bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2022–03–13
fifty-two papers selected by
Catalina Vasilescu, University of Helsinki
  1. The Splicing of the Mitochondrial Calcium Uniporter Genuine Activator MICU1 Is Driven by RBFOX2 Splicing Factor during Myogenic Differentiation.
  2. Genes Involved in Maintaining Mitochondrial Membrane Potential Upon Electron Transport Chain Disruption.
  3. Mito-FUNCAT-FACS reveals cellular heterogeneity in mitochondrial translation.
  4. Novel Pathogenic Sequence Variation m.5789T>C Causes NARP Syndrome and Promotes Formation of Deletions of the Mitochondrial Genome.
  5. The Complicated Nature of Somatic mtDNA Mutations in Aging.
  6. Protein methylation in mitochondria.
  7. Iron chelation promotes mitophagy through SENP3-mediated deSUMOylation of FIS1.
  8. Mutant CHCHD10 causes an extensive metabolic rewiring that precedes OXPHOS dysfunction in a murine model of mitochondrial cardiomyopathy.
  9. How many molecules of mitochondrial complex I are in a cell?
  10. Methyltransferase METTL8 is required for 3-methylcytosine modification in human mitochondrial tRNAs.
  11. Ultra-deep whole genome bisulfite sequencing reveals a single methylation hotspot in human brain mitochondrial DNA.
  12. Serum Creatine, Not Neurofilament Light, Is Elevated in CHCHD10-Linked Spinal Muscular Atrophy.
  13. Frequent recurrence of pancreatitis in a patient with Leigh syndrome.
  14. MQuad enables clonal substructure discovery using single cell mitochondrial variants.
  15. Mitochondria in Pathological Cardiac Remodeling.
  16. Mitochondrial Function and Reactive Oxygen/Nitrogen Species in Skeletal Muscle.
  17. The multi-factor modulated biogenesis of the mitochondrial multi-span protein Om14.
  18. Case Report: A Case of β-Ureidopropionase Deficiency Complicated With MELAS Syndrome Caused by UPB1 Variant and Mitochondrial Gene Variant.
  19. Energy transfer between the mitochondrial network and lipid droplets in insulin resistant skeletal muscle.
  20. Nicotinamide Adenine Dinucleotide in the Development and Treatment of Cardiac Remodeling and Aging.
  21. Box C/D small nucleolar ribonucleoproteins regulate mitochondrial surveillance and innate immunity.
  22. Clinicopathologic Features of Mitochondrial Nephropathy.
  23. Gel-Based and Gel-Free Phosphoproteomics to Measure and Characterize Mitochondrial Phosphoproteins.
  24. Hunger games in the host cell: Toxoplasma traps and skins host mitochondria.
  25. Micropeptides Identified from Human Genomes.
  26. Imaging and analysis of neuronal mitochondria in murine acute brain slices.
  27. Mammalian HEMK1 methylates glutamine residue of the GGQ motif of mitochondrial release factors.
  28. Iron Supplementation Delays Aging and Extends Cellular Lifespan through Potentiation of Mitochondrial Function.
  29. seqr: a web-based analysis and collaboration tool for rare disease genomics.
  30. A serotonergic circuit regulates aversive associative learning under mitochondrial stress in C. elegans.
  31. Immunonutrition for the acute treatment of MELAS syndrome.
  32. Mitochondria-lysosome contact site dynamics and misregulation in neurodegenerative diseases.
  33. Elovl2-Ablation Leads to Mitochondrial Membrane Fatty Acid Remodeling and Reduced Efficiency in Mouse Liver Mitochondria.
  34. Evaluation of Parkin in the Regulation of Myocardial Mitochondria-Associated Membranes and Cardiomyopathy During Endotoxemia.
  35. βIII-Tubulin Structural Domains Regulate Mitochondrial Network Architecture in an Isotype-Specific Manner.
  36. The Role of l-Carnitine in Mitochondria, Prevention of Metabolic Inflexibility and Disease Initiation.
  37. Loss of intermediate filament IFB-1 reduces mobility, density and physiological function of mitochondria in C. elegans sensory neurons.
  38. Intertwined Relationship of Mitochondrial Metabolism, Gut Microbiome and Exercise Potential.
  39. Loss of Function of mtHsp70 Chaperone Variants Leads to Mitochondrial Dysfunction in Congenital Sideroblastic Anemia.
  40. Quantitative transportomics identifies Kif5a as a major regulator of neurodegeneration.
  41. The Mitochondrial Deubiquitinase USP30 Regulates AKT/mTOR Signaling.
  42. A non-canonical tricarboxylic acid cycle underlies cellular identity.
  43. Mitochondrial respiration supports autophagy to provide stress resistance during quiescence.
  44. OpenCell: Endogenous tagging for the cartography of human cellular organization.
  45. Improved prediction of protein-protein interactions using AlphaFold2.
  46. Assessing the contribution of rare variants to complex trait heritability from whole-genome sequence data.
  47. A pan-tissue DNA methylation atlas enables in silico decomposition of human tissue methylomes at cell-type resolution.
  48. Multicenter Consensus Approach to Evaluation of Neonatal Hypotonia in the Genomic Era: A Review.
  49. Distinct and diverse chromatin-proteomes of ageing mouse organs reveal protein signatures that correlate with physiological functions.
  50. Metabolic Regulation of Stem Cells in Aging.
  51. UK recommendations for SDHA germline genetic testing and surveillance in clinical practice.
  52. Invertebrate Model Organisms as a Platform to Investigate Rare Human Neurological Diseases.
  1. Int J Mol Sci. 2022 Feb 24. pii: 2517. [Epub ahead of print]23(5):
    The Splicing of the Mitochondrial Calcium Uniporter Genuine Activator MICU1 Is Driven by RBFOX2 Splicing Factor during Myogenic Differentiation.
    Denis Vecellio Reane, Cristina Cerqua, Sabrina Sacconi, Leonardo Salviati, Eva Trevisson, Anna Raffaello.
      Alternative splicing, the process by which exons within a pre-mRNA transcript are differentially joined or skipped, is crucial in skeletal muscle since it is required both during myogenesis and in post-natal life to reprogram the transcripts of contractile proteins, metabolic enzymes, and transcription factors in functionally distinct muscle fiber types. The importance of such events is underlined by the numerosity of pathological conditions caused by alternative splicing aberrations. Importantly, many skeletal muscle Ca2+ homeostasis genes are also regulated by alternative splicing mechanisms, among which is the Mitochondrial Ca2+ Uniporter (MCU) genuine activator MICU1 which regulates MCU opening upon cell stimulation. We have previously shown that murine skeletal muscle MICU1 is subjected to alternative splicing, thereby generating a splice variant-which was named MICU1.1-that confers unique properties to the mitochondrial Ca2+ uptake and ensuring sufficient ATP production for muscle contraction. Here we extended the analysis of MICU1 alternative splicing to human tissues, finding two additional splicing variants that were characterized by their ability to regulate mitochondrial Ca2+ uptake. Furthermore, we found that MICU1 alternative splicing is induced during myogenesis by the splicing factor RBFOX2. These results highlight the complexity of the alternative splicing mechanisms in skeletal muscle and the regulation of mitochondrial Ca2+ among tissues.
    Keywords:  alternative splicing; mitochondrial calcium homeostasis; myogenic differentiation; skeletal muscle
    DOI:  https://doi.org/10.3390/ijms23052517
  2. Front Cell Dev Biol. 2022 ;10 781558
    Genes Involved in Maintaining Mitochondrial Membrane Potential Upon Electron Transport Chain Disruption.
    Karthik Vasan, Matt Clutter, Sara Fernandez Dunne, Mariam D George, Chi-Hao Luan, Navdeep S Chandel, Inmaculada Martínez-Reyes.
      Mitochondria are biosynthetic, bioenergetic, and signaling organelles with a critical role in cellular physiology. Dysfunctional mitochondria are associated with aging and underlie the cause of a wide range of diseases, from neurodegeneration to cancer. Through signaling, mitochondria regulate diverse biological outcomes. The maintenance of the mitochondrial membrane potential, for instance, is essential for proliferation, the release of mitochondrial reactive oxygen species, and oxygen sensing. The loss of mitochondrial membrane potential triggers pathways to clear damaged mitochondria and often results in cell death. In this study, we conducted a genome-wide positive selection CRISPR screen using a combination of mitochondrial inhibitors to uncover genes involved in sustaining a mitochondrial membrane potential, and therefore avoid cell death when the electron transport chain is impaired. Our screen identified genes involved in mitochondrial protein translation and ATP synthesis as essential for the induction of cell death when cells lose their mitochondrial membrane potential. This report intends to provide potential targets for the treatment of diseases associated with mitochondrial dysfunction.
    Keywords:  ATP synthase; CRISPR screen; cell death; mitochondria; mitochondrial membrane potential; mitochondrial protein translation
    DOI:  https://doi.org/10.3389/fcell.2022.781558
  3. RNA. 2022 Mar 07. pii: rna.079097.122. [Epub ahead of print]
    Mito-FUNCAT-FACS reveals cellular heterogeneity in mitochondrial translation.
    Yusuke Kimura, Hironori Saito, Tatsuya Osaki, Yasuhiro Ikegami, Taisei Wakigawa, Yoshiho Ikeuchi, Shintaro Iwasaki.
      Mitochondria possess their own genome that encodes components of oxidative phosphorylation (OXPHOS) complexes, and mitochondrial ribosomes within the organelle translate the mRNAs expressed from the mitochondrial genome. Given the differential OXPHOS activity observed in diverse cell types, cell growth conditions, and other circumstances, cellular heterogeneity in mitochondrial translation can be expected. Although individual protein products translated in mitochondria have been monitored, the lack of techniques that address the variation in overall mitochondrial protein synthesis in cell populations poses analytic challenges. Here, we adapted mitochondrial-specific fluorescent noncanonical amino acid tagging (FUNCAT) for use with fluorescence-activated cell sorting (FACS) and developed mito-FUNCAT-FACS. The click chemistry-compatible methionine analog L-homopropargylglycine (HPG) enabled the metabolic labeling of newly synthesized proteins. In the presence of cytosolic translation inhibitors, HPG was selectively incorporated into mitochondrial nascent proteins and conjugated to fluorophores via the click reaction (mito-FUNCAT). The application of in situ mito-FUNCAT to flow cytometry allowed us to separate changes in net mitochondrial translation activity from those of the organelle mass and detect variations in mitochondrial translation in cancer cells. Our approach provides a useful methodology for examining mitochondrial protein synthesis in individual cells.
    Keywords:  FACS; FUNCAT; HPG; Mitochondria; Translation
    DOI:  https://doi.org/10.1261/rna.079097.122
  4. Neurol Genet. 2022 Apr;8(2): e660
    Novel Pathogenic Sequence Variation m.5789T>C Causes NARP Syndrome and Promotes Formation of Deletions of the Mitochondrial Genome.
    Marius Hippen, Gábor Zsurka, Viktoriya Peeva, Judith Machts, Kati Schwiecker, Grazyna Debska-Vielhaber, Rudolf J Wiesner, Stefan Vielhaber, Wolfram S Kunz.
       Background and Objectives: We report the pathogenic sequence variant m.5789T>C in the anticodon stem of the mitochondrial tRNA for cysteine as a novel cause of neuropathy, ataxia, and retinitis pigmentosa (NARP), which is usually associated with pathogenic variants in the MT-ATP6 gene.
