bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2022‒04‒10
48 papers selected by
Catalina Vasilescu
University of Helsinki
  1. FGF21 modulates mitochondrial stress response in cardiomyocytes only under mild mitochondrial dysfunction.
  2. Gene therapy restores mitochondrial function and protects retinal ganglion cells in optic neuropathy induced by a mito-targeted mutant ND1 gene.
  3. Coupling to Pam16 differentially controls the dual role of Pam18 in protein import and respiratory chain formation.
  4. DELE1 tracks perturbed protein import and processing in human mitochondria.
  5. Mitochondrial-derived vesicles in skeletal muscle remodeling and adaptation.
  6. Whole exome sequencing is an alternative method in the diagnosis of mitochondrial DNA diseases.
  7. Clinical implementation of RNA sequencing for Mendelian disease diagnostics.
  8. The role of the individual TOM subunits in the association of PINK1 with depolarized mitochondria.
  9. A mitochondrial long-chain fatty acid oxidation defect leads to tRNA uncharging and activation of the integrated stress response in the mouse heart.
  10. Pterostilbene in Combination With Mitochondrial Cofactors Improve Mitochondrial Function in Cellular Models of Mitochondrial Diseases.
  11. Mitochondrial complex I subunit deficiency promotes pancreatic α-cell proliferation.
  12. Mitochondrial transfer in BAT.
  13. Genetic, biochemical and clinical spectrum of patients with mitochondrial trifunctional protein deficiency identified after introduction of newborn screening in the Netherlands.
  14. Mitophagy and Neurodegeneration: Between the Knowns and the Unknowns.
  15. Activated glia cells cause bioenergetic impairment of neurons that can be rescued by knock-down of the mitochondrial calcium uniporter.
  16. Decompensation of cardiorespiratory function and emergence of anemia during pregnancy in a case of mitochondrial myopathy, lactic acidosis, and sideroblastic anemia 2 with compound heterozygous YARS2 pathogenic variants.
  17. WIPI2 positively regulates mitophagy by promoting mitochondrial recruitment of VCP.
  18. Emerging Roles of SIRT3 in Cardiac Metabolism.
  19. A Ca2+-dependent mechanism boosting glycolysis and OXPHOS by activating Aralar-malate-aspartate shuttle, upon neuronal stimulation.
  20. CRISPR-free base editors with enhanced activity and expanded targeting scope in mitochondrial and nuclear DNA.
  21. Longitudinal associations between blood lysophosphatidylcholines and skeletal muscle mitochondrial function.
  22. Praseodymium trivalent ion is an effective inhibitor of mitochondrial basic amino acids and carnitine/acylcarnitine carriers.
  23. Tomatidine-stimulated maturation of human embryonic stem cell-derived cardiomyocytes for modeling mitochondrial dysfunction.
  24. Transcriptome-based variant calling and aberrant mRNA discovery enhance diagnostic efficiency for neuromuscular diseases.
  25. Clinical outcomes of treatment with idebenone in Leber's hereditary optic neuropathy in the Netherlands: A national cohort study.
  26. Mitochondria-associated myosin 19 processively transports mitochondria on actin tracks in living cells.
  27. Prevalence and health care costs of mitochondrial disease in Ontario, Canada: A population-based cohort study.
  28. Letter by Belmadani and Matrougui Regarding Article, "Integrated Stress Response Couples Mitochondrial Protein Translation With Oxidative Stress Control".
  29. Dynamic Mitochondrial Proteome Under Polyamines Treatment in Cardiac Aging.
  30. Serine/Threonine Protein Phosphatase 2A Regulates the Transport of Axonal Mitochondria.
  31. Compartmentalized metabolism supports midgestation mammalian development.
  32. Elucidating arrhythmogenic right ventricular cardiomyopathy with stem cells.
  33. DiMeLo-seq: a long-read, single-molecule method for mapping protein-DNA interactions genome wide.
  34. Precise and long-term tracking of mitochondria in neurons using a bioconjugatable and photostable AIE luminogen.
  35. Mutant ANP induces mitochondrial and ion channel remodeling in a human iPSC-derived atrial fibrillation model.
  36. Best practices for the interpretation and reporting of clinical whole genome sequencing.
  37. Uncompensated mitochondrial oxidative stress underlies heart failure in an iPSC-derived model of congenital heart disease.
  38. Mitochondrial Reactive Oxygen Species Mediate Activation of TRPV1 and Calcium Entry Following Peripheral Sensory Axotomy.
  39. Hepatocyte-specific activity of TSC22D4 triggers progressive NAFLD by impairing mitochondrial function.
  40. High-resolution Slide-seqV2 spatial transcriptomics enables discovery of disease-specific cell neighborhoods and pathways.
  41. Genetic disorders of cellular trafficking.
  42. Population-based high-throughput toxicity screen of human iPSC-derived cardiomyocytes and neurons.
  43. Inborn errors of metabolism screening in neonates: current perspective with diagnosis and therapy.
  44. Ischemia-induced cleavage of OPA1 at S1 site aggravates mitochondrial fragmentation and reperfusion injury in neurons.
  45. Searching thousands of genomes to classify somatic and novel structural variants using STIX.
  46. Phenotype-driven approaches to enhance variant prioritization and diagnosis of rare disease.
  47. RNA sequencing role and application in clinical diagnostic.
  48. Ultrastructural and proteomic profiling of mitochondria-associated endoplasmic reticulum membranes reveal aging signatures in striated muscle.
  1. Sci Adv. 2022 Apr 08. 8(14): eabn7105
    FGF21 modulates mitochondrial stress response in cardiomyocytes only under mild mitochondrial dysfunction.
    Marijana Croon, Karolina Szczepanowska, Milica Popovic, Christina Lienkamp, Katharina Senft, Christoph Paul Brandscheid, Theresa Bock, Leoni Gnatzy-Feik, Artem Ashurov, Richard James Acton, Harshita Kaul, Claire Pujol, Stephan Rosenkranz, Marcus Krüger, Aleksandra Trifunovic.
      The mitochondrial integrated stress response (mitoISR) has emerged as a major adaptive pathway to respiratory chain deficiency, but both the tissue specificity of its regulation, and how mitoISR adapts to different levels of mitochondrial dysfunction are largely unknown. Here, we report that diverse levels of mitochondrial cardiomyopathy activate mitoISR, including high production of FGF21, a cytokine with both paracrine and endocrine function, shown to be induced by respiratory chain dysfunction. Although being fully dispensable for the cell-autonomous and systemic responses to severe mitochondrial cardiomyopathy, in the conditions of mild-to-moderate cardiac OXPHOS dysfunction, FGF21 regulates a portion of mitoISR. In the absence of FGF21, a large part of the metabolic adaptation to mitochondrial dysfunction (one-carbon metabolism, transsulfuration, and serine and proline biosynthesis) is strongly blunted, independent of the primary mitoISR activator ATF4. Collectively, our work highlights the complexity of mitochondrial stress responses by revealing the importance of the tissue specificity and dose dependency of mitoISR.
    DOI:  https://doi.org/10.1126/sciadv.abn7105
  2. Gene Ther. 2022 Apr 06.
    Gene therapy restores mitochondrial function and protects retinal ganglion cells in optic neuropathy induced by a mito-targeted mutant ND1 gene.
    Yuan Liu, Jeremy D Eastwood, Diego E Alba, Sindhu Velmurugan, Ning Sun, Vittorio Porciatti, Richard K Lee, William W Hauswirth, John Guy, Hong Yu.
