluctuate rhythmically and rely on coordination between the circadian clock and nutrient-sensing signalling pathways, yet mechanisms of their interaction remain not fully understood. Surprisingly, we find that class 3 phosphatidylinositol-3-kinase (PI3K), known best for its essential role as a lipid kinase in endocytosis and lysosomal degradation by autophagy, has an overlooked nuclear function in gene transcription as a coactivator of the heterodimeric transcription factor and circadian driver Bmal1-Clock. Canonical pro-catabolic functions of class 3 PI3K in trafficking rely on the indispensable complex between the lipid kinase Vps34 and regulatory subunit Vps15. We demonstrate that although both subunits of class 3 PI3K interact with RNA polymerase II and co-localize with active transcription sites, exclusive loss of Vps15 in cells blunts the transcriptional activity of Bmal1-Clock. Thus, we establish non-redundancy between nuclear Vps34 and Vps15, reflected by the persistent nuclear pool of Vps15 in Vps34-depleted cells and the ability of Vps15 to coactivate Bmal1-Clock independently of its complex with Vps34. In physiology we find that Vps15 is required for metabolic rhythmicity in liver and, unexpectedly, it promotes pro-anabolic de novo purine nucleotide synthesis. We show that Vps15 activates the transcription of Ppat, a key enzyme for the production of inosine monophosphate, a central metabolic intermediate for purine synthesis. Finally, we demonstrate that in fasting, which represses clock transcriptional activity, Vps15 levels are decreased on the promoters of Bmal1 targets, Nr1d1 and Ppat. Our findings open avenues for establishing the complexity for nuclear class 3 PI3K signalling for temporal regulation of energy homeostasis.

DOI: https://doi.org/10.1038/s41556-023-01171-3
Front Endocrinol (Lausanne). 2023 ;14 1160155

Impaired mitochondrial dynamics and removal of the damaged mitochondria in diabetic retinopathy.

Kumari Alka, Jay Kumar, Renu A Kowluru.

  Introduction: Mitochondrial dynamic plays a major role in their quality control, and the damaged mitochondrial components are removed by autophagy. In diabetic retinopathy, mitochondrial fusion enzyme, mitofusin 2 (Mfn2), is downregulated and mitochondrial dynamic is disturbed resulting in depolarized and dysfunctional mitochondria. Our aim was to investigate the mechanism of inhibition of Mfn2, and its role in the removal of the damaged mitochondria, in diabetic retinopathy.Methods: Using human retinal endothelial cells, effect of high glucose (20mM) on the GTPase activity of Mfn2 and its acetylation were determined. Role of Mfn2 in the removal of the damaged mitochondria was confirmed by regulating its acetylation, or by Mfn2 overexpression, on autophagosomes- autolysosomes formation and the mitophagy flux.
Results: High glucose inhibited GTPase activity and increased acetylation of Mfn2. Inhibition of acetylation, or Mfn2 overexpression, attenuated decrease in GTPase activity and mitochondrial fragmentation, and increased the removal of the damaged mitochondria. Similar phenomenon was observed in diabetic mice; overexpression of sirtuin 1 (a deacetylase) ameliorated diabetes-induced inhibition of retinal Mfn2 and facilitated the removal of the damaged mitochondria.
Conclusions: Acetylation of Mfn2 has dual roles in mitochondrial homeostasis in diabetic retinopathy, it inhibits GTPase activity of Mfn2 and increases mitochondrial fragmentation, and also impairs removal of the damaged mitochondria. Thus, protecting Mfn2 activity should maintain mitochondrial homeostasis and inhibit the development/progression of diabetic retinopathy.

Keywords:  diabetic retinopathy; mitochondria; mitochondrial dynamics; mitofusin; mitophagy; retina

DOI:  https://doi.org/10.3389/fendo.2023.1160155
Chem Res Toxicol. 2023 Jul 06.

Predicting the Mitochondrial Toxicity of Small Molecules: Insights from Mechanistic Assays and Cell Painting Data.

Marina Garcia de Lomana, Paula Andrea Marin Zapata, Floriane Montanari.