    Methods: To address the correlation of oxidative phosphorylation deficiency with mutation loads, we performed genotyping on single laser-dissected skeletal muscle fibers. Stability of the mitochondrial tRNACys was investigated by Northern blotting. Accompanying deletions of the mitochondrial genome were detected by long-range PCR and their breakpoints were determined by sequencing of single-molecule amplicons.
    Results: The sequence variant m.5789T>C, originating from the patient's mother, decreases the stability of the mitochondrial tRNA for cysteine by disrupting the anticodon stem, which subsequently leads to a combined oxidative phosphorylation deficiency. In parallel, we observed a prominent cluster of low-abundance somatic deletions with breakpoints in the immediate vicinity of the m.5789T>C variant. Strikingly, all deletion-carrying mitochondrial DNA (mtDNA) species, in which the corresponding nucleotide position was not removed, harbored the mutant allele, and none carried the wild-type allele.
    Discussion: In addition to providing evidence for the novel association of a tRNA sequence alteration with NARP syndrome, our observations support the hypothesis that single nucleotide changes can lead to increased occurrence of site-specific mtDNA deletions through the formation of an imperfect repeat. This finding might be relevant for understanding mechanisms of deletion generation in the human mitochondrial genome.
    DOI:  https://doi.org/10.1212/NXG.0000000000000660
  5. Front Aging. 2022 ;pii: 805126. [Epub ahead of print]2
    The Complicated Nature of Somatic mtDNA Mutations in Aging.
    Monica Sanchez-Contreras, Scott R Kennedy.
      Mitochondria are the main source of energy used to maintain cellular homeostasis. This aspect of mitochondrial biology underlies their putative role in age-associated tissue dysfunction. Proper functioning of the electron transport chain (ETC), which is partially encoded by the extra-nuclear mitochondrial genome (mtDNA), is key to maintaining this energy production. The acquisition of de novo somatic mutations that interrupt the function of the ETC have long been associated with aging and common diseases of the elderly. Yet, despite over 30 years of study, the exact role(s) mtDNA mutations play in driving aging and its associated pathologies remains under considerable debate. Furthermore, even fundamental aspects of age-related mtDNA mutagenesis, such as when mutations arise during aging, where and how often they occur across tissues, and the specific mechanisms that give rise to them, remain poorly understood. In this review, we address the current understanding of the somatic mtDNA mutations, with an emphasis of when, where, and how these mutations arise during aging. Additionally, we highlight current limitations in our knowledge and critically evaluate the controversies stemming from these limitations. Lastly, we highlight new and emerging technologies that offer potential ways forward in increasing our understanding of somatic mtDNA mutagenesis in the aging process.
    Keywords:  aging; mitochondria; mtDNA; mutagenesis; sequencing; somatic mutations
    DOI:  https://doi.org/10.3389/fragi.2021.805126
  6. J Biol Chem. 2022 Mar 02. pii: S0021-9258(22)00231-9. [Epub ahead of print] 101791
    Protein methylation in mitochondria.
    Jędrzej M Małecki, Erna Davydova, Pål Ø Falnes.
      Many proteins are modified by post-translational methylation, introduced by a number of methyltransferases (MTases). Protein methylation plays important roles in modulating protein function, and thus in optimizing and regulating cellular and physiological processes. Research has mainly focused on nuclear and cytosolic protein methylation, but it has been known for many years that also mitochondrial proteins are methylated. During the last decade, significant progress has been made on identifying the MTases responsible for mitochondrial protein methylation and addressing its functional significance. In particular, several novel human MTases have been uncovered that methylate lysine, arginine, histidine, and glutamine residues in various mitochondrial substrates. Several of these substrates are key components of the bioenergetics machinery, e.g. respiratory Complex I, citrate synthase and the ATP synthase. In the present review we report the status of the field of mitochondrial protein methylation, with a particular emphasis on recently discovered human MTases. We also discuss evolutionary aspects and functional significance of mitochondrial protein methylation, and present an outlook for this emergent research field.
    Keywords:  ATP synthase; bioenergetics; electron transport chain; methyltransferase; mitochondria; oxidative phosphorylation; protein methylation
    DOI:  https://doi.org/10.1016/j.jbc.2022.101791
  7. Autophagy. 2022 Mar 11. 1-3
    Iron chelation promotes mitophagy through SENP3-mediated deSUMOylation of FIS1.
    Kevin A Wilkinson, Chun Guo.
      The selective clearance of mitochondria by mitophagy is an important quality control mechanism for maintaining mitochondrial and cellular health. Iron chelation, for example by the compound deferiprone (DFP), leads to a specific form of PINK1-PRKN/Parkin-independent mitophagy; however, the molecular mechanisms underlying this are poorly understood. In our recent paper, we examined the role of the deSUMOylating enzyme SENP3 in DFP-induced mitophagy. We observed that SENP3 levels are enhanced by DFP treatment, and that SENP3 is essential for DFP-induced mitophagy. Furthermore, we identified the mitochondrial protein FIS1, which is also required for DFP-induced mitophagy, as a novel SUMO substrate. Our data demonstrate that SENP3-dependent deSUMOylation of FIS1 enhances FIS1 mitochondrial targeting, to promote mitophagy in response to DFP treatment. These findings offer new insight into the mechanisms underlying mitophagy upon iron chelation, and have relevance to the therapeutic potential of DFP in a number of disorders, including Parkinson disease. Abbreviations DFP: deferiprone; OMM: outer mitochondrial membrane. PD: Parkinson disease; SUMO: small ubiquitin like modifier.
    Keywords:  FIS1; SENP3; SUMO; iron chelation; mitophagy
    DOI:  https://doi.org/10.1080/15548627.2022.2046898
  8. Cell Rep. 2022 Mar 08. pii: S2211-1247(22)00208-X. [Epub ahead of print]38(10): 110475
    Mutant CHCHD10 causes an extensive metabolic rewiring that precedes OXPHOS dysfunction in a murine model of mitochondrial cardiomyopathy.
    Nicole M Sayles, Nneka Southwell, Kevin McAvoy, Kihwan Kim, Alba Pesini, Corey J Anderson, Catarina Quinzii, Suzanne Cloonan, Hibiki Kawamata, Giovanni Manfredi.
      Mitochondrial cardiomyopathies are fatal diseases, with no effective treatment. Alterations of heart mitochondrial function activate the mitochondrial integrated stress response (ISRmt), a transcriptional program affecting cell metabolism, mitochondrial biogenesis, and proteostasis. In humans, mutations in CHCHD10, a mitochondrial protein with unknown function, were recently associated with dominant multi-system mitochondrial diseases, whose pathogenic mechanisms remain to be elucidated. Here, in CHCHD10 knockin mutant mice, we identify an extensive cardiac metabolic rewiring triggered by proteotoxic ISRmt. The stress response arises early on, before the onset of bioenergetic impairments, triggering a switch from oxidative to glycolytic metabolism, enhancement of transsulfuration and one carbon (1C) metabolism, and widespread metabolic imbalance. In parallel, increased NADPH oxidases elicit antioxidant responses, leading to heme depletion. As the disease progresses, the adaptive metabolic stress response fails, resulting in fatal cardiomyopathy. Our findings suggest that early interventions to counteract metabolic imbalance could ameliorate mitochondrial cardiomyopathy associated with proteotoxic ISRmt.
    Keywords:  1C metabolism; CHCHD10; coiled-coil-helix-coiled-coil-helix domain containing 10; heart, cardiomyopathy; heme; integrated stress response; metabolic rewiring; mitochondria
    DOI:  https://doi.org/10.1016/j.celrep.2022.110475
  9. Anal Biochem. 2022 Mar 05. pii: S0003-2697(22)00102-6. [Epub ahead of print] 114646
    How many molecules of mitochondrial complex I are in a cell?
    Fariha Ansari, Belem Yoval, Zoya Niatsetskaya, Vadim Ten, Ilka Wittig, Alexander Galkin.
      Mitochondrial complex I is the only enzyme responsible for oxidation of matrix NADH and regeneration of NAD+ for catabolism. Nuclear and mtDNA mutations, assembly impairments, and enzyme damage are implicated in inherited diseases, ischemia-reperfusion injury, neurodegeneration, and tumorogenesis. Here we introduce a novel method to measure the absolute content of complex I. The method is based on flavin fluorescence scanning of a polyacrylamide gel after separation of complexes by Clear Native electrophoresis. Using mouse primary astrocytes as an example, we calculated an average value of 2.2 × 105 complex I molecules/cell. Our method can be used for accurate quantification of complex I content.
    Keywords:  Astrocytes; Flavin mononucleotide; Fluorescence; Mitochondrial complex I; Respiratory chain
    DOI:  https://doi.org/10.1016/j.ab.2022.114646
  10. J Biol Chem. 2022 Mar 02. pii: S0021-9258(22)00228-9. [Epub ahead of print] 101788
    Methyltransferase METTL8 is required for 3-methylcytosine modification in human mitochondrial tRNAs.
    Jenna M Lentini, Rachel Bargabos, Chen Chen, Dragony Fu.
      A subset of eukaryotic tRNAs is methylated in the anticodon loop, forming 3-methylcytosine (m3C) modifications. In mammals, the number of tRNAs containing m3C modifications has been expanded to include mitochondrial (mt) tRNA-Ser-UGA and mt-tRNA-Thr-UGU. However, whereas the enzymes catalyzing m3C formation in nuclear-encoded tRNAs have been identified, the proteins responsible for m3C modification in mt-tRNAs are unknown. Here, we show that m3C formation in human mt-tRNAs is dependent upon the Methyltransferase-Like 8 (METTL8) enzyme. We find that METTL8 is a mitochondria-associated protein that interacts with mitochondrial seryl-tRNA synthetase, as well as with mt-tRNAs containing m3C. We demonstrate that human cells deficient in METTL8 exhibit loss of m3C modification in mt-tRNAs, but not nuclear-encoded tRNAs. Consistent with the mitochondrial import of METTL8, the formation of m3C in METTL8-deficient cells could be rescued by re-expression of wildtype METTL8, but not by a METTL8 variant lacking the N-terminal mitochondrial localization signal. Notably, we found METTL8-deficiency in human cells causes alterations in the native migration pattern of mt-tRNA-Ser-UGA, suggesting a role for m3C in tRNA folding. Altogether, these findings demonstrate that METTL8 is required for m3C formation in mitochondrial tRNAs and uncover a potential function for m3C modification in mitochondrial tRNA structure.
    Keywords:  3-methylcytosine; METTL8; m(3)C; mitochondria; tRNA; tRNA modification
    DOI:  https://doi.org/10.1016/j.jbc.2022.101788
  11. Epigenetics. 2022 Mar 07. 1-16
    Ultra-deep whole genome bisulfite sequencing reveals a single methylation hotspot in human brain mitochondrial DNA.
    Romain Guitton, Christian Dölle, Guido Alves, Tysnes Ole-Bjørn, Gonzalo S Nido, Charalampos Tzoulis.