      Therapies for genetic disorders caused by mutated mitochondrial DNA are an unmet need, in large part due barriers in delivering DNA to the organelle and the absence of relevant animal models. We injected into mouse eyes a mitochondrially targeted Adeno-Associated-Virus (MTS-AAV) to deliver the mutant human NADH ubiquinone oxidoreductase subunit I (hND1/m.3460 G > A) responsible for Leber's hereditary optic neuropathy, the most common primary mitochondrial genetic disease. We show that the expression of the mutant hND1 delivered to retinal ganglion cells (RGC) layer colocalizes with the mitochondrial marker PORIN and the assembly of the expressed hND1 protein into host respiration complex I. The hND1-injected eyes exhibit hallmarks of the human disease with progressive loss of RGC function and number, as well as optic nerve degeneration. We also show that gene therapy in the hND1 eyes by means of an injection of a second MTS-AAV vector carrying wild-type human ND1 restores mitochondrial respiratory complex I activity, the rate of ATP synthesis and protects RGCs and their axons from dysfunction and degeneration. These results prove that MTS-AAV is a highly efficient gene delivery approach with the ability to create mito-animal models and has the therapeutic potential to treat mitochondrial genetic diseases.
    DOI:  https://doi.org/10.1038/s41434-022-00333-6
  3. Cell Rep. 2022 Apr 05. pii: S2211-1247(22)00367-9. [Epub ahead of print]39(1): 110619
    Coupling to Pam16 differentially controls the dual role of Pam18 in protein import and respiratory chain formation.
    Chantal Priesnitz, Lena Böttinger, Nicole Zufall, Michael Gebert, Bernard Guiard, Martin van der Laan, Thomas Becker.
      The presequence translocase (TIM23 complex) imports precursor proteins into the mitochondrial inner membrane and matrix. The presequence translocase-associated motor (PAM) provides a driving force for transport into the matrix. The J-protein Pam18 stimulates the ATPase activity of the mitochondrial Hsp70 (mtHsp70). Pam16 recruits Pam18 to the TIM23 complex to ensure protein import. The Pam16-Pam18 module also associates with components of the respiratory chain, but the function of the dual localization of Pam16-Pam18 is largely unknown. Here, we show that disruption of the Pam16-Pam18 heterodimer causes redistribution of Pam18 to the respiratory chain supercomplexes, where it forms a homodimer. Redistribution of Pam18 decreases protein import into mitochondria but stimulates mtHsp70-dependent assembly of respiratory chain complexes. We conclude that coupling to Pam16 differentially controls the dual function of Pam18. It recruits Pam18 to the TIM23 complex to promote protein import but attenuates the Pam18 function in the assembly of respiratory chain complexes.
    Keywords:  CP: Cell biology; CP: Metabolism; Pam18; TIM23 complex; cytochrome c oxidase; mitochondria; mtHsp70; protein sorting; respiratory chain
    DOI:  https://doi.org/10.1016/j.celrep.2022.110619
  4. Nat Commun. 2022 Apr 06. 13(1): 1853
    DELE1 tracks perturbed protein import and processing in human mitochondria.
    Evelyn Fessler, Luisa Krumwiede, Lucas T Jae.
      Protein homeostatic control of mitochondria is key to age-related diseases and organismal decline. However, it is unknown how the diverse types of stress experienced by mitochondria can be integrated and appropriately responded to in human cells. Here we identify perturbations in the ancient conserved processes of mitochondrial protein import and processing as sources of DELE1 activation: DELE1 is continuously sorted across both mitochondrial membranes into the matrix and detects different types of perturbations along the way. DELE1 molecules in transit can become licensed for mitochondrial release and stress signaling through proteolytic removal of N-terminal sorting signals. Import defects that occur at the mitochondrial surface allow DELE1 precursors to bind and activate downstream factor HRI without the need for cleavage. Genome-wide genetics reveal that DELE1 additionally responds to compromised presequence processing by the matrix proteases PITRM1 and MPP, which are mutated in neurodegenerative diseases. These mechanisms rationalize DELE1-dependent mitochondrial stress integration in the human system and may inform future therapies of neuropathies.
    DOI:  https://doi.org/10.1038/s41467-022-29479-y
  5. Semin Cell Dev Biol. 2022 Mar 30. pii: S1084-9521(22)00095-7. [Epub ahead of print]
    Mitochondrial-derived vesicles in skeletal muscle remodeling and adaptation.
    Anna Picca, Flora Guerra, Riccardo Calvani, Roberta Romano, Hélio José Coelho-Junior, Cecilia Bucci, Christiaan Leeuwenburgh, Emanuele Marzetti.
      Mitochondrial remodeling is crucial to meet the bioenergetic demand to support muscle contractile activity during daily tasks and muscle regeneration following injury. A set of mitochondrial quality control (MQC) processes, including mitochondrial biogenesis, dynamics, and mitophagy, are in place to maintain a well-functioning mitochondrial network and support muscle regeneration. Alterations in any of these pathways compromises mitochondrial quality and may potentially lead to impaired myogenesis, defective muscle regeneration, and ultimately loss of muscle function. Among MQC processes, mitophagy has gained special attention for its implication in the clearance of dysfunctional mitochondria via crosstalk with the endo-lysosomal system, a major cell degradative route. Along this pathway, additional opportunities for mitochondrial disposal have been identified that may also signal at the systemic level. This communication occurs via inclusion of mitochondrial components within membranous shuttles named mitochondrial-derived vesicles (MDVs). Here, we discuss MDV generation and release as a mitophagy-complementing route for the maintenance of mitochondrial homeostasis in skeletal myocytes. We also illustrate the possible role of muscle-derived MDVs in immune signaling during muscle remodeling and adaptation.
    Keywords:  Extracellular vesicles; Mitochondrial DNA damage; Mitochondrial biogenesis; Mitochondrial quality control; Mitophagy; Skeletal muscle
    DOI:  https://doi.org/10.1016/j.semcdb.2022.03.023
  6. Mol Genet Genomic Med. 2022 Apr 07. e1943
    Whole exome sequencing is an alternative method in the diagnosis of mitochondrial DNA diseases.
    Chong Sun, Shengyang Wu, Ruiguo Chen, Junwu Liu, Jiasen Wang, Yanyun Ma, Zhulin Yuan, Yuezhen Li.
      BACKGROUND: Mitochondrial disease (MD) is genetically a heterogeneous group of disorders with impairment in respiratory chain complexes or pathways associated with the mitochondrial function. Nowadays, it is still a challenge for the genetic screening of MD due to heteroplasmy of mitochondrial genome and the complex model of inheritance. This study was designed to investigate the feasibility of whole exome sequencing (WES)-based testing as an alternative option for the diagnosis of MD.METHODS: A Chinese Han cohort of 48 patients with suspect MD features was tested using nanoWES, which was a self-designed WES technique that covered the complete mtDNA genome and 21,019 nuclear genes. Fourteen patients were identified with a single genetic variant and three with single deletion in mtDNA.
    RESULTS: The heteroplasmy levels of variants in mitochondrial genome range from 11% to 100%. NanoWES failed to identify multiple deletions in mtDNA compared with long range PCR and massively parallel sequencing (LR-PCR/MPS). However, our testing showed obvious advantages in identifying variations in nuclear DNA. Based on nanoWES, we identified two patients with nuclear DNA variation. One of them showed Xp22.33-q28 duplication, which indicated a possibility of Klinefelter syndrome.
    CONCLUSION: NanoWES yielded a diagnostic rate of 35.4% for MD. With the rapid advances of next generation sequencing technique and decrease in cost, we recommend the usage of nanoWES as a first-line method in clinical diagnosis.
    Keywords:  genetic diagnosis; mitochondrial disease; next generation sequencing; whole exome sequencing
    DOI:  https://doi.org/10.1002/mgg3.1943
  7. Genome Med. 2022 Apr 05. 14(1): 38
    Clinical implementation of RNA sequencing for Mendelian disease diagnostics.