Mitochondrial toxicity is a significant concern in the drug discovery process, as compounds that disrupt the function of these organelles can lead to serious side effects, including liver injury and cardiotoxicity. Different in vitro assays exist to detect mitochondrial toxicity at varying mechanistic levels: disruption of the respiratory chain, disruption of the membrane potential, or general mitochondrial dysfunction. In parallel, whole cell imaging assays like Cell Painting provide a phenotypic overview of the cellular system upon treatment and enable the assessment of mitochondrial health from cell profiling features. In this study, we aim to establish machine learning models for the prediction of mitochondrial toxicity, making the best use of the available data. For this purpose, we first derived highly curated datasets of mitochondrial toxicity, including subsets for different mechanisms of action. Due to the limited amount of labeled data often associated with toxicological endpoints, we investigated the potential of using morphological features from a large Cell Painting screen to label additional compounds and enrich our dataset. Our results suggest that models incorporating morphological profiles perform better in predicting mitochondrial toxicity than those trained on chemical structures alone (up to +0.08 and +0.09 mean MCC in random and cluster cross-validation, respectively). Toxicity labels derived from Cell Painting images improved the predictions on an external test set up to +0.08 MCC. However, we also found that further research is needed to improve the reliability of Cell Painting image labeling. Overall, our study provides insights into the importance of considering different mechanisms of action when predicting a complex endpoint like mitochondrial disruption as well as into the challenges and opportunities of using Cell Painting data for toxicity prediction.

DOI: https://doi.org/10.1021/acs.chemrestox.3c00086
Biochem J. 2023 Jul 12. 480(13): 909-919

Shaping mitochondria through fed-fast and circadian cycles.

Subhash Khatri, Rubina Kazi, Ullas Kolthur-Seetharam.

  Energy and metabolic homeostasis at the level of the whole body are dictated by the balance between nutrient intake/utilization, bioenergetic potential, and energy expenditure, which are tightly coupled with fed/fast cycles and circadian oscillation. Emerging literature has highlighted the importance of each of these mechanisms that are essential to maintain physiological homeostasis. Lifestyle changes predominantly associated with altered fed-fast and circadian cycles are well established to affect systemic metabolism and energetics, and hence contribute to pathophysiological states. Therefore, it is not surprising that mitochondria have emerged as being pivotal in maintaining physiological homeostasis through daily oscillations/fluctuations in nutrient inputs and light-dark/sleep-wake cycles. Moreover, given the inherent association between mitochondrial dynamics/morphology and functions, it is important to understand the phenomenological and mechanistic underpinnings of fed-fast and circadian cycles dependent remodeling of mitochondria. In this regard, we have summarized the current status of the field in addition to providing a perspective vis-a-vis the complexity of cell-autonomous and non-cell-autonomous signals that dictate mitochondrial dynamics. We also highlight the lacunae besides speculating on prospective efforts that will possibly redefine our insights into the diurnal orchestration of fission/fusion events, which are ultimately coupled to the mitochondrial output.

Keywords:  circadian clock; fed–fast cycles; fission/fusion; metabolic sensing; mitochondrial biogenesis; mitochondrial functions

DOI:  https://doi.org/10.1042/BCJ20220378
Epigenetics. 2023 Dec;18(1): 2230670

Epimutation detection in the clinical context: guidelines and a use case from a new Bioconductor package.

Carlos Ruiz-Arenas, Leire Abarrategui, Carles Hernandez-Ferrer, Xavier Escribà-Montagut, Dolors Pelegrí-Sisó, Patricia Ryser-Welch, Martine Vrijheid, Mariona Bustamante, Regina Grazuleviciene, Johanna Lepeule, Mathew Mathai, Marina Vafeiadi, Sergi Beltran, Luis A Pérez-Jurado, Juan R González.

  Epimutations are rare alterations of the normal DNA methylation pattern at specific loci, which can lead to rare diseases. Methylation microarrays enable genome-wide epimutation detection, but technical limitations prevent their use in clinical settings: methods applied to rare diseases' data cannot be easily incorporated to standard analyses pipelines, while epimutation methods implemented in R packages (ramr) have not been validated for rare diseases. We have developed epimutacions, a Bioconductor package (https://bioconductor.org/packages/release/bioc/html/epimutacions.html). epimutacions implements two previously reported methods and four new statistical approaches to detect epimutations, along with functions to annotate and visualize epimutations. Additionally, we have developed an user-friendly Shiny app to facilitate epimutations detection (https://github.com/isglobal-brge/epimutacionsShiny) to non-bioinformatician users. We first compared the performance of epimutacions and ramr packages using three public datasets with experimentally validated epimutations. Methods in epimutacions had a high performance at low sample sizes and outperformed methods in ramr. Second, we used two general population children cohorts (INMA and HELIX) to determine the technical and biological factors that affect epimutations detection, providing guidelines on how designing the experiments or preprocessing the data. In these cohorts, most epimutations did not correlate with detectable regional gene expression changes. Finally, we exemplified how epimutacions can be used in a clinical context. We run epimutacions in a cohort of children with autism disorder and identified novel recurrent epimutations in candidate genes for autism. Overall, we present epimutacions a new Bioconductor package for incorporating epimutations detection to rare disease diagnosis and provide guidelines for the design and data analyses.

Keywords:  Epigenetics; bioinformatics; epidemiology; rare disease

DOI:  https://doi.org/10.1080/15592294.2023.2230670