      While DNA methylation is established as a major regulator of gene expression in the nucleus, the existence of mitochondrial DNA (mtDNA) methylation remains controversial. Here, we characterized the mtDNA methylation landscape in the prefrontal cortex of neurological healthy individuals (n=26) and patients with Parkinson's disease (n=27), using a combination of whole-genome bisulphite sequencing (WGBS) and bisulphite-independent methods. Accurate mtDNA mapping from WGBS data required alignment to an mtDNA reference only, to avoid misalignment to nuclear mitochondrial pseudogenes. Once correctly aligned, WGBS data provided ultra-deep mtDNA coverage (16,723 ± 7,711) and revealed overall very low levels of cytosine methylation. The highest methylation levels (5.49 ± 0.97%) were found on CpG position m.545, located in the heavy-strand promoter 1 region. The m.545 methylation was validated using a combination of methylation-sensitive DNA digestion and quantitative PCR analysis. We detected no association between mtDNA methylation profile and Parkinson's disease. Interestingly, m.545 methylation correlated with the levels of mtDNA transcripts, suggesting a putative role in regulating mtDNA gene expression. In addition, we propose a robust framework for methylation analysis of mtDNA from WGBS data, which is less prone to false-positive findings due to misalignment of nuclear mitochondrial pseudogene sequences.
    Keywords:  NUMTs; epigenetics; mitochondria; mtDNA; parkinson’s disease
    DOI:  https://doi.org/10.1080/15592294.2022.2045754
  12. Front Neurol. 2022 ;13 793937
    Serum Creatine, Not Neurofilament Light, Is Elevated in CHCHD10-Linked Spinal Muscular Atrophy.
    Julius Järvilehto, Sandra Harjuhaahto, Edouard Palu, Mari Auranen, Jouni Kvist, Henrik Zetterberg, Johanna Koskivuori, Marko Lehtonen, Anna Maija Saukkonen, Manu Jokela, Emil Ylikallio, Henna Tyynismaa.
       Objective: To characterize serum biomarkers in mitochondrial CHCHD10-linked spinal muscular atrophy Jokela (SMAJ) type for disease monitoring and for the understanding of pathogenic mechanisms.
    Methods: We collected serum samples from a cohort of 49 patients with SMAJ, all carriers of the heterozygous c.197G>T p.G66V variant in CHCHD10. As controls, we used age- and sex-matched serum samples obtained from Helsinki Biobank. Creatine kinase and creatinine were measured by standard methods. Neurofilament light (NfL) and glial fibrillary acidic protein (GFAP) were measured with single molecule array (Simoa), fibroblast growth factor 21 (FGF-21), and growth differentiation factor 15 (GDF-15) with an enzyme-linked immunosorbent assay. For non-targeted plasma metabolite profiling, samples were analyzed with liquid chromatography high-resolution mass spectrometry. Disease severity was evaluated retrospectively by calculating a symptom-based score.
    Results: Axon degeneration marker, NfL, was unexpectedly not altered in the serum of patients with SMAJ, whereas astrocytic activation marker, GFAP, was slightly decreased. Creatine kinase was elevated in most patients, particularly men. We identified six metabolites that were significantly altered in serum of patients with SMAJ in comparison to controls: increased creatine and pyruvate, and decreased creatinine, taurine, N-acetyl-carnosine, and succinate. Creatine correlated with disease severity. Altered pyruvate and succinate indicated a metabolic response to mitochondrial dysfunction; however, lactate or mitochondrial myopathy markers FGF-21 or GDF-15 was not changed.
    Conclusions: Biomarkers of muscle mass and damage are altered in SMAJ serum, indicating a role for skeletal muscle in disease pathogenesis in addition to neurogenic damage. Despite the minimal mitochondrial pathology in skeletal muscle, signs of a metabolic shift can be detected.
    Keywords:  CHCHD10; NEFL; SMAJ; biomarker; creatine
    DOI:  https://doi.org/10.3389/fneur.2022.793937
  13. Pediatr Int. 2022 Jan;64(1): e15021
    Frequent recurrence of pancreatitis in a patient with Leigh syndrome.
    Kengo Nakashima, Ryosuke Bo, Hiroyuki Awano, Masahiro Nishiyama, Kazumoto Iijima.
      
    Keywords:  Leigh syndrome; mitochondrial disease; pancreatitis
    DOI:  https://doi.org/10.1111/ped.15021
  14. Nat Commun. 2022 Mar 08. 13(1): 1205
    MQuad enables clonal substructure discovery using single cell mitochondrial variants.
    Aaron Wing Cheung Kwok, Chen Qiao, Rongting Huang, Mai-Har Sham, Joshua W K Ho, Yuanhua Huang.
      Mitochondrial mutations are increasingly recognised as informative endogenous genetic markers that can be used to reconstruct cellular clonal structure using single-cell RNA or DNA sequencing data. However, identifying informative mtDNA variants in noisy and sparse single-cell sequencing data is still challenging with few computation methods available. Here we present an open source computational tool MQuad that accurately calls clonally informative mtDNA variants in a population of single cells, and an analysis suite for complete clonality inference, based on single cell RNA, DNA or ATAC sequencing data. Through a variety of simulated and experimental single cell sequencing data, we showed that MQuad can identify mitochondrial variants with both high sensitivity and specificity, outperforming existing methods by a large extent. Furthermore, we demonstrate its wide applicability in different single cell sequencing protocols, particularly in complementing single-nucleotide and copy-number variations to extract finer clonal resolution.
    DOI:  https://doi.org/10.1038/s41467-022-28845-0
  15. Curr Opin Physiol. 2022 Feb;pii: 100489. [Epub ahead of print]25
    Mitochondria in Pathological Cardiac Remodeling.
    Michael P Lazaropoulos, John W Elrod.
      Adverse cardiac remodeling is often precipitated by chronic stress or injury inflicted upon the heart during the progression of cardiovascular diseases. Mitochondria play an important role in the cardiomyocyte response to stress by serving as a signaling hub for changes in cellular energetics, redox balance, contractile function, and cell death. Cardiac remodeling involves alterations to mitochondrial form and function that are either compensatory to maintain contractility or maladaptive, which promotes heart failure progression. In this mini-review, we focus on three mitochondrial processes that contribution to cardiac remodeling: Ca2+ signaling, mitochondrial dynamics, and mitochondrial metabolism.
    Keywords:  calcium; heart failure; metabolism; mitochondria; remodeling
    DOI:  https://doi.org/10.1016/j.cophys.2022.100489
  16. Front Cell Dev Biol. 2022 ;10 826981
    Mitochondrial Function and Reactive Oxygen/Nitrogen Species in Skeletal Muscle.
    Ming-Ming Chen, Yan Li, Shou-Long Deng, Yue Zhao, Zheng-Xing Lian, Kun Yu.
      Skeletal muscle fibers contain a large number of mitochondria, which produce ATP through oxidative phosphorylation (OXPHOS) and provide energy for muscle contraction. In this process, mitochondria also produce several types of "reactive species" as side product, such as reactive oxygen species and reactive nitrogen species which have attracted interest. Mitochondria have been proven to have an essential role in the production of skeletal muscle reactive oxygen/nitrogen species (RONS). Traditionally, the elevation in RONS production is related to oxidative stress, leading to impaired skeletal muscle contractility and muscle atrophy. However, recent studies have shown that the optimal RONS level under the action of antioxidants is a critical physiological signal in skeletal muscle. Here, we will review the origin and physiological functions of RONS, mitochondrial structure and function, mitochondrial dynamics, and the coupling between RONS and mitochondrial oxidative stress. The crosstalk mechanism between mitochondrial function and RONS in skeletal muscle and its regulation of muscle stem cell fate and myogenesis will also be discussed. In all, this review aims to describe a comprehensive and systematic network for the interaction between skeletal muscle mitochondrial function and RONS.
    Keywords:  RONS; mitochondrial dynamics; mitochondrial function; oxidative stress; skeletal muscle
    DOI:  https://doi.org/10.3389/fcell.2022.826981
  17. J Cell Biol. 2022 Apr 04. pii: e202112030. [Epub ahead of print]221(4):
    The multi-factor modulated biogenesis of the mitochondrial multi-span protein Om14.
    Jialin Zhou, Martin Jung, Kai S Dimmer, Doron Rapaport.
      The mitochondrial outer membrane (MOM) harbors proteins that traverse the membrane via several helical segments and are called multi-span proteins. To obtain new insights into the biogenesis of these proteins, we utilized yeast mitochondria and the multi-span protein Om14. Testing different truncation variants, we show that while only the full-length protein contains all the information that assures perfect targeting specificity, shorter variants are targeted to mitochondria with compromised fidelity. Employing a specific insertion assay and various deletion strains, we show that proteins exposed to the cytosol do not contribute significantly to the biogenesis process. We further demonstrate that Mim1 and Porin support optimal membrane integration of Om14 but none of them are absolutely required. Unfolding of newly synthesized Om14, its optimal hydrophobicity, and higher fluidity of the membrane enhanced the import capacity of Om14. Collectively, these findings suggest that MOM multi-span proteins follow different biogenesis pathways in which proteinaceous elements and membrane behavior contribute to a variable extent to the combined efficiency.
    DOI:  https://doi.org/10.1083/jcb.202112030
  18. Front Pediatr. 2022 ;10 838341
    Case Report: A Case of β-Ureidopropionase Deficiency Complicated With MELAS Syndrome Caused by UPB1 Variant and Mitochondrial Gene Variant.
    Jianbo Shu, Xiufang Zhi, Jing Chen, Meifang Lei, Jie Zheng, Wenchao Sheng, Chunhua Zhang, Dong Li, Chunquan Cai.
       Background: β-Ureidopropionase deficiency is a rare autosomal recessive disease affecting the last step of pyrimidine degradation. Mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes (MELAS) syndrome is a rare inherited disorder caused by genetic defects in mitochondrial DNA.
    Case Presentation: One 8-year-old boy presented with dizziness, vomiting, and convulsions. The gas chromatography-mass spectrometry results suggested β-ureidopropionase deficiency. The whole-exome sequencing results revealed homozygous missense variant c.977G>A (p.R326Q) in UPB1. However, the patient presented with persistent hyperlactacidemia and metabolic acidosis, which did not correspond to the classic features of β-ureidopropionase deficiency. Combined with the manifestations of developmental delay, poor academic performance, and poor sports stamina, whole-mitochondrial-genome sequencing was performed. The results exhibited the variant m.3243A>G of MT-TL1 gene. The level of heterogeneity was 65% in the patient and 17.8% in his mother. Eventually, the final diagnosis of β-ureidopropionase deficiency combined with MELAS syndrome was made.
    Conclusion: The report about β-ureidopropionase deficiency caused by a nuclear gene variant and MELAS syndrome caused by a mitochondrial gene variant coexisting in the same patient enriches the clinical study of these two rare diseases.
    Keywords:  MELAS syndrome; UPB1 gene; mitochondrial DNA; whole-exome sequencing; β-ureidopropionase deficiency
    DOI:  https://doi.org/10.3389/fped.2022.838341
  19. Curr Opin Physiol. 2021 Dec;pii: 100487. [Epub ahead of print]24
    Energy transfer between the mitochondrial network and lipid droplets in insulin resistant skeletal muscle.
    Hailey A Parry, Brian Glancy.