    Vicente A Yépez, Mirjana Gusic, Robert Kopajtich, Christian Mertes, Nicholas H Smith, Charlotte L Alston, Rui Ban, Skadi Beblo, Riccardo Berutti, Holger Blessing, Elżbieta Ciara, Felix Distelmaier, Peter Freisinger, Johannes Häberle, Susan J Hayflick, Maja Hempel, Yulia S Itkis, Yoshihito Kishita, Thomas Klopstock, Tatiana D Krylova, Costanza Lamperti, Dominic Lenz, Christine Makowski, Signe Mosegaard, Michaela F Müller, Gerard Muñoz-Pujol, Agnieszka Nadel, Akira Ohtake, Yasushi Okazaki, Elena Procopio, Thomas Schwarzmayr, Joél Smet, Christian Staufner, Sarah L Stenton, Tim M Strom, Caterina Terrile, Frederic Tort, Rudy Van Coster, Arnaud Vanlander, Matias Wagner, Manting Xu, Fang Fang, Daniele Ghezzi, Johannes A Mayr, Dorota Piekutowska-Abramczuk, Antonia Ribes, Agnès Rötig, Robert W Taylor, Saskia B Wortmann, Kei Murayama, Thomas Meitinger, Julien Gagneur, Holger Prokisch.
      BACKGROUND: Lack of functional evidence hampers variant interpretation, leaving a large proportion of individuals with a suspected Mendelian disorder without genetic diagnosis after whole genome or whole exome sequencing (WES). Research studies advocate to further sequence transcriptomes to directly and systematically probe gene expression defects. However, collection of additional biopsies and establishment of lab workflows, analytical pipelines, and defined concepts in clinical interpretation of aberrant gene expression are still needed for adopting RNA sequencing (RNA-seq) in routine diagnostics.METHODS: We implemented an automated RNA-seq protocol and a computational workflow with which we analyzed skin fibroblasts of 303 individuals with a suspected mitochondrial disease that previously underwent WES. We also assessed through simulations how aberrant expression and mono-allelic expression tests depend on RNA-seq coverage.
    RESULTS: We detected on average 12,500 genes per sample including around 60% of all disease genes-a coverage substantially higher than with whole blood, supporting the use of skin biopsies. We prioritized genes demonstrating aberrant expression, aberrant splicing, or mono-allelic expression. The pipeline required less than 1 week from sample preparation to result reporting and provided a median of eight disease-associated genes per patient for inspection. A genetic diagnosis was established for 16% of the 205 WES-inconclusive cases. Detection of aberrant expression was a major contributor to diagnosis including instances of 50% reduction, which, together with mono-allelic expression, allowed for the diagnosis of dominant disorders caused by haploinsufficiency. Moreover, calling aberrant splicing and variants from RNA-seq data enabled detecting and validating splice-disrupting variants, of which the majority fell outside WES-covered regions.
    CONCLUSION: Together, these results show that streamlined experimental and computational processes can accelerate the implementation of RNA-seq in routine diagnostics.
    Keywords:  Genetic diagnostics; Mendelian diseases; RNA-seq
    DOI:  https://doi.org/10.1186/s13073-022-01019-9
  8. J Mol Med (Berl). 2022 Apr 07.
    The role of the individual TOM subunits in the association of PINK1 with depolarized mitochondria.
    Klaudia K Maruszczak, Martin Jung, Shafqat Rasool, Jean-François Trempe, Doron Rapaport.
      Mitochondria dysfunction is involved in the pathomechanism of many illnesses including Parkinson's disease. PINK1, which is mutated in some cases of familial Parkinsonism, is a key component in the degradation of damaged mitochondria by mitophagy. The accumulation of PINK1 on the mitochondrial outer membrane (MOM) of compromised organelles is crucial for the induction of mitophagy, but the molecular mechanism of this process is still unresolved. Here, we investigate the association of PINK1 with the TOM complex. We demonstrate that PINK1 heavily relies on the import receptor TOM70 for its association with mitochondria and directly interacts with this receptor. The structural protein TOM7 appears to play only a moderate role in PINK1 association with the TOM complex, probably due to its role in stabilizing this complex. PINK1 requires the TOM40 pore lumen for its stable interaction with the TOM complex and apparently remains there during its further association with the MOM. Overall, this study provides new insights on the role of the individual TOM subunits in the association of PINK1 with the MOM of depolarized mitochondria. KEY MESSAGES: TOM70 is the main receptor for the import of PINK1 into mitochondria. TOM20 plays only a minor role in PINK1 recognition at the organellar outer membrane. PINK1 association with the TOM complex is reduced upon knock-down of TOM7. The lumen of the TOM pore is crucial for PINK1 association with the outer membrane. TcPINK1 blocks the TOM pore in depolarized mitochondria.
    Keywords:  Mitochondria; Outer membrane; PINK1; Parkinson’s disease; TOM complex
    DOI:  https://doi.org/10.1007/s00109-022-02191-6
  9. Cardiovasc Res. 2022 Apr 07. pii: cvac050. [Epub ahead of print]
    A mitochondrial long-chain fatty acid oxidation defect leads to tRNA uncharging and activation of the integrated stress response in the mouse heart.
    Pablo Ranea-Robles, Natalya N Pavlova, Aaron Bender, Andrea S Pereyra, Jessica M Ellis, Brandon Stauffer, Chunli Yu, Craig B Thompson, Carmen Argmann, Michelle Puchowicz, Sander M Houten.
      AIMS: Cardiomyopathy and arrhythmias can be severe presentations in patients with inherited defects of mitochondrial long-chain fatty acid β-oxidation (FAO). The pathophysiological mechanisms that underlie these cardiac abnormalities remain largely unknown. We investigated the molecular adaptations to a FAO deficiency in the heart using the long-chain acyl-CoA dehydrogenase (LCAD) knockout (KO) mouse model.METHODS AND RESULTS: We observed enrichment of amino acid metabolic pathways and of ATF4 target genes among the upregulated genes in the LCAD KO heart transcriptome. We also found a prominent activation of the eIF2α/ATF4 axis at the protein level that was independent of the feeding status, in addition to a reduction of cardiac protein synthesis during a short period of food withdrawal. These findings are consistent with an activation of the integrated stress response (ISR) in the LCAD KO mouse heart. Notably, charging of several tRNAs, such as tRNAGln was decreased in LCAD KO hearts, reflecting a reduced availability of cardiac amino acids, in particular, glutamine. We replicated the activation of the ISR in hearts of mice with a muscle-specific deletion of carnitine palmitoyltransferase 2.
    CONCLUSIONS: Our results show that perturbations in amino acid metabolism caused by long-chain FAO deficiency impact on cardiac metabolic signaling, in particular the ISR. These results may serve as a foundation for investigating the role of the ISR in the cardiac pathology associated with long-chain FAO defects.Translational Perspective: The heart relies mainly on mitochondrial fatty acid β-oxidation (FAO) for its high energy requirements. The heart disease observed in patients with a genetic defect in this pathway highlights the importance of FAO for cardiac health. We show that the consequences of a FAO defect extend beyond cardiac energy homeostasis and include amino acid metabolism and associated signaling pathways such as the integrated stress response.
    Keywords:  LCAD; amino acids; fatty acid oxidation; hypertrophy; tRNA
    DOI:  https://doi.org/10.1093/cvr/cvac050
  10. Front Pharmacol. 2022 ;13 862085
    Pterostilbene in Combination With Mitochondrial Cofactors Improve Mitochondrial Function in Cellular Models of Mitochondrial Diseases.
    Juan M Suárez-Rivero, Carmen J Pastor-Maldonado, Ana Romero-González, David Gómez-Fernandez, Suleva Povea-Cabello, Mónica Álvarez-Córdoba, Irene Villalón-García, Marta Talaverón-Rey, Alejandra Suárez-Carrillo, Manuel Munuera-Cabeza, José A Sánchez-Alcázar.