      Mitochondria and lipid droplets in the insulin resistant skeletal muscle of type 2 diabetic individuals have both been heavily investigated independently and are characterized by more fragmented, dysfunctional mitochondrial networks and larger lipid droplets compared to skeletal muscle of healthy individuals. Specialized contacts between mitochondrial and lipid droplet membranes are known to decrease in diabetic muscle, though it remains unclear how energy transfer at the remaining mitochondria-lipid droplet contact sites may be altered by type 2 diabetes. The purpose of this review is to highlight recent data on mitochondrial structure and function and lipid droplet dynamics in type 2 diabetic skeletal muscle and to underscore the need for more detailed investigations into the functional nature of mitochondria-lipid droplet interactions in type 2 diabetes.
    Keywords:  Mitochondria; diabetes; insulin resistance; lipid droplets; mitochondrial network
    DOI:  https://doi.org/10.1016/j.cophys.2022.100487
  20. Mini Rev Med Chem. 2022 Mar 04.
    Nicotinamide Adenine Dinucleotide in the Development and Treatment of Cardiac Remodeling and Aging.
    Zuowei Pei, Fang Wang, Kanglin Wang, Lei Wang.
       BACKGROUND: Recently, the beneficial effects of nicotinamide adenine dinucleotide (NAD+) as an antiaging and antioxidant molecule have become a focus of research. However, the mechanisms by which NAD+ supplementation affects the associated metabolites under physiological conditions remain unclear. Specifically, although NAD+ is involved in several processes that are dysregulated in cardiovascular diseases, some effects of NAD+ precursors and NAD+ on cardiac diseases have started to gain recognition only recently.
    OBJECTIVE: To discuss the influence of NAD+ supplementation on adverse cardiac remodeling and aging.
    RESULTS: Supplementation with NAD+ precursors or nicotinamide riboside, which enhances or supplements the NAD+ metabolome, might have a protective effect on the heart. NAD+ can alleviate chronic heart failure via a mitochondrial oxidation-reduction (redox) state mechanism. Furthermore, NAD+ replenishment can improve the life span of mice.
    CONCLUSION: NAD+ exerts considerable antiaging and antioxidant effects with promising therapeutic effects. However, its effect in humans and use as a dietary supplement need to be studied further.
    Keywords:  Cardiac remodeling; aging; antioxidant; dietary supplement; metabolome; nicotinamide adenine dinucleotide; oxidation-reduction; redox
    DOI:  https://doi.org/10.2174/1389557522666220304121917
  21. PLoS Genet. 2022 Mar 11. 18(3): e1010103
    Box C/D small nucleolar ribonucleoproteins regulate mitochondrial surveillance and innate immunity.
    Elissa Tjahjono, Alexey V Revtovich, Natalia V Kirienko.
      Monitoring mitochondrial function is crucial for organismal survival. This task is performed by mitochondrial surveillance or quality control pathways, which are activated by signals originating from mitochondria and relayed to the nucleus (retrograde response) to start transcription of protective genes. In Caenorhabditis elegans, several systems are known to play this role, including the UPRmt, MAPKmt, and the ESRE pathways. These pathways are highly conserved and their loss compromises survival following mitochondrial stress. In this study, we found a novel interaction between the box C/D snoRNA core proteins (snoRNPs) and mitochondrial surveillance and innate immune pathways. We showed that box C/D, but not box H/ACA, snoRNPs are required for the full function of UPRmt and ESRE upon stress. The loss of box C/D snoRNPs reduced mitochondrial mass, mitochondrial membrane potential, and oxygen consumption rate, indicating overall degradation of mitochondrial function. Concomitantly, the loss of C/D snoRNPs increased immune response and reduced host intestinal colonization by infectious bacteria, improving host resistance to pathogenesis. Our data may indicate a model wherein box C/D snoRNP machinery regulates a "switch" of the cell's activity between mitochondrial surveillance and innate immune activation. Understanding this mechanism is likely to be important for understanding multifactorial processes, including responses to infection and aging.
    DOI:  https://doi.org/10.1371/journal.pgen.1010103
  22. Kidney Int Rep. 2022 Mar;7(3): 580-590
    Clinicopathologic Features of Mitochondrial Nephropathy.
    J-SMiN Collaborators
       Introduction: The clinicopathologic characteristics of nephropathy associated with mitochondrial disease (MD) remain unknown. We retrospectively analyzed a cohort of patients with proteinuria, decreased glomerular filtration rate, or Fanconi syndrome who had a genetic mutation confirmed as the cause of MD, defined as mitochondrial nephropathy.
    Methods: This nationwide survey included 757 nephrology sections throughout Japan, and consequently, data on 81 cases of mitochondrial nephropathy were collected.
    Results: The most common renal manifestation observed during the disease course was proteinuria. Hearing loss was the most common comorbidity; a renal-limited phenotype was observed only in mitochondrial DNA (mtDNA) point mutation and COQ8B mutation cases. We found a median time delay of 6.0 years from onset of renal manifestations to diagnosis. Focal segmental glomerular sclerosis (FSGS) was the most common pathologic diagnosis. We then focused on 63 cases with the m.3243A>G mutation. The rate of cases with diabetes was significantly higher among adult-onset cases than among childhood-onset cases. Pathologic diagnoses were more variable in adult-onset cases, including diabetic nephropathy, nephrosclerosis, tubulointerstitial nephropathy, and minor glomerular abnormalities. During the median observation period of 11.0 years from the first onset of renal manifestations in patients with m.3243A>G, renal replacement therapy (RRT) was initiated in 50.8% of patients. Death occurred in 25.4% of the patients during the median observation period of 12.0 years. The median estimated glomerular filtration rate (eGFR) decline was 5.4 ml/min per 1.73 m2/yr in the cases, especially 8.3 ml/min per 1.73 m2/yr in FSGS cases, with m.3243A>G.
    Conclusion: Here, we described the clinicopathologic features and prognosis of mitochondrial nephropathy using large-scale data.
    Keywords:  clinicopathologic feature; m.3243A>G; mitochondria; mitochondrial nephropathy; national survey; prognosis
    DOI:  https://doi.org/10.1016/j.ekir.2021.12.028
  23. Curr Protoc. 2022 Mar;2(3): e390
    Gel-Based and Gel-Free Phosphoproteomics to Measure and Characterize Mitochondrial Phosphoproteins.
    Visith Thongboonkerd, Sakdithep Chaiyarit.
      The mitochondrion is a key intracellular organelle regulating metabolic processes, oxidative stress, energy production, calcium homeostasis, and cell survival. Protein phosphorylation plays an important role in regulating mitochondrial functions and cellular signaling pathways. Dysregulation of protein phosphorylation status can cause protein malfunction and abnormal signal transduction, leading to organ dysfunction and disease. Investigating the mitochondrial phosphoproteins is therefore crucial to better understand the molecular and pathogenic mechanisms of many metabolic disorders. Conventional analyses of phosphoproteins, for instance, via western blotting, can be done only for proteins for which specific antibodies to their phosphorylated forms are available. Moreover, such an approach is not suitable for large-scale study of phosphoproteins. Currently, proteomics represents an important tool for large-scale analysis of proteins and their post-translational modifications, including phosphorylation. Here, we provide step-by-step protocols for the proteomics analysis of mitochondrial phosphoproteins (the phosphoproteome), using renal tubular cells as an example. These protocols include methods to effectively isolate mitochondria and to validate the efficacy of mitochondrial enrichment as well as its purity. We also provide detailed protocols for performing both gel-based and gel-free phosphoproteome analyses. The gel-based analysis involves two-dimensional gel electrophoresis and phosphoprotein-specific staining, followed by protein identification via mass spectrometry, whereas the gel-free approach is based on in-solution mass spectrometric identification of specific phosphorylation sites and residues. In all, these approaches allow large-scale analyses of mitochondrial phosphoproteins that can be applied to other cells and tissues of interest. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Mitochondrial isolation/purification from renal tubular cells Support Protocol: Validation of enrichment efficacy and purity of mitochondrial isolation Basic Protocol 2: Gel-based phosphoproteome analysis Basic Protocol 3: Gel-free phosphoproteome analysis.
    Keywords:  PTMs ; mass spectrometry; mitochondria; phosphoproteome; phosphorylation; proteome; proteomics
    DOI:  https://doi.org/10.1002/cpz1.390
  24. Cell Host Microbe. 2022 Mar 09. pii: S1931-3128(22)00096-8. [Epub ahead of print]30(3): 274-276
    Hunger games in the host cell: Toxoplasma traps and skins host mitochondria.
    Mohamed-Ali Hakimi.
      Toxoplasma gondii actively tethers host mitochondria to its vacuole, altering their function. In a recent issue of Science, Li et al. demonstrate that Toxoplasma disarms host metabolic defenses by inducing the organelle to shed atypical large structures from its outer membrane to trap mitochondrial proteins that restrict parasite growth.
    DOI:  https://doi.org/10.1016/j.chom.2022.02.010
  25. J Proteome Res. 2022 Mar 07.
    Micropeptides Identified from Human Genomes.
    Jing Yuanyuan, Yin Xinqiang.
      Advanced analytic techniques, such as ribosome profiling and mass spectrometry, as well as improved bioinformatics technology, have promoted the field of genome annotation forward and have identified thousands of likely coding short open reading frames (sORFs) in the human genome. The discovery of sORFs and their products allows us to realize that the complexity of the human genome is far greater than previously assumed. Here, we provide a review of human micropeptides encoded by various transcripts such as mitochondrial rRNAs, long noncoding RNAs, circular RNAs, upstream of mRNAs, and so on.
    Keywords:  human genome; micropeptides; sORFs
    DOI:  https://doi.org/10.1021/acs.jproteome.1c00889
  26. J Neurosci Methods. 2022 Mar 07. pii: S0165-0270(22)00085-1. [Epub ahead of print] 109558
    Imaging and analysis of neuronal mitochondria in murine acute brain slices.
    Bimala Malla, Anja Hauser, Raluca Niesner, Carmen Infante-Duarte.
       BACKGROUND: Mitochondrial alterations are common to many inflammatory, degenerative as well as metabolic diseases. However, due to the vulnerability of mitochondria in explanted tissue, there is a general lack of ex vivo models, especially of CNS tissue, that preserve mitochondria and allow investigation of mitochondrial dynamics.
    NEW METHODS: Here, we present a model of acute hippocampal slices to study neuronal mitochondria ex vivo. We used two-photon microscopy to image CFP fluorescent neuronal mitochondria in B6.Cg-Tg(Thy1-CFP/COX8A)S2Lich mice brain slices. To define the optimal processing and culturing conditions, we compared mitochondrial morphology and motility with three different sets of slicing and incubation solutions. The investigation of mitochondrial dynamics was performed on deconvoluted images. For morphological investigation, images were segmented into three different categories according to the shape of mitochondria, while motility was investigated using semi-automated tracking.
    RESULTS: The imaging of acute brain slices by two-photon microscopy represented a suitable tool to monitor neuronal mitochondria ex vivo. We observed that mitochondrial dynamics were better preserved in slices incubated with HEPES aCSF, maintaining elongated rod-shaped morphology and the motility.
    COMPARISON WITH EXISTING METHODS: We showed for the first time a method that allows live imaging of mitochondria and its quantification, while the existing in vitro protocol are not suitable to investigate mitochondria in live tissue.
    CONCLUSION: We have established the best incubation conditions and microscopy tools to investigate living mitochondria in acute slices. We showed that preventing initial swelling with HEPES and addition of glucose, pyruvate, ascorbate and thiourea preserved mitochondria in adult brain slices, which could be monitored by two-photon microscopy.
    Keywords:  Acute brain slices; HEPES aCSF; N-Methyl-D-glucamin (NMDG) aCSF; mitochondria; sucrose cutting solution; two-photon microscopy
    DOI:  https://doi.org/10.1016/j.jneumeth.2022.109558
  27. Sci Rep. 2022 Mar 08. 12(1): 4104
    Mammalian HEMK1 methylates glutamine residue of the GGQ motif of mitochondrial release factors.
    Qi Fang, Yusuke Kimura, Tadahiro Shimazu, Takehiro Suzuki, Ayumi Yamada, Naoshi Dohmae, Shintaro Iwasaki, Yoichi Shinkai.
      Despite limited reports on glutamine methylation, methylated glutamine is found to be highly conserved in a "GGQ" motif in both prokaryotes and eukaryotes. In bacteria, glutamine methylation of peptide chain release factors 1/2 (RF1/2) by the enzyme PrmC is essential for translational termination and transcript recycling. Two PrmC homologs, HEMK1 and HEMK2, are found in mammals. In contrast to those of HEMK2, the biochemical properties and biological significance of HEMK1 remain largely unknown. In this study, we demonstrated that HEMK1 is an active methyltransferase for the glutamine residue of the GGQ motif of all four putative mitochondrial release factors (mtRFs)-MTRF1, MTRF1L, MRPL58, and MTRFR. In HEMK1-deficient HeLa cells, GGQ motif glutamine methylation was absent in all the mtRFs. We examined cell growth and mitochondrial properties, but disruption of the HEMK1 gene had no considerable impact on the overall cell growth, mtDNA copy number, mitochondrial membrane potential, and mitochondrial protein synthesis under regular culture condition with glucose as a carbon source. Furthermore, cell growth potential of HEMK1 KO cells was still maintained in the respiratory condition with galactose medium. Our results suggest that HEMK1 mediates the GGQ methylation of all four mtRFs in human cells; however, this specific modification seems mostly dispensable in cell growth and mitochondrial protein homeostasis at least for HeLa cells under fermentative culture condition.
    DOI:  https://doi.org/10.1038/s41598-022-08061-y
  28. Cells. 2022 Mar 02. pii: 862. [Epub ahead of print]11(5):
    Iron Supplementation Delays Aging and Extends Cellular Lifespan through Potentiation of Mitochondrial Function.
    Jovian Lin Jing, Trishia Cheng Yi Ning, Federica Natali, Frank Eisenhaber, Mohammad Alfatah.
      Aging is the greatest challenge to humankind worldwide. Aging is associated with a progressive loss of physiological integrity due to a decline in cellular metabolism and functions. Such metabolic changes lead to age-related diseases, thereby compromising human health for the remaining life. Thus, there is an urgent need to identify geroprotectors that regulate metabolic functions to target the aging biological processes. Nutrients are the major regulator of metabolic activities to coordinate cell growth and development. Iron is an important nutrient involved in several biological functions, including metabolism. In this study using yeast as an aging model organism, we show that iron supplementation delays aging and increases the cellular lifespan. To determine how iron supplementation increases lifespan, we performed a gene expression analysis of mitochondria, the main cellular hub of iron utilization. Quantitative analysis of gene expression data reveals that iron supplementation upregulates the expression of the mitochondrial tricarboxylic acid (TCA) cycle and electron transport chain (ETC) genes. Furthermore, in agreement with the expression profiles of mitochondrial genes, ATP level is elevated by iron supplementation, which is required for increasing the cellular lifespan. To confirm, we tested the role of iron supplementation in the AMPK knockout mutant. AMPK is a highly conserved controller of mitochondrial metabolism and energy homeostasis. Remarkably, iron supplementation rescued the short lifespan of the AMPK knockout mutant and confirmed its anti-aging role through the enhancement of mitochondrial functions. Thus, our results suggest a potential therapeutic use of iron supplementation to delay aging and prolong healthspan.
    Keywords:  AMPK; Saccharomyces cerevisiae; cellular lifespan extension; chronological aging; iron; mitochondria
    DOI:  https://doi.org/10.3390/cells11050862
  29. Hum Mutat. 2022 Mar 09.
    seqr: a web-based analysis and collaboration tool for rare disease genomics.
    Lynn S Pais, Hana Snow, Ben Weisburd, Shifa Zhang, Samantha M Baxter, Stephanie DiTroia, Emily O'Heir, Eleina England, Katherine R Chao, Gabrielle Lemire, Ikeoluwa Osei-Owusu, Grace E VanNoy, Michael Wilson, Kevin Nguyen, Harindra Arachchi, William Phu, Matthew Solomonson, Stacy Mano, Melanie O'Leary, Alysia Lovgren, Lawrence Babb, Christina A Austin-Tse, Heidi L Rehm, Daniel G MacArthur, Anne O'Donnell-Luria.
      Exome and genome sequencing have become the tools of choice for rare disease diagnosis, leading to large amounts of data available for analyses. To identify causal variants in these datasets, powerful filtering and decision support tools that can be efficiently used by clinicians and researchers are required. To address this need, we developed seqr - an open source, web-based tool for family-based monogenic disease analysis that allows researchers to work collaboratively to search and annotate genomic callsets. To date, seqr is being used in several research pipelines and one clinical diagnostic lab. In our own experience through the Broad Institute Center for Mendelian Genomics, seqr has enabled analyses of over 10,000 families, supporting the diagnosis of more than 3,800 individuals with rare disease and discovery of over 300 novel disease genes. Here we describe a framework for genomic analysis in rare disease that leverages seqr's capabilities for variant filtration, annotation, and causal variant identification, as well as support for research collaboration and data sharing. The seqr platform is available as open source software, allowing low-cost participation in rare disease research, and a community effort to support diagnosis and gene discovery in rare disease. This article is protected by copyright. All rights reserved.
    Keywords:  data sharing; genomic analysis; novel gene discovery; rare disease diagnosis; research collaboration; variant filtration
    DOI:  https://doi.org/10.1002/humu.24366
  30. Proc Natl Acad Sci U S A. 2022 03 15. 119(11): e2115533119
    A serotonergic circuit regulates aversive associative learning under mitochondrial stress in C. elegans.
    Yueh-Chen Chiang, Chien-Po Liao, Chun-Liang Pan.
      SignificancePhysiological stress triggers avoidance behavior, allowing the animals to stay away from potential threats and optimize their chance of survival. Mitochondrial disruption, a common physiological stress in diverse species, induces the nematode Caenorhabditis elegans to avoid non-pathogenic bacteria through a serotonergic neuronal circuit. We find that distinct neurons, communicated through serotonin and a specific serotonin receptor, are required for the formation and retrieval of this learned aversive behavior. This learned avoidance behavior is associated with increased serotonin synthesis, altered neuronal response property, and reprogramming of locomotion patterns. The circuit and neuromodulatory mechanisms described here offer important insights for stress-induced avoidance behavior.
    Keywords:  C. elegans; aversive learning; mitochondria; serotonin; stress
    DOI:  https://doi.org/10.1073/pnas.2115533119
  31. Endocrinol Diabetes Nutr (Engl Ed). 2022 Feb;pii: S2530-0180(22)00023-3. [Epub ahead of print]69(2): 144-148
    Immunonutrition for the acute treatment of MELAS syndrome.
    Elizabeth Pérez-Cruz, Carolina González-Rivera, Luz Del Carmen Gabriela Valencia-Olvera.
      MELAS syndrome (Mitochondrial Encephalopathy, Lactic Acidosis and Stroke-like episodes) is one of the most frequent mitochondrial pathologies. Its diagnosis is based on the classic triad of symptoms its acronym stands for and the presence of ragged red fibres. There is currently no curative therapy for MELAS, and treatment focuses on managing complications that affect specific organs and functions. However, some immunonutrients can be used as a therapeutic alternative in patients with MELAS. We present a scientific literature review accompanied by the clinical case of a patient with dementia and seizures admitted to the intensive care unit.
    Keywords:  Arginina; Arginine; Carnitina; Carnitine; Immunonutrition; Inmunonutrición; MELAS syndrome; Síndrome MELAS
    DOI:  https://doi.org/10.1016/j.endien.2022.02.006
  32. Trends Neurosci. 2022 Mar 03. pii: S0166-2236(22)00017-0. [Epub ahead of print]
    Mitochondria-lysosome contact site dynamics and misregulation in neurodegenerative diseases.
    Jasmine Cisneros, Tayler B Belton, George C Shum, Catherine G Molakal, Yvette C Wong.
      Neurons rely heavily on properly regulated mitochondrial and lysosomal homeostasis, with multiple neurodegenerative diseases linked to dysfunction in these two organelles. Interestingly, mitochondria-lysosome membrane contact sites have been identified as a key pathway mediating their crosstalk in neurons. Recent studies have further elucidated the regulation of mitochondria-lysosome contact dynamics via distinct tethering/untethering protein machinery. Moreover, this pathway has been shown to have additional functions in regulating organelle network dynamics and metabolite transfer between lysosomes and mitochondria. In this review, we highlight recent advances in the field of mitochondria-lysosome contact sites and their misregulation across multiple neurodegenerative disorders, which further underscore a potential role for this pathway in neuronal homeostasis and disease.
    Keywords:  Charcot-Marie-Tooth disease; Parkinson’s disease; inter-organelle contact sites; lysosomal storage disorders; lysosomes; mitochondria
    DOI:  https://doi.org/10.1016/j.tins.2022.01.005
  33. Nutrients. 2022 Jan 27. pii: 559. [Epub ahead of print]14(3):
    Elovl2-Ablation Leads to Mitochondrial Membrane Fatty Acid Remodeling and Reduced Efficiency in Mouse Liver Mitochondria.
    Alexia Gómez Rodríguez, Emanuela Talamonti, Alba Naudi, Anastasia V Kalinovich, Anna M Pauter, Gustavo Barja, Tore Bengtsson, Anders Jacobsson, Reinald Pamplona, Irina G Shabalina.
      The fatty acid elongase elongation of very long-chain fatty acids protein 2 (ELOVL2) controls the elongation of polyunsaturated fatty acids (PUFA) producing precursors for omega-3, docosahexaenoic acid (DHA), and omega-6, docosapentaenoic acid (DPAn-6) in vivo. Expectedly, Elovl2-ablation drastically reduced the DHA and DPAn-6 in liver mitochondrial membranes. Unexpectedly, however, total PUFAs levels decreased further than could be explained by Elovl2 ablation. The lipid peroxidation process was not involved in PUFAs reduction since malondialdehyde-lysine (MDAL) and other oxidative stress biomarkers were not enhanced. The content of mitochondrial respiratory chain proteins remained unchanged. Still, membrane remodeling was associated with the high voltage-dependent anion channel (VDAC) and adenine nucleotide translocase 2 (ANT2), a possible reflection of the increased demand on phospholipid transport to the mitochondria. Mitochondrial function was impaired despite preserved content of the respiratory chain proteins and the absence of oxidative damage. Oligomycin-insensitive oxygen consumption increased, and coefficients of respiratory control were reduced by 50%. The mitochondria became very sensitive to fatty acid-induced uncoupling and permeabilization, where ANT2 is involved. Mitochondrial volume and number of peroxisomes increased as revealed by transmission electron microscopy. In conclusion, the results imply that endogenous DHA production is vital for the normal function of mouse liver mitochondria and could be relevant not only for mice but also for human metabolism.