      Mitochondrial diseases are genetic disorders caused by mutations in genes in the nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) that encode mitochondrial structural or functional proteins. Although considered "rare" due to their low incidence, such diseases affect thousands of patients' lives worldwide. Despite intensive research efforts, most mitochondrial diseases are still incurable. Recent studies have proposed the modulation of cellular compensatory pathways such as mitophagy, AMP-activated protein kinase (AMPK) activation or the mitochondrial unfolded protein response (UPRmt) as novel therapeutic approaches for the treatment of these pathologies. UPRmt is an intracellular compensatory pathway that signals mitochondrial stress to the nucleus for the activation of mitochondrial proteostasis mechanisms including chaperones, proteases and antioxidants. In this work a potentially beneficial molecule, pterostilbene (a resveratrol analogue), was identified as mitochondrial booster in drug screenings. The positive effects of pterostilbene were significantly increased in combination with a mitochondrial cocktail (CoC3) consisting of: pterostilbene, nicotinamide, riboflavin, thiamine, biotin, lipoic acid and l-carnitine. CoC3 increases sirtuins' activity and UPRmt activation, thus improving pathological alterations in mutant fibroblasts and induced neurons.
    Keywords:  UPRmt; mitochondrial cofactors; mitochondrial diseases; pterostilbene; sirt3
    DOI:  https://doi.org/10.3389/fphar.2022.862085
  11. Mol Metab. 2022 Apr 04. pii: S2212-8778(22)00058-8. [Epub ahead of print] 101489
    Mitochondrial complex I subunit deficiency promotes pancreatic α-cell proliferation.
    Xuefei Yu, Catherine Arden, Rolando Berlinguer-Palmini, Chun Chen, Carla Bradshaw, Julia Whitehall, Michael White, Scott Anderson, Nicole Kattner, James Shaw, Doug Turnbull, Laura Greaves, Mark Walker.
      OBJECTIVE: There is strong evidence that mitochondrial DNA mutations and mitochondrial dysfunction play a role in diabetes pathogenesis. The homozygous knock-in mtDNA mutator mouse is a model of premature aging due to the accumulation of mitochondrial DNA mutations. We used this mouse model to investigate the relationship between mitochondrial subunit expression and pancreatic islet cell composition.METHODS: Quadruple immunofluorescence was used to quantify mitochondrial subunit expression (complex I and IV) and cell composition in pancreatic islets from mitochondrial DNA mutator mice (PolgAmut/mut) and control C57BL/6 mice at 12 and 44 weeks of age.
    RESULTS: Mitochondrial complex I subunit expression was decreased in islets from 12 week PolgAmut/mut mice. This complex I deficiency persisted with age and was associated with decreased insulin staining intensity at 44 weeks. Complex I deficiency was greater in α-cells compared with β-cells in islets from 44 week PolgAmut/mut mice. Islet cell composition was normal in 12 week PolgAmut/mut mice, but the β: α cell ratio was decreased in islets from 44 week PolgAmut/mut mice. This was due to an increase in α-cell number linked to an increase in α-cell proliferation.
    CONCLUSION: Complex I deficiency promotes α-cell proliferation and alters islet cell composition.
    Keywords:  Mitochondria; mtDNA; mtDNA mutator mice; pancreatic islets
    DOI:  https://doi.org/10.1016/j.molmet.2022.101489
  12. Nat Rev Endocrinol. 2022 Apr 07.
    Mitochondrial transfer in BAT.
    Shimona Starling.
      
    DOI:  https://doi.org/10.1038/s41574-022-00674-7
  13. J Inherit Metab Dis. 2022 Apr 05.
    Genetic, biochemical and clinical spectrum of patients with mitochondrial trifunctional protein deficiency identified after introduction of newborn screening in the Netherlands.
    Marit Schwantje, Sabine A Fuchs, Lonneke de Boer, Annet M Bosch, Inge Cuppen, Eugenie Dekkers, Terry G J Derks, Sacha Ferdinandusse, Lodewijk IJlst, Riekelt H Houtkooper, Rose Maase, W Ludo van der Pol, Maaike C de Vries, Rendelien K Verschoof-Puite, Ronald J A Wanders, Monique Williams, Frits Wijburg, Gepke Visser.
      INTRODUCTION: Long-chain 3-hydroxyacyl-CoA dehydrogenase deficiency (LCHADD) is included in many newborn screening (NBS) programs. Acylcarnitine-based NBS for LCHADD not only identifies LCHADD, but all different deficiencies of the mitochondrial trifunctional protein (MTP), a multi-enzyme complex involved in long-chain fatty acid β-oxidation. Besides LCHAD, MTP harbors two additional enzyme activities: long-chain enoyl-CoA hydratase (LCEH), and long-chain ketoacyl-CoA thiolase (LCKAT). Deficiency of one or more MTP activities causes generalized MTP deficiency (MTPD), LCHADD, LCEH deficiency (not yet reported), or LCKAT deficiency (LCKATD).AIM: To gain insight in the outcomes of MTP-deficient patients diagnosed after introduction of NBS for LCHADD in the Netherlands.
    METHODS: Retrospective evaluation of genetic, biochemical and clinical characteristics of MTP-deficient patients, identified since 2007.
    RESULTS: Thirteen patients were identified: seven with LCHADD, five with MTPD and one with LCKATD. All LCHADD patients (one missed by NBS, clinical diagnosis) and one MTPD patient (clinical diagnosis) were alive. Four MTPD patients and one LCKATD patient developed cardiomyopathy and died within one month and 13 months of life, respectively. Surviving patients did not develop symptomatic hypoglycemia, but experienced reversible cardiomyopathy and rhabdomyolysis. Five LCHADD patients developed subclinical neuropathy and/or retinopathy.
    CONCLUSION: Patient outcomes were highly variable, stressing the need for accurate classification of and discrimination between the MTP deficiencies to improve insight in the yield of NBS for LCHADD. NBS allowed prevention of symptomatic hypoglycemia, but current treatment options failed to treat cardiomyopathy and prevent long-term complications. Moreover, milder patients, who might benefit from NBS, were missed due to normal acylcarnitine profiles.
    DOI:  https://doi.org/10.1002/jimd.12502
  14. Front Cell Dev Biol. 2022 ;10 837337
    Mitophagy and Neurodegeneration: Between the Knowns and the Unknowns.
    Cuckoo Teresa Jetto, Akshaya Nambiar, Ravi Manjithaya.
      Macroautophagy (henceforth autophagy) an evolutionary conserved intracellular pathway, involves lysosomal degradation of damaged and superfluous cytosolic contents to maintain cellular homeostasis. While autophagy was initially perceived as a bulk degradation process, a surfeit of studies in the last 2 decades has revealed that it can also be selective in choosing intracellular constituents for degradation. In addition to the core autophagy machinery, these selective autophagy pathways comprise of distinct molecular players that are involved in the capture of specific cargoes. The diverse organelles that are degraded by selective autophagy pathways are endoplasmic reticulum (ERphagy), lysosomes (lysophagy), mitochondria (mitophagy), Golgi apparatus (Golgiphagy), peroxisomes (pexophagy) and nucleus (nucleophagy). Among these, the main focus of this review is on the selective autophagic pathway involved in mitochondrial turnover called mitophagy. The mitophagy pathway encompasses diverse mechanisms involving a complex interplay of a multitude of proteins that confers the selective recognition of damaged mitochondria and their targeting to degradation via autophagy. Mitophagy is triggered by cues that signal the mitochondrial damage such as disturbances in mitochondrial fission-fusion dynamics, mitochondrial membrane depolarisation, enhanced ROS production, mtDNA damage as well as developmental cues such as erythrocyte maturation, removal of paternal mitochondria, cardiomyocyte maturation and somatic cell reprogramming. As research on the mechanistic aspects of this complex pathway is progressing, emerging roles of new players such as the NIPSNAP proteins, Miro proteins and ER-Mitochondria contact sites (ERMES) are being explored. Although diverse aspects of this pathway are being investigated in depth, several outstanding questions such as distinct molecular players of basal mitophagy, selective dominance of a particular mitophagy adapter protein over the other in a given physiological condition, molecular mechanism of how specific disease mutations affect this pathway remain to be addressed. In this review, we aim to give an overview with special emphasis on molecular and signalling pathways of mitophagy and its dysregulation in neurodegenerative disorders.
    Keywords:  mitochondrial dynamics; mitochondrial dysfunction; mitophagy; neurodegenaration; phosphorylation; ubiquitination
    DOI:  https://doi.org/10.3389/fcell.2022.837337
  15. Biochem Biophys Res Commun. 2022 Mar 25. pii: S0006-291X(22)00465-X. [Epub ahead of print]608 45-51
    Activated glia cells cause bioenergetic impairment of neurons that can be rescued by knock-down of the mitochondrial calcium uniporter.
    Angela Maria Casaril, Athanasios Katsalifis, Rolf M Schmidt, Carlos Bas-Orth.
      Neuroinflammation is a hallmark of various neurological disorders including autoimmune-, neurodegenerative and neuropsychiatric diseases. In neuroinflammation, activated microglia and astrocytes release soluble mediators such as cytokines, glutamate, and reactive oxygen species that negatively affect neuronal function and viability, and thus contribute to neurodegeneration during disease progression. Therefore, the development of neuroprotective strategies might be important in addition to treating inflammation in these diseases. Mitochondria are promising cellular targets for neuroprotective interventions: They are among the first structures affected in many neuroinflammatory diseases, with mitochondrial impairment ranging from impaired respiratory activity and reduced mitochondrial membrane potential to mitochondrial oxidation and fragmentation. Therefore, we developed a cell culture model that resembles an early state of inflammation-induced neuronal mitochondrial dysfunction preceding neuronal cell death, and can be used to test mito- and neuroprotective strategies. Rat primary cortical neurons were challenged with conditioned medium from mixed primary cultures of rat microglia and astrocytes that had been activated with lipopolysaccharide and ATP. When sublethal amounts of glia-conditioned medium were added to neurons for 24 h, mitochondrial membrane potential and ATP levels were decreased, whereas mitochondrial redox state remained unaffected. Effects on mitochondrial membrane potential and ATP levels were ameliorated by knock-down of the mitochondrial calcium uniporter in neurons. This study suggests that neuronal bioenergetic failure is an early event during neuroinflammation and it identifies the mitochondrial calcium uniporter as a candidate target for neuroprotection in this context.
    Keywords:  Astrocytes; Energy depletion; Microglia; Mitochondria; Neuroinflammation
    DOI:  https://doi.org/10.1016/j.bbrc.2022.03.120
  16. Am J Med Genet A. 2022 Apr 08.
    Decompensation of cardiorespiratory function and emergence of anemia during pregnancy in a case of mitochondrial myopathy, lactic acidosis, and sideroblastic anemia 2 with compound heterozygous YARS2 pathogenic variants.
    Laura I Rudaks, Eloise Watson, Carly Oboudiyat, Kishore R Kumar, Patricia Sullivan, Mark J Cowley, Ryan L Davis, Carolyn M Sue.
      Myopathy, lactic acidosis, and sideroblastic anemia 2 (MLASA2) is an autosomal recessive mitochondrial disorder caused by pathogenic variants in YARS2. YARS2 variants confer heterogeneous phenotypes ranging from the full MLASA syndrome to a clinically unaffected state. Symptom onset is most common in the first decade of life but can occur in adulthood and has been reported following intercurrent illness. Early death can result from respiratory muscle weakness and cardiomyopathy. We report a case of MLASA2 with compound heterozygous YARS2 pathogenic variants; a known pathogenic nonsense variant [NM_001040436.3:c.98C>A (p.Ser33Ter)] and a likely pathogenic missense variant not previously associated with disease [NM_001040436.3:c.948G>T (p.Arg316Ser)]. The proband initially presented with a relatively mild phenotype of myopathy and lactic acidosis. During pregnancy, anemia emerged as an additional feature and in the postpartum period she experienced severe decompensation of cardiorespiratory function. This is the first reported case of pregnancy-related complications in a patient with YARS2-related mitochondrial disease. This case highlights the need for caution and careful counseling when considering pregnancy in mitochondrial disease, due to the risk of disease exacerbation and pregnancy complications.
    Keywords:  MLASA2; YARS2; mitochondrial myopathy; pregnancy; sideroblastic anemia
    DOI:  https://doi.org/10.1002/ajmg.a.62755
  17. Autophagy. 2022 Apr 07. 1-15
    WIPI2 positively regulates mitophagy by promoting mitochondrial recruitment of VCP.
    Guang Lu, Hayden Weng Siong Tan, Tomas Schmauck-Medina, Liming Wang, Jiaqing Chen, Yik-Lam Cho, Kelie Chen, Jing-Zi Zhang, Weifeng He, Yihua Wu, Dajing Xia, Jing Zhou, Evandro F Fang, Lei Fang, Wei Liu, Han-Ming Shen.
      The mammalian Atg18 ortholog WIPI2 is a key regulator of LC3 lipidation to promote autophagosome biogenesis during nonselective macroautophagy, while its functions in selective autophagy such as mitophagy remain largely unexplored. In this study, we explored the role of WIPI2 in PINK1-PRKN/parkin-mediated mitophagy. First, we found that WIPI2 is recruited to damaged mitochondria upon mitophagy induction. Second, loss of WIPI2 impedes mitochondrial damaging agents-induced mitophagy. Third, at molecular level, WIPI2 binds to and promotes AAA-ATPase VCP/p97 (valosin containing protein) to damaged mitochondria; and WIPI2 depletion blunts the recruitment of VCP to damaged mitochondria, leading to reduction in degradation of outer mitochondrial membrane (OMM) proteins and mitophagy. Finally, WIPI2 is implicated in cell fate decision as cells deficient in WIPI2 are largely resistant to cell death induced by mitochondrial damage. In summary, our study reveals a critical regulatory role of WIPI2 in mitochondrial recruitment of VCP to promote OMM protein degradation and eventual mitophagy.Abbreviations: ATG, autophagy related; CALCOCO2/NDP52, calcium binding and coiled-coil domain 2; CCCP, carbonyl cyanide chlorophenylhydrazone; CYCS, cytochrome c, somatic; HSPD1/HSP60, heat shock protein family D (Hsp60) member 1; IMM, inner mitochondrial membrane; MAP1LC3/LC3, microtubule associated protein 1 light chain 3; NPLOC4, NPL4 homolog, ubiquitin recognition factor; OMM, outer mitochondrial membrane; OPTN, optineurin; PtdIns3P, phosphatidylinositol-3-phosphate; PINK1, PTEN induced kinase 1; PRKN/Parkin, parkin RBR E3 ubiquitin protein ligase; UBXN6/UBXD1, UBX domain protein 6; UFD1, ubiquitin recognition factor in ER associated degradation 1; VCP/p97, valosin containing protein; WIPI2, WD repeat domain, phosphoinositide interacting 2.
    Keywords:  Autophagy; PINK1; PRKN; VCP; WIPI2; cell death; mitophagy
    DOI:  https://doi.org/10.1080/15548627.2022.2052461
  18. Front Cardiovasc Med. 2022 ;9 850340
    Emerging Roles of SIRT3 in Cardiac Metabolism.
    Krishnega Murugasamy, Aastha Munjal, Nagalingam Ravi Sundaresan.