    Keywords:  adenine nucleotide translocase; docosahexaenoic acid (DHA) deficiency; membrane permeabilization; mitochondrial function; oxidative damage markers; polyunsaturated fatty acids
    DOI:  https://doi.org/10.3390/nu14030559
  34. Front Cell Dev Biol. 2022 ;10 796061
    Evaluation of Parkin in the Regulation of Myocardial Mitochondria-Associated Membranes and Cardiomyopathy During Endotoxemia.
    Matthew Kim, Azadeh Nikouee, Yuxiao Sun, Qing-Jun Zhang, Zhi-Ping Liu, Qun Sophia Zang.
      Background: Mitochondrial deficiency is a known pathology in sepsis-induced organ failure. We previously found that mitochondria-associated membranes (MAMs), a subcellular domain supporting mitochondrial status, are impaired in the heart during endotoxemia, suggesting a mechanism of mitochondrial damage occurred in sepsis. Mitophagy pathway via E3 ubiquitin ligase Parkin and PTEN-induced kinase 1 (PINK1) controls mitochondrial quality. Studies described here examined the impact of Parkin on cardiac MAMs and endotoxemia-induced cardiomyopathy. Additionally, point mutation W403A in Parkin was previously identified as a constitutively active mutation in vitro. In vivo effects of forced expression of this mutation were evaluated in the endotoxemia model. Methods: Mice of wild type (WT), Parkin-deficiency (Park2 -/- ), and knock-in expression of Parkin W402A (human Parkin W403A) were given lipopolysaccharide (LPS) challenge. Cardiac function was evaluated by echocardiography. In the harvested heart tissue, MAM fractions were isolated by ultracentrifugation, and their amount and function were quantified. Ultrastructure of MAMs and mitochondria was examined by electron microscopy. Mitochondrial respiratory activities were measured by enzyme assays. Myocardial inflammation was estimated by levels of pro-inflammatory cytokine IL-6. Myocardial mitophagy was assessed by levels of mitophagy factors associated with mitochondria and degrees of mitochondria-lysosome co-localization. Parkin activation, signified by phosphorylation on serine 65 of Parkin, was also evaluated. Results: Compared with WT, Park2 -/- mice showed more severely impaired cardiac MAMs during endotoxemia, characterized by disrupted structure, reduced quantity, and weakened transporting function. Endotoxemia-induced cardiomyopathy was intensified in Park2 -/- mice, shown by worsened cardiac contractility and higher production of IL-6. Mitochondria from the Park2 -/- hearts were more deteriorated, indicated by losses in both structural integrity and respiration function. Unexpectedly, mice carrying Parkin W402A showed similar levels of cardiomyopathy and mitochondrial damage when compared with their WT counterparts. Further, Parkin W402A mutation neither enhanced mitophagy nor increased Parkin activation in myocardium under the challenge of endotoxemia. Conclusion: our results suggest that Parkin/PINK1 mitophagy participates in the regulation of cardiac MAMs during endotoxemia. Point mutation W402A (human W403A) in Parkin is not sufficient to alleviate cardiomyopathy induced by endotoxemia in vivo.
    Keywords:  cardiac dysfunction; endotoxemia; inflammation; mitochondria; mitophagy; parkin; sepsis
    DOI:  https://doi.org/10.3389/fcell.2022.796061
  35. Cells. 2022 Feb 23. pii: 776. [Epub ahead of print]11(5):
    βIII-Tubulin Structural Domains Regulate Mitochondrial Network Architecture in an Isotype-Specific Manner.
    Amelia L Parker, Wee Siang Teo, Simon Brayford, Ullhas K Moorthi, Senthil Arumugam, Charles Ferguson, Robert G Parton, Joshua A McCarroll, Maria Kavallaris.
      βIII-tubulin is a neuronal microtubule protein that is aberrantly expressed in epithelial cancers. The microtubule network is implicated in regulating the architecture and dynamics of the mitochondrial network, although the isotype-specific role for β-tubulin proteins that constitute this microtubule network remains unclear. High-resolution electron microscopy revealed that manipulation of βIII-tubulin expression levels impacts the volume and shape of mitochondria. Analysis of the structural domains of the protein identifies that the C-terminal tail of βIII-tubulin, which distinguishes this protein from other β-tubulin isotypes, significantly contributes to the isotype-specific effects of βIII-tubulin on mitochondrial architecture. Mass spectrometry analysis of protein-protein interactions with β-tubulin isotypes identifies that βIII-tubulin specifically interacts with regulators of mitochondrial dynamics that may mediate these functional effects. Advanced quantitative dynamic lattice light sheet imaging of the mitochondrial network reveals that βIII-tubulin promotes a more dynamic and extended reticular mitochondrial network, and regulates mitochondrial volume. A regulatory role for the βIII-tubulin C-terminal tail in mitochondrial network dynamics and architecture has widespread implications for the maintenance of mitochondrial homeostasis in health and disease.
    Keywords:  carboxy-terminal tail; microtubules; mitochondria; tubulin isotype
    DOI:  https://doi.org/10.3390/cells11050776
  36. Int J Mol Sci. 2022 Feb 28. pii: 2717. [Epub ahead of print]23(5):
    The Role of l-Carnitine in Mitochondria, Prevention of Metabolic Inflexibility and Disease Initiation.
    Mohamed Ashraf Virmani, Maria Cirulli.
      Mitochondria control cellular fate by various mechanisms and are key drivers of cellular metabolism. Although the main function of mitochondria is energy production, they are also involved in cellular detoxification, cellular stabilization, as well as control of ketogenesis and glucogenesis. Conditions like neurodegenerative disease, insulin resistance, endocrine imbalances, liver and kidney disease are intimately linked to metabolic disorders or inflexibility and to mitochondrial dysfunction. Mitochondrial dysfunction due to a relative lack of micronutrients and substrates is implicated in the development of many chronic diseases. l-carnitine is one of the key nutrients for proper mitochondrial function and is notable for its role in fatty acid oxidation. l-carnitine also plays a major part in protecting cellular membranes, preventing fatty acid accumulation, modulating ketogenesis and glucogenesis and in the elimination of toxic metabolites. l-carnitine deficiency has been observed in many diseases including organic acidurias, inborn errors of metabolism, endocrine imbalances, liver and kidney disease. The protective effects of micronutrients targeting mitochondria hold considerable promise for the management of age and metabolic related diseases. Preventing nutrient deficiencies like l-carnitine can be beneficial in maintaining metabolic flexibility via the optimization of mitochondrial function. This paper reviews the critical role of l-carnitine in mitochondrial function, metabolic flexibility and in other pathophysiological cellular mechanisms.
    Keywords:  beta oxidation; diabetes; fatty acid oxidation; glycolysis; ketogenesis; l-carnitine; liver disease; metabolic inflexibility; mitochondrial function; neurodegeneration
    DOI:  https://doi.org/10.3390/ijms23052717
  37. Traffic. 2022 Mar 08.
    Loss of intermediate filament IFB-1 reduces mobility, density and physiological function of mitochondria in C. elegans sensory neurons.
    Syed Nooruzuha Barmaver, Muniesh Muthaiyan Shanmugam, Yen Chang, Odvogmed Bayansan, Prerana Bhan, Gong-Her Wu, Oliver I Wagner.
      Mitochondria and intermediate filament (IF) accumulations often occur during imbalanced axonal transport leading to various types of neurological diseases. It is still poorly understood whether a link between neuronal IFs and mitochondrial mobility exist. In C. elegans, among the 11 cytoplasmic IF family proteins, IFB-1 is of particular interest as it is expressed in a subset of sensory neurons. Depletion of IFB-1 leads to mild dye-filling and significant chemotaxis defects as well as reduced life span. Sensory neuron development is affected and mitochondria transport is slowed down leading to reduced densities of these organelles. Mitochondria tend to cluster in neurons of IFB-1 mutants likely independent of the fission and fusion machinery. Oxygen consumption and mitochondrial membrane potential is measurably reduced in worms carrying mutations in the ifb-1 gene. Membrane potential also seems to play a role in transport such as FCCP treatment led to increased directional switching of mitochondria. Mitochondria colocalize with IFB-1 in worm neurons and appear in a complex with IFB-1 in pull-down assays. In summary, we propose a model in which neuronal intermediate filaments may serve as critical (transient) anchor points for mitochondria during their long-range transport in neurons for steady and balanced transport. This article is protected by copyright. All rights reserved.
    Keywords:  ATP5B1; Axonal transport; C. elegans; FCCP; IFA; IFB-1; amphid sensory neuron bundle; chemotaxis quadrant assay; intermediate filaments; mitochondria; nematode oxygen consumption
    DOI:  https://doi.org/10.1111/tra.12838
  38. Int J Mol Sci. 2022 Feb 28. pii: 2679. [Epub ahead of print]23(5):
    Intertwined Relationship of Mitochondrial Metabolism, Gut Microbiome and Exercise Potential.
    Saba Imdad, Wonchung Lim, Jin-Hee Kim, Chounghun Kang.
      The microbiome has emerged as a key player contributing significantly to the human physiology over the past decades. The potential microbial niche is largely unexplored in the context of exercise enhancing capacity and the related mitochondrial functions. Physical exercise can influence the gut microbiota composition and diversity, whereas a sedentary lifestyle in association with dysbiosis can lead to reduced well-being and diseases. Here, we have elucidated the importance of diverse microbiota, which is associated with an individual's fitness, and moreover, its connection with the organelle, the mitochondria, which is the hub of energy production, signaling, and cellular homeostasis. Microbial by-products, such as short-chain fatty acids, are produced during regular exercise that can enhance the mitochondrial capacity. Therefore, exercise can be employed as a therapeutic intervention to circumvent or subside various metabolic and mitochondria-related diseases. Alternatively, the microbiome-mitochondria axis can be targeted to enhance exercise performance. This review furthers our understanding about the influence of microbiome on the functional capacity of the mitochondria and exercise performance, and the interplay between them.
    Keywords:  gut microbiome; metabolism; microbial metabolites; mitochondrial plasticity; regular exercise training; short chain fatty acids
    DOI:  https://doi.org/10.3390/ijms23052679
  39. Front Cell Dev Biol. 2022 ;10 847045
    Loss of Function of mtHsp70 Chaperone Variants Leads to Mitochondrial Dysfunction in Congenital Sideroblastic Anemia.
    Vinaya Vishwanathan, Patrick D'Silva.
      Congenital Sideroblastic Anemias (CSA) is a group of rare genetic disorders characterized by the abnormal accumulation of iron in erythrocyte precursors. A common hallmark underlying these pathological conditions is mitochondrial dysfunction due to altered protein homeostasis, heme biosynthesis, and oxidative phosphorylation. A clinical study on congenital sideroblastic anemia has identified mutations in mitochondrial Hsp70 (mtHsp70/Mortalin). Mitochondrial Hsp70 plays a critical role in maintaining mitochondrial function by regulating several pathways, including protein import and folding, and iron-sulfur cluster synthesis. Owing to the structural and functional homology between human and yeast mtHsp70, we have utilized the yeast system to delineate the role of mtHsp70 variants in the etiology of CSA's. Analogous mutations in yeast mtHsp70 exhibited temperature-sensitive growth phenotypes under non-respiratory and respiratory conditions. In vivo analyses indicate a perturbation in mitochondrial mass and functionality accompanied by an alteration in the organelle network and cellular redox levels. Preliminary in vitro biochemical studies of mtHsp70 mutants suggest impaired import function, altered ATPase activity and substrate interaction. Together, our findings suggest the loss of chaperone activity to be a pivotal factor in the pathophysiology of congenital sideroblastic anemia.