      The heart is a highly metabolically active organ that predominantly utilizes fatty acids as an energy substrate. The heart also derives some part of its energy by oxidation of other substrates, including glucose, lactose, amino acids and ketones. The critical feature of cardiac pathology is metabolic remodeling and loss of metabolic flexibility. Sirtuin 3 (SIRT3) is one of the seven mammalian sirtuins (SIRT1 to SIRT7), with NAD+ dependent deacetylase activity. SIRT3 is expressed in high levels in healthy hearts but downregulated in the aged or diseased hearts. Experimental evidence shows that increasing SIRT3 levels or activity can ameliorate several cardiac pathologies. The primary deacetylation targets of SIRT3 are mitochondrial proteins, most of which are involved in energy metabolism. Thus, SIRT3 improves cardiac health by modulating cardiac energetics. In this review, we discuss the essential role of SIRT3 in regulating cardiac metabolism in the context of physiology and pathology. Specifically, we summarize the recent advancements that emphasize the critical role of SIRT3 as a master regulator of cardiac metabolism. We also present a comprehensive view of all known activators of SIRT3, and elaborate on their therapeutic potential to ameliorate energetic abnormalities in various cardiac pathologies.
    Keywords:  SIRT3; glycolysis; heart failure; metabolism; mitochondrial oxidation
    DOI:  https://doi.org/10.3389/fcvm.2022.850340
  19. J Neurosci. 2022 Apr 06. pii: JN-RM-1463-21. [Epub ahead of print]
    A Ca2+-dependent mechanism boosting glycolysis and OXPHOS by activating Aralar-malate-aspartate shuttle, upon neuronal stimulation.
    Irene Pérez-Liébana, Inés Juaristi, Paloma González-Sánchez, Luis González-Moreno, Eduardo Rial, Maša Podunavac, Armen Zakarian, Jordi Molgó, Ainara Vallejo-Illarramendi, Laura Mosqueira-Martín, Adolfo López de Munain, Beatriz Pardo, Jorgina Satrústegui, Araceli Del Arco.
      Calcium is an important second messenger regulating a bioenergetic response to the workloads triggered by neuronal activation. In embryonic mouse cortical neurons using glucose as only fuel, activation by NMDA elicits a strong workload (ATP demand) dependent on Na+ and Ca2+ entry, and stimulates glucose uptake, glycolysis, pyruvate and lactate production and OXPHOS in a Ca2+-dependent way. We find that Ca2+-upregulation of glycolysis, pyruvate levels and respiration, but not glucose uptake, all depend on Aralar/AGC1/Slc25a12, the mitochondrial aspartate-glutamate carrier, component of the malate-aspartate shuttle (MAS). MAS activation increases glycolysis, pyruvate production and respiration, a process inhibited in the presence of BAPTA-AM suggesting that the Ca2+ binding motifs in Aralar may be involved in the activation. MCU silencing had no effect indicating that none of these processes required MCU-dependent mitochondrial Ca2+ uptake. The neuronal respiratory response to carbachol was also dependent on Aralar, but not on MCU. We find that mouse cortical neurons are endowed with a constitutive ER-to-mitochondria Ca2+ flow maintaining basal cell bioenergetics in which Ryanodine receptors, RyR2, rather than InsP3R, are responsible for Ca2+ release, and in which MCU does not participate. The results reveal that in neurons using glucose MCU does not participate in OXPHOS regulation under basal or stimulated conditions, while Aralar-MAS appears as the major Ca2+-dependent pathway tuning simultaneously glycolysis and OXPHOS to neuronal activation.SIGNIFICANT STATEMENTSNeuronal activation increases cell workload to restore ion gradients altered by activation. Ca2+ is involved in matching increased workload with ATP production, but the mechanisms are still unknown. We find that glycolysis, pyruvate production and neuronal respiration are stimulated upon neuronal activation in a Ca2+ dependent way, independently of effects of Ca2+ as workload inducer. MCU does not play a relevant role in Ca2+ stimulated pyruvate production and oxygen consumption as both are unchanged in MCU silenced neurons. However, Ca2+ stimulation is blunt in the absence of Aralar, a Ca2+-binding mitochondrial carrier component of Malate-Aspartate Shuttle (MAS). The results suggest that Ca2+-regulated Aralar-MAS activation upregulates glycolysis and pyruvate production which fuels mitochondrial respiration, through regulation of cytosolic NAD+/NADH ratio.
    Keywords:  Aralar/AGC1/Slc25a12; Neuronal metabolism; calcium regulation; glycolysis; malate aspartate shuttle; mitochondrial calcium uniporter
    DOI:  https://doi.org/10.1523/JNEUROSCI.1463-21.2022
  20. Nat Biotechnol. 2022 Apr 04.
    CRISPR-free base editors with enhanced activity and expanded targeting scope in mitochondrial and nuclear DNA.
    Beverly Y Mok, Anna V Kotrys, Aditya Raguram, Tony P Huang, Vamsi K Mootha, David R Liu.
      The all-protein cytosine base editor DdCBE uses TALE proteins and a double-stranded DNA-specific cytidine deaminase (DddA) to mediate targeted C•G-to-T•A editing. To improve editing efficiency and overcome the strict TC sequence-context constraint of DddA, we used phage-assisted non-continuous and continuous evolution to evolve DddA variants with improved activity and expanded targeting scope. Compared to canonical DdCBEs, base editors with evolved DddA6 improved mitochondrial DNA (mtDNA) editing efficiencies at TC by 3.3-fold on average. DdCBEs containing evolved DddA11 offered a broadened HC (H = A, C or T) sequence compatibility for both mitochondrial and nuclear base editing, increasing average editing efficiencies at AC and CC targets from less than 10% for canonical DdCBE to 15-30% and up to 50% in cell populations sorted to express both halves of DdCBE. We used these evolved DdCBEs to efficiently install disease-associated mtDNA mutations in human cells at non-TC target sites. DddA6 and DddA11 substantially increase the effectiveness and applicability of all-protein base editing.
    DOI:  https://doi.org/10.1038/s41587-022-01256-8
  21. Geroscience. 2022 Apr 07.
    Longitudinal associations between blood lysophosphatidylcholines and skeletal muscle mitochondrial function.
    Qu Tian, Brendan A Mitchell, Marta Zampino, Luigi Ferrucci.
      Lysophosphatidylcholines (LPCs) are phospholipids critical in the synthesis of cardiolipin, an essential component of mitochondrial membranes. Lower plasma LPCs have been cross-sectionally associated with lower skeletal muscle mitochondrial function, but whether lower LPCs and their decline over time are longitudinally associated with an accelerated decline of mitochondria function is unknown. We analyzed data from 184 participants in the Baltimore Longitudinal Study of Aging (mean age: 74.5 years, 57% women, 25% black) who had repeated measures of plasma LPCs (16:0, 16:1, 17:0, 18:0, 18:1, 18:2, 20:3, 20:4, 24:0, and 28:1) by liquid chromatography-tandem mass spectrometry and repeated measures of skeletal muscle oxidative capacity (kPCr) assessed by 31P magnetic resonance spectroscopy over an average of 2.4 years. Rates of change in kPCr and each LPC were first estimated using simple linear regression. In multivariable linear regression models adjusted for baseline demographics and PCr % depletion, lower baseline LPC 16:1 and faster rates of decline in LPC 16:1 and 18:1 were significantly associated with a faster rate of decline in kPCr (B =  - 0.169, 95% CI: - 0.328, - 0.010, p = 0.038; B = 0.209, 95% CI: 0.065, 0.352, p = 0.005; B = 0.156, 95% CI: 0.011, 0.301, p = 0.035, respectively). Rates of change in other LPCs were not significantly associated with change in kPCr (all p > 0.05). Lower baseline concentrations and faster decline in selected plasma lysophosphatidylcholines over time are associated with faster decline in skeletal muscle mitochondrial function. Strategies to prevent the decline of plasma LPCs at an early stage may slow down mitochondrial function decline and impairment during aging.
    Keywords:  Cardiolipin synthesis; Lysophosphatidylcholines; Mitochondrial function
    DOI:  https://doi.org/10.1007/s11357-022-00548-w
  22. Biochim Biophys Acta Bioenerg. 2022 Mar 31. pii: S0005-2728(22)00026-3. [Epub ahead of print] 148557
    Praseodymium trivalent ion is an effective inhibitor of mitochondrial basic amino acids and carnitine/acylcarnitine carriers.
    Giovanna Incampo, Nicola Giangregorio, Nicola Gambacorta, Orazio Nicolotti, Concetta Pacifico, Luigi Palmieri, Annamaria Tonazzi.
      We herein report the identification of the lantanide praseodymium trivalent ion Pr3+ as inhibitor of mitochondrial transporters for basic amino acids and phylogenetically related carriers belonging to the Slc25 family. The inhibitory effect of Pr3+ has been tested using mitochondrial transporters reconstituted into liposomes being effective in the micromolar range, acting as a competitive inhibitor of the human basic amino acids carrier (BAC, Slc25A29), the human carnitine/acylcarnitine carrier (CAC, Slc25A20). Furthermore, we provide computational evidence that the complete inhibition of the transport activity of the recombinant proteins is due to the Pr3+ coordination to key acidic residues of the matrix salt bridge network. Besides being used as a first choice stop inhibitor for functional studies in vitro of mitochondrial carriers reconstituted in proteoliposomes, Pr3+ might also represent a useful tool for structural studies of the mitochondrial carrier family.
    Keywords:  Inhibitor; Liposomes; Mitochondria; Praseodymium; Reconstitution; Slc25 family transporters; Transport
    DOI:  https://doi.org/10.1016/j.bbabio.2022.148557
  23. Exp Mol Med. 2022 Apr 04.
    Tomatidine-stimulated maturation of human embryonic stem cell-derived cardiomyocytes for modeling mitochondrial dysfunction.
    Ye Seul Kim, Jung Won Yoon, Dasol Kim, Seunghak Choi, Hyoung Kyu Kim, Jae Boum Youm, Jin Han, Soon Chul Heo, Sung-Ae Hyun, Jung-Wook Seo, Deok-Ho Kim, Jae Ho Kim.
      Human embryonic stem cell-derived cardiomyocytes (hESC-CMs) have been reported to exhibit immature embryonic or fetal cardiomyocyte-like phenotypes. To enhance the maturation of hESC-CMs, we identified a natural steroidal alkaloid, tomatidine, as a new substance that stimulates the maturation of hESC-CMs. Treatment of human embryonic stem cells with tomatidine during cardiomyocyte differentiation stimulated the expression of several cardiomyocyte-specific markers and increased the density of T-tubules. Furthermore, tomatidine treatment augmented the number and size of mitochondria and enhanced the formation of mitochondrial lamellar cristae. Tomatidine treatment stimulated mitochondrial functions, including mitochondrial membrane potential, oxidative phosphorylation, and ATP production, in hESC-CMs. Tomatidine-treated hESC-CMs were more sensitive to doxorubicin-induced cardiotoxicity than the control cells. In conclusion, the present study suggests that tomatidine promotes the differentiation of stem cells to adult cardiomyocytes by accelerating mitochondrial biogenesis and maturation and that tomatidine-treated mature hESC-CMs can be used for cardiotoxicity screening and cardiac disease modeling.
    DOI:  https://doi.org/10.1038/s12276-022-00746-8
  24. J Med Genet. 2022 Apr 06. pii: jmedgenet-2021-108307. [Epub ahead of print]
    Transcriptome-based variant calling and aberrant mRNA discovery enhance diagnostic efficiency for neuromuscular diseases.
    Sung Eun Hong, Jana Kneissl, Anna Cho, Man Jin Kim, Soojin Park, Jeongeun Lee, Sijae Woo, Sora Kim, Jun-Soon Kim, Soo Yeon Kim, Sungwon Jung, Jinkuk Kim, Je-Young Shin, Jong-Hee Chae, Murim Choi.
      BACKGROUND: Whole-exome sequencing-based diagnosis of rare diseases typically yields 40%-50% of success rate. Precise diagnosis of the patients with neuromuscular disorders (NMDs) has been hampered by locus heterogeneity or phenotypic heterogeneity. We evaluated the utility of transcriptome sequencing as an independent approach in diagnosing NMDs.METHODS: The RNA sequencing (RNA-Seq) of muscle tissues from 117 Korean patients with suspected Mendelian NMD was performed to evaluate the ability to detect pathogenic variants. Aberrant splicing and CNVs were inspected to identify additional causal genetic factors for NMD. Aberrant splicing events in Dystrophin (DMD) were investigated by using antisense oligonucleotides (ASOs). A non-negative matrix factorisation analysis of the transcriptome data followed by cell type deconvolution was performed to cluster samples by expression-based signatures and identify cluster-specific gene ontologies.
    RESULTS: Our pipeline called 38.1% of pathogenic variants exclusively from the muscle transcriptomes, demonstrating a higher diagnostic rate than that achieved via exome analysis (34.9%). The discovery of variants causing aberrant splicing allowed the application of ASOs to the patient-derived cells, providing a therapeutic approach tailored to individual patients. RNA-Seq data further enabled sample clustering by distinct gene expression profiles that corresponded to clinical parameters, conferring additional advantages over exome sequencing.
    CONCLUSION: The RNA-Seq-based diagnosis of NMDs achieves an increased diagnostic rate and provided pathogenic status information, which is not easily accessible through exome analysis.
    Keywords:  RNA-Seq; diagnosis; neuromuscular diseases
    DOI:  https://doi.org/10.1136/jmedgenet-2021-108307
  25. Acta Ophthalmol. 2022 Apr 08.
    Clinical outcomes of treatment with idebenone in Leber's hereditary optic neuropathy in the Netherlands: A national cohort study.
    Judith A M van Everdingen, Jan Willem R Pott, Noël J C Bauer, Anna M Krijnen, Tanya Lushchyk, René J Wubbels.
      PURPOSE: The purpose of the study was to present results from a national Dutch cohort of patients with Leber's Hereditary Optic Neuropathy (LHON) treated with idebenone.METHODS: The multicentre, open-label, retrospective evaluation of the long-term outcome of idebenone treatment of Dutch LHON patients on visual function and on thickness of the retinal ganglion cell layer. Patients included in the analysis had a confirmed mutation in their mitochondrial DNA encoding either of the seven subunits of complex I, had a reported loss of vision in at least one eye and had a follow-up of more than 6 months after their treatment was started. Control visits involved routine clinical examinations of visual function and retinal structure at (1) the start of treatment, (2) nadir (time of lowest visual acuity), (3) the time of recovery (if any), (4) the time of termination of treatment and (5) more than 6 months after termination of the treatment.
    RESULTS: Data from 72 patients were analysed. Treatment duration was 23.8 ± 14.4 (mean ± SD) months. A positive response, that is either a clinically relevant recovery (CRR) or a clinically relevant stabilization (CRS), occurred in 53% and 11% of the patients, respectively. The magnitude of CRR was 0.41 ± 1.54 logMAR. CRR of visual acuity is associated with recovery of colour discrimination. The thickness of both the ganglion cell complex (GCC) and the retinal nerve fibre layer (RNFL) is irreversibly reduced.
    CONCLUSION: Our results confirm that idebenone may help to restore or maintain visual function. Whether this effect will persist is still unknown. Thinning of retinal neural tissue appears to be permanent.