    Keywords:  Ssc1; congenital sideroblastic anemia; molecular chaperone; mortalin; mtHsp70; protein folding
    DOI:  https://doi.org/10.3389/fcell.2022.847045
  40. Elife. 2022 Mar 08. pii: e68148. [Epub ahead of print]11
    Quantitative transportomics identifies Kif5a as a major regulator of neurodegeneration.
    Sahil H Shah, Lucio M Schiapparelli, Yuanhui Ma, Satoshi Yokota, Melissa Atkins, Xin Xia, Evan G Cameron, Thanh Huang, Sarah Saturday, Catalin B Sun, Cara Knasel, Seth Blackshaw, John R Yates Iii, Hollis T Cline, Jeffrey L Goldberg.
      Many neurons in the adult central nervous system, including retinal ganglion cells (RGCs), degenerate and die after injury. Early axon protein and organelle trafficking failure is a key component in many neurodegenerative disorders yet changes to axoplasmic transport in disease models have not been quantified. We analyzed early changes in the protein 'transportome' from (RGC somas to their axons after optic nerve injury and identified transport failure of an anterograde motor protein Kif5a early in RGC degeneration. We demonstrated that manipulating Kif5a expression affects anterograde mitochondrial trafficking in RGCs and characterized axon transport in Kif5a knockout mice to identify proteins whose axon localization was Kif5a-dependent. Finally, we found that knockout of Kif5a in RGCs resulted in progressive RGC degeneration in the absence of injury. Together with expression data localizing Kif5a to human RGCs, these data identify Kif5a transport failure as a cause of RGC neurodegeneration and point to a mechanism for future therapeutics.
    Keywords:  mouse; neuroscience; rat; regenerative medicine; stem cells
    DOI:  https://doi.org/10.7554/eLife.68148
  41. Front Pharmacol. 2022 ;13 816551
    The Mitochondrial Deubiquitinase USP30 Regulates AKT/mTOR Signaling.
    Ruohan Zhang, Serra Ozgen, Hongke Luo, Judith Krigman, Yutong Zhao, Gang Xin, Nuo Sun.
      Mitophagy is an intracellular mechanism to maintain mitochondrial health by removing dysfunctional mitochondria. The E3 ligase Parkin ubiquitinates the membrane proteins on targeted mitochondria to initiate mitophagy, whereas USP30 antagonizes Parkin-dependent mitophagy by removing ubiquitin from Parkin substrates. The AKT/mTOR signaling is a master regulator of cell proliferation, differentiation, apoptosis, and autophagy. Although mounting evidence suggests that perturbations in the AKT/mTOR signaling pathway may contribute to mitophagy regulation, the specific mechanisms between Parkin/USP30 and AKT/mTOR signaling have not been elucidated. In this study, we employ a set of genetic reagents to investigate the role of Parkin and USP30 in regulating the AKT/mTOR signaling during mitophagy. We demonstrated that, in the setting of mitochondrial stress, the AKT/mTOR signaling is regulated, at least in part, by the activity of Parkin and USP30. Parkin inhibits AKT/mTOR signaling following an in vitro mitochondrial stress, thereby promoting apoptosis. However, USP30 overexpression antagonizes the activity of Parkin to sustain AKT/mTOR activity and inhibit apoptosis. These findings provide new insights into Parkin and USP30's role in apoptosis and suggest that inhibiting USP30 might provide a specific strategy to synergize with AKT/mTOR inhibitors in cancer treatment.
    Keywords:  USP30; akt; cancer; leukemia; mTOR; mitophagy; parkin
    DOI:  https://doi.org/10.3389/fphar.2022.816551
  42. Nature. 2022 Mar 09.
    A non-canonical tricarboxylic acid cycle underlies cellular identity.
    Paige K Arnold, Benjamin T Jackson, Katrina I Paras, Julia S Brunner, Madeleine L Hart, Oliver J Newsom, Sydney P Alibeckoff, Jennifer Endress, Esther Drill, Lucas B Sullivan, Lydia W S Finley.
      The tricarboxylic acid (TCA) cycle is a central hub of cellular metabolism, oxidizing nutrients to generate reducing equivalents for energy production and critical metabolites for biosynthetic reactions. Despite the importance of the products of the TCA cycle for cell viability and proliferation, mammalian cells display diversity in TCA-cycle activity1,2. How this diversity is achieved, and whether it is critical for establishing cell fate, remains poorly understood. Here we identify a non-canonical TCA cycle that is required for changes in cell state. Genetic co-essentiality mapping revealed a cluster of genes that is sufficient to compose a biochemical alternative to the canonical TCA cycle, wherein mitochondrially derived citrate exported to the cytoplasm is metabolized by ATP citrate lyase, ultimately regenerating mitochondrial oxaloacetate to complete this non-canonical TCA cycle. Manipulating the expression of ATP citrate lyase or the canonical TCA-cycle enzyme aconitase 2 in mouse myoblasts and embryonic stem cells revealed that changes in the configuration of the TCA cycle accompany cell fate transitions. During exit from pluripotency, embryonic stem cells switch from canonical to non-canonical TCA-cycle metabolism. Accordingly, blocking the non-canonical TCA cycle prevents cells from exiting pluripotency. These results establish a context-dependent alternative to the traditional TCA cycle and reveal that appropriate TCA-cycle engagement is required for changes in cell state.
    DOI:  https://doi.org/10.1038/s41586-022-04475-w
  43. Autophagy. 2022 Mar 08. 1-18
    Mitochondrial respiration supports autophagy to provide stress resistance during quiescence.
    Silvia Magalhaes-Novais, Jan Blecha, Ravindra Naraine, Jana Mikesova, Pavel Abaffy, Alena Pecinova, Mirko Milosevic, Romana Bohuslavova, Jan Prochazka, Shawez Khan, Eliska Novotna, Radek Sindelka, Radek Machan, Mieke Dewerchin, Erik Vlcak, Joanna Kalucka, Sona Stemberkova Hubackova, Ales Benda, Jermaine Goveia, Tomas Mracek, Cyril Barinka, Peter Carmeliet, Jiri Neuzil, Katerina Rohlenova, Jakub Rohlena.
      Mitochondrial oxidative phosphorylation (OXPHOS) generates ATP, but OXPHOS also supports biosynthesis during proliferation. In contrast, the role of OXPHOS during quiescence, beyond ATP production, is not well understood. Using mouse models of inducible OXPHOS deficiency in all cell types or specifically in the vascular endothelium that negligibly relies on OXPHOS-derived ATP, we show that selectively during quiescence OXPHOS provides oxidative stress resistance by supporting macroautophagy/autophagy. Mechanistically, OXPHOS constitutively generates low levels of endogenous ROS that induce autophagy via attenuation of ATG4B activity, which provides protection from ROS insult. Physiologically, the OXPHOS-autophagy system (i) protects healthy tissue from toxicity of ROS-based anticancer therapy, and (ii) provides ROS resistance in the endothelium, ameliorating systemic LPS-induced inflammation as well as inflammatory bowel disease. Hence, cells acquired mitochondria during evolution to profit from oxidative metabolism, but also built in an autophagy-based ROS-induced protective mechanism to guard against oxidative stress associated with OXPHOS function during quiescence.Abbreviations: AMPK: AMP-activated protein kinase; AOX: alternative oxidase; Baf A: bafilomycin A1; CI, respiratory complexes I; DCF-DA: 2',7'-dichlordihydrofluorescein diacetate; DHE: dihydroethidium; DSS: dextran sodium sulfate; ΔΨmi: mitochondrial inner membrane potential; EdU: 5-ethynyl-2'-deoxyuridine; ETC: electron transport chain; FA: formaldehyde; HUVEC; human umbilical cord endothelial cells; IBD: inflammatory bowel disease; LC3B: microtubule associated protein 1 light chain 3 beta; LPS: lipopolysaccharide; MEFs: mouse embryonic fibroblasts; MTORC1: mechanistic target of rapamycin kinase complex 1; mtDNA: mitochondrial DNA; NAC: N-acetyl cysteine; OXPHOS: oxidative phosphorylation; PCs: proliferating cells; PE: phosphatidylethanolamine; PEITC: phenethyl isothiocyanate; QCs: quiescent cells; ROS: reactive oxygen species; PLA2: phospholipase A2, WB: western blot.
    Keywords:  ATG4B; biosynthesis; cell death; electron transport chain; endothelial cells; mitochondria; oxidative phosphorylation; oxidative stress; reactive oxygen species
    DOI:  https://doi.org/10.1080/15548627.2022.2038898
  44. Science. 2022 Mar 11. 375(6585): eabi6983
    OpenCell: Endogenous tagging for the cartography of human cellular organization.
    Nathan H Cho, Keith C Cheveralls, Andreas-David Brunner, Kibeom Kim, André C Michaelis, Preethi Raghavan, Hirofumi Kobayashi, Laura Savy, Jason Y Li, Hera Canaj, James Y S Kim, Edna M Stewart, Christian Gnann, Frank McCarthy, Joana P Cabrera, Rachel M Brunetti, Bryant B Chhun, Greg Dingle, Marco Y Hein, Bo Huang, Shalin B Mehta, Jonathan S Weissman, Rafael Gómez-Sjöberg, Daniel N Itzhak, Loïc A Royer, Matthias Mann, Manuel D Leonetti.
      Elucidating the wiring diagram of the human cell is a central goal of the postgenomic era. We combined genome engineering, confocal live-cell imaging, mass spectrometry, and data science to systematically map the localization and interactions of human proteins. Our approach provides a data-driven description of the molecular and spatial networks that organize the proteome. Unsupervised clustering of these networks delineates functional communities that facilitate biological discovery. We found that remarkably precise functional information can be derived from protein localization patterns, which often contain enough information to identify molecular interactions, and that RNA binding proteins form a specific subgroup defined by unique interaction and localization properties. Paired with a fully interactive website (opencell.czbiohub.org), our work constitutes a resource for the quantitative cartography of human cellular organization.
    DOI:  https://doi.org/10.1126/science.abi6983
  45. Nat Commun. 2022 Mar 10. 13(1): 1265
    Improved prediction of protein-protein interactions using AlphaFold2.
    Patrick Bryant, Gabriele Pozzati, Arne Elofsson.
      Predicting the structure of interacting protein chains is a fundamental step towards understanding protein function. Unfortunately, no computational method can produce accurate structures of protein complexes. AlphaFold2, has shown unprecedented levels of accuracy in modelling single chain protein structures. Here, we apply AlphaFold2 for the prediction of heterodimeric protein complexes. We find that the AlphaFold2 protocol together with optimised multiple sequence alignments, generate models with acceptable quality (DockQ ≥ 0.23) for 63% of the dimers. From the predicted interfaces we create a simple function to predict the DockQ score which distinguishes acceptable from incorrect models as well as interacting from non-interacting proteins with state-of-art accuracy. We find that, using the predicted DockQ scores, we can identify 51% of all interacting pairs at 1% FPR.
    DOI:  https://doi.org/10.1038/s41467-022-28865-w
  46. Nat Genet. 2022 Mar 07.
    Assessing the contribution of rare variants to complex trait heritability from whole-genome sequence data.
    TOPMed Anthropometry Working Group
      Analyses of data from genome-wide association studies on unrelated individuals have shown that, for human traits and diseases, approximately one-third to two-thirds of heritability is captured by common SNPs. However, it is not known whether the remaining heritability is due to the imperfect tagging of causal variants by common SNPs, in particular whether the causal variants are rare, or whether it is overestimated due to bias in inference from pedigree data. Here we estimated heritability for height and body mass index (BMI) from whole-genome sequence data on 25,465 unrelated individuals of European ancestry. The estimated heritability was 0.68 (standard error 0.10) for height and 0.30 (standard error 0.10) for body mass index. Low minor allele frequency variants in low linkage disequilibrium (LD) with neighboring variants were enriched for heritability, to a greater extent for protein-altering variants, consistent with negative selection. Our results imply that rare variants, in particular those in regions of low linkage disequilibrium, are a major source of the still missing heritability of complex traits and disease.
    DOI:  https://doi.org/10.1038/s41588-021-00997-7
  47. Nat Methods. 2022 Mar;19(3): 296-306
    A pan-tissue DNA methylation atlas enables in silico decomposition of human tissue methylomes at cell-type resolution.
    Tianyu Zhu, Jacklyn Liu, Stephan Beck, Sun Pan, David Capper, Matt Lechner, Chrissie Thirlwell, Charles E Breeze, Andrew E Teschendorff.
      Bulk-tissue DNA methylomes represent an average over many different cell types, hampering our understanding of cell-type-specific contributions to disease development. As single-cell methylomics is not scalable to large cohorts of individuals, cost-effective computational solutions are needed, yet current methods are limited to tissues such as blood. Here we leverage the high-resolution nature of tissue-specific single-cell RNA-sequencing datasets to construct a DNA methylation atlas defined for 13 solid tissue types and 40 cell types. We comprehensively validate this atlas in independent bulk and single-nucleus DNA methylation datasets. We demonstrate that it correctly predicts the cell of origin of diverse cancer types and discovers new prognostic associations in olfactory neuroblastoma and stage 2 melanoma. In brain, the atlas predicts a neuronal origin for schizophrenia, with neuron-specific differential DNA methylation enriched for corresponding genome-wide association study risk loci. In summary, the DNA methylation atlas enables the decomposition of 13 different human tissue types at a high cellular resolution, paving the way for an improved interpretation of epigenetic data.
    DOI:  https://doi.org/10.1038/s41592-022-01412-7
  48. JAMA Neurol. 2022 Mar 07.
    Multicenter Consensus Approach to Evaluation of Neonatal Hypotonia in the Genomic Era: A Review.
    Sarah U Morton, John Christodoulou, Gregory Costain, Francesco Muntoni, Emma Wakeling, Monica H Wojcik, Courtney E French, Anna Szuto, James J Dowling, Ronald D Cohn, F Lucy Raymond, Basil T Darras, David A Williams, Sebastian Lunke, Zornitza Stark, David H Rowitch, Pankaj B Agrawal.
       Importance: Infants with hypotonia can present with a variety of potentially severe clinical signs and symptoms and often require invasive testing and multiple procedures. The wide range of clinical presentations and potential etiologies leaves diagnosis and prognosis uncertain, underscoring the need for rapid elucidation of the underlying genetic cause of disease.
    Observations: The clinical application of exome sequencing or genome sequencing has dramatically improved the timely yield of diagnostic testing for neonatal hypotonia, with diagnostic rates of greater than 50% in academic neonatal intensive care units (NICUs) across Australia, Canada, the UK, and the US, which compose the International Precision Child Health Partnership (IPCHiP). A total of 74% (17 of 23) of patients had a change in clinical care in response to genetic diagnosis, including 2 patients who received targeted therapy. This narrative review discusses the common causes of neonatal hypotonia, the relative benefits and limitations of available testing modalities used in NICUs, and hypotonia management recommendations.
    Conclusions and Relevance: This narrative review summarizes the causes of neonatal hypotonia and the benefits of prompt genetic diagnosis, including improved prognostication and identification of targeted treatments which can improve the short-term and long-term outcomes. Institutional resources can vary among different NICUs; as a result, consideration should be given to rule out a small number of relatively unique conditions for which rapid targeted genetic testing is available. Nevertheless, the consensus recommendation is to use rapid genome or exome sequencing as a first-line testing option for NICU patients with unexplained hypotonia. As part of the IPCHiP, this diagnostic experience will be collected in a central database with the goal of advancing knowledge of neonatal hypotonia and improving evidence-based practice.
    DOI:  https://doi.org/10.1001/jamaneurol.2022.0067
  49. Elife. 2022 Mar 08. pii: e73524. [Epub ahead of print]11
    Distinct and diverse chromatin-proteomes of ageing mouse organs reveal protein signatures that correlate with physiological functions.
    Giorgio Oliviero, Sergey Kovalchuk, Adelina Rogowska-Wrzesinska, Veit Schwämmle, Ole N Jensen.
      Temporal molecular changes in ageing mammalian organs are of relevance to disease etiology because many age-related diseases are linked to changes in the transcriptional and epigenetic machinery that regulate gene expression. We performed quantitative proteome analysis of chromatin-enriched protein extracts to investigate the dynamics of the chromatin-proteomes of the mouse brain, heart, lung, kidney, liver, and spleen at 3, 5, 10, and 15 months of age. Each organ exhibited a distinct chromatin-proteome and sets of unique proteins. The brain and spleen chromatin-proteomes were the most extensive, diverse, and heterogenous among the six organs. The spleen chromatin proteome appeared static during the lifespan, presenting a young phenotype that reflects the permanent alertness state and important role of this organ in physiological defense and immunity. We identified a total of 5928 proteins, including 2472 nuclear or chromatin associated proteins across the six mouse organs. Up to 3125 proteins were quantified in each organ demonstrating distinct and organ-specific temporal protein expression timelines and regulation at the post-translational level. Bioinformatics meta-analysis of these chromatin proteomes revealed distinct physiological and ageing-related features for each organ. Our results demonstrate the efficiency of organelle specific proteomics for in vivo studies of a model organism and consolidate the hypothesis that chromatin-associated proteins are involved in distinct and specific physiological functions in ageing organs.
    Keywords:  cell biology; developmental biology; mouse
    DOI:  https://doi.org/10.7554/eLife.73524
  50. Curr Stem Cell Rep. 2021 Jun;7(2): 72-84
    Metabolic Regulation of Stem Cells in Aging.
    Andrea Keller, Tyus Temple, Behnam Sayanjali, Maria M Mihaylova.
       Purpose of Review: From invertebrates to vertebrates, the ability to sense nutrient availability is critical for survival. Complex organisms have evolved numerous signaling pathways to sense nutrients and dietary fluctuations, which influence many cellular processes. Although both overabundance and extreme depletion of nutrients can lead to deleterious effects, dietary restriction without malnutrition can increase lifespan and promote overall health in many model organisms. In this review, we focus on age-dependent changes in stem cell metabolism and dietary interventions used to modulate stem cell function in aging.
    Recent Findings: Over the last half-century, seminal studies have illustrated that dietary restriction confers beneficial effects on longevity in many model organisms. Many researchers have now turned to dissecting the molecular mechanisms by which these diets affect aging at the cellular level. One subpopulation of cells of particular interest are adult stem cells, the most regenerative cells of the body. It is generally accepted that the regenerative capacity of stem cells declines with age, and while the metabolic requirements of each vary across tissues, the ability of dietary interventions to influence stem cell function is striking.
    Summary: In this review, we will focus primarily on how metabolism plays a role in adult stem cell homeostasis with respect to aging, with particular emphasis on intestinal stem cells while also touching on hematopoietic, skeletal muscle, and neural stem cells. We will also discuss key metabolic signaling pathways influenced by both dietary restriction and the aging process, and will examine their role in improving tissue homeostasis and lifespan. Understanding the mechanisms behind the metabolic needs of stem cells will help bridge the divide between a basic science interpretation of stem cell function and a whole-organism view of nutrition, thereby providing insight into potential dietary or therapeutic interventions.
    Keywords:  Aging; Metabolism; stem cells
    DOI:  https://doi.org/10.1007/s40778-021-00186-6
  51. J Med Genet. 2022 Mar 08. pii: jmedgenet-2021-108355. [Epub ahead of print]
    UK recommendations for SDHA germline genetic testing and surveillance in clinical practice.
    UK Cancer Genetics Centres
      SDHA pathogenic germline variants (PGVs) are identified in up to 10% of patients with paraganglioma and phaeochromocytoma and up to 30% with wild-type gastrointestinal stromal tumours. Most SDHA PGV carriers present with an apparently sporadic tumour, but often the pathogenic variant has been inherited from parent who has the variant, but has not developed any clinical features. Studies of SDHA PGV carriers suggest that lifetime penetrance for SDHA-associated tumours is low, particularly when identified outside the context of a family history. Current recommended surveillance for SDHA PGV carriers follows an intensive protocol. With increasing implementation of tumour and germline large panel and whole-genome sequencing, it is likely more SDHA PGV carriers will be identified in patients with tumours not strongly associated with SDHA, or outside the context of a strong family history. This creates a complex situation about what to recommend in clinical practice considering low penetrance for tumour development, surveillance burden and patient anxiety. An expert SDHA working group was formed to discuss and consider this situation. This paper outlines the recommendations from this working group for testing and management of SDHA PGV carriers in clinical practice.
    Keywords:  endocrinology; genetic counselling; genetic predisposition to disease; genetic testing
    DOI:  https://doi.org/10.1136/jmedgenet-2021-108355
  52. Exp Neurobiol. 2022 Feb 28. 31(1): 1-16
    Invertebrate Model Organisms as a Platform to Investigate Rare Human Neurological Diseases.
    Ji-Hye Lee.
      Patients suffering from rare human diseases often go through a painful journey for finding a definite molecular diagnosis prerequisite of appropriate cures. With a novel variant isolated from a single patient, determination of its pathogenicity to end such "diagnostic odyssey" requires multi-step processes involving experts in diverse areas of interest, including clinicians, bioinformaticians and research scientists. Recent efforts in building large-scale genomic databases and in silico prediction platforms have facilitated identification of potentially pathogenic variants causative of rare human diseases of a Mendelian basis. However, the functional significance of individual variants remains elusive in many cases, thus requiring incorporation of versatile and rapid model organism (MO)-based platforms for functional analyses. In this review, the current scope of rare disease research is briefly discussed. In addition, an overview of invertebrate MOs for their key features relevant to rare neurological diseases is provided, with the characteristics of two representative invertebrate MOs, Drosophila melanogaster and Caenorhabditis elegans, as well as the challenges against them. Finally, recently developed research networks integrating these MOs in collaborative research are portraited with an array of bioinformatical analyses embedded. A comprehensive survey of MO-based research activities provided in this review will help us to design a wellstructured analysis of candidate genes or potentially pathogenic variants for their roles in rare neurological diseases in future.
    Keywords:  Caenorhabditis elegans; Disease models; Drosophila melanogaster; Invertebrates; Nervous system diseases; Rare diseases
    DOI:  https://doi.org/10.5607/en22003
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