    Keywords:  LHON; complex I deficiency; ganglion cells; mitochondrial hereditary disease; retina
    DOI:  https://doi.org/10.1111/aos.15153
  26. J Biol Chem. 2022 Mar 30. pii: S0021-9258(22)00323-4. [Epub ahead of print] 101883
    Mitochondria-associated myosin 19 processively transports mitochondria on actin tracks in living cells.
    Osamu Sato, Tsuyoshi Sakai, Young-Yeon Choo, Reiko Ikebe, Tomonobu M Watanabe, Mitsuo Ikebe.
      Mitochondria are fundamentally important in cell function and their malfunction can cause the development of cancer, cardiovascular disease, and neuronal disorders. Myosin 19 (Myo19) shows discrete localization with mitochondria and is thought to play an important role in mitochondrial dynamics and function; however, the function of Myo19 in mitochondrial dynamics at the cellular and molecular levels is poorly understood. Critical missing information is whether Myo19 is a processive motor that is suitable for transportation of mitochondria. Here we show for the first time that single Myo19 molecules processively move on actin filaments and can transport mitochondria in cells. We demonstrate that Myo19 dimers having a leucine-zipper processively moved on cellular actin tracks in de-membraned cells with a velocity of 50-60 nm/s and a run length of ∼0.4 μm, similar to the movement of isolated mitochondria from Myo19 dimer-transfected cells on actin tracks, suggesting that the Myo19 dimer can transport mitochondria. Furthermore, we show single molecules of Myo19 dimers processively moved on single actin filaments with a large step size of ∼34 nm. Importantly, wild type Myo19 single molecules without the leucine-zipper processively move in filopodia in living cells similar to Myo19 dimers, while deletion of the tail domain abolished such active movement. These results suggest that Myo19 can processively move on actin filaments when two Myo19 monomers form a dimer, presumably as a result of tail-tail association. In conclusion, Myo19 molecules can directly transport mitochondria on actin tracks within living cells.
    Keywords:  TIRF microscopy; Unconventional myosin; intracellular movement; mitochondria; single-molecule
    DOI:  https://doi.org/10.1016/j.jbc.2022.101883
  27. PLoS One. 2022 ;17(4): e0265744
    Prevalence and health care costs of mitochondrial disease in Ontario, Canada: A population-based cohort study.
    Emmalin Buajitti, Laura C Rosella, Ersi Zabzuni, L Trevor Young, Ana C Andreazza.
      BACKGROUND: Mitochondrial disease prevalence has been estimated at 1 in 4000 in the United States, and 1 in 5000 worldwide. Prevalence in Canada has not been established, though multi-linked health administrative data resources present a unique opportunity to establish robust population-based estimates in a single-payer health system. This study used administrative data for the Ontario, Canada population between April 1988 and March 2019 to measure mitochondrial disease prevalence and describe patient characteristics and health care costs.RESULTS: 3069 unique individuals were hospitalized with mitochondrial disease in Ontario and eligible for the study cohort, representing a period prevalence of 2.51 per 10,000 or 1 in 3989. First hospitalization was most common between ages 0-9 or 50-69. The mitochondrial disease population experiences a high need for health care and incurred high costs (mean = CAD$24,023 in 12 months before first hospitalization) within the single-payer Ontario health care system.
    CONCLUSIONS: This study provides needed insight into mitochondrial disease in Canada, and demonstrates the high health burden on patients. The methodology used can be adapted across jurisdictions with similar routine collection of health data, such as in other Canadian provinces. Future work should seek to validate this approach via record linkage of existing disease cohorts in Ontario, and identify specific comorbidities with mitochondrial disease that may contribute to high health resource utilization.
    DOI:  https://doi.org/10.1371/journal.pone.0265744
  28. Circulation. 2022 Apr 05. 145(14): e802-e803
    Letter by Belmadani and Matrougui Regarding Article, "Integrated Stress Response Couples Mitochondrial Protein Translation With Oxidative Stress Control".
    Souad Belmadani, Khalid Matrougui.
      
    DOI:  https://doi.org/10.1161/CIRCULATIONAHA.121.058242
  29. Front Cell Dev Biol. 2022 ;10 840389
    Dynamic Mitochondrial Proteome Under Polyamines Treatment in Cardiac Aging.
    Hao Zhang, Meng Yan, Ting Liu, Peiling Wei, Nannan Chai, Lingxu Li, Junying Wang, Xue Yu, Yan Lin, Bintao Qiu, Yajun Zhao.
      Age-related alteration of mitochondria causes impaired cardiac function, along with cellular and molecular changes. Polyamines can extend the life span in mice. However, whether polyamines can affect the dynamic mitochondrial proteome, thereby preventing age-related changes in cardiac function and cardiac aging, remains unclear. In this study, we found that spermine (Spm) and spermidine (Spd) injection for 6 weeks could prevent 24-month-old rats heart dysfunction, improve mitochondrial function, and downregulate apoptosis. Using iTRAQ tools, we identify 75 mitochondrial proteins of statistically significant alteration in aging hearts, which mainly participate in important mitochondrial physiological activity, such as metabolism, translation, transport, apoptosis, and oxidative phosphorylation. Moreover, four proteins of differential expression, pyruvate dehydrogenase kinase (PDK4), trifunctional enzyme subunit alpha (HADHA), nicotinamide nucleotide transhydrogenase (NNT), and Annexin6, which were significantly associated with heart aging, were validated by Western blotting. In vitro, we further demonstrated polyamines could retard cardiomyocytes aging through downregulating the expression of PDK4 and thereby inhibiting cell apoptosis. In summary, the distinct mitochondrial proteins identified in this study suggested some candidates involved in the anti-aging of the heart after polyamines treatment, and PDK4 may provide molecular clues for polyamines to inhibit apoptosis and thus retard aging-induced cardiac dysfunction.
    Keywords:  aging; heart; mitochondria; polyamines; proteome; rat
    DOI:  https://doi.org/10.3389/fcell.2022.840389
  30. Front Cell Neurosci. 2022 ;16 852245
    Serine/Threonine Protein Phosphatase 2A Regulates the Transport of Axonal Mitochondria.
    Keunjung Heo, Himanish Basu, Amos Gutnick, Wei Wei, Evgeny Shlevkov, Thomas L Schwarz.
      Microtubule-based transport provides mitochondria to distant regions of neurons and is essential for neuronal health. To identify compounds that increase mitochondrial motility, we screened 1,641 small-molecules in a high-throughput screening platform. Indirubin and cantharidin increased mitochondrial motility in rat cortical neurons. Cantharidin is known to inhibit protein phosphatase 2A (PP2A). We therefore tested two other inhibitors of PP2A: LB-100 and okadaic acid. LB-100 increased mitochondrial motility, but okadaic acid did not. To resolve this discrepancy, we knocked down expression of the catalytic subunit of PP2A (PP2CA). This long-term inhibition of PP2A more than doubled retrograde transport of axonal mitochondria, confirming the importance of PP2A as a regulator of mitochondrial motility and as the likely mediator of cantharidin's effect.
    Keywords:  cantharidin; high-throughput screen; indirubin; mitochondrial transport; protein phosphatase 2A
    DOI:  https://doi.org/10.3389/fncel.2022.852245
  31. Nature. 2022 Apr 06.
    Compartmentalized metabolism supports midgestation mammalian development.
    Ashley Solmonson, Brandon Faubert, Wen Gu, Aparna Rao, Mitzy A Cowdin, Ivan Menendez-Montes, Sherwin Kelekar, Thomas J Rogers, Chunxiao Pan, Gerardo Guevara, Amy Tarangelo, Lauren G Zacharias, Misty S Martin-Sandoval, Duyen Do, Panayotis Pachnis, Dennis Dumesnil, Thomas P Mathews, Alpaslan Tasdogan, An Pham, Ling Cai, Zhiyu Zhao, Min Ni, Ondine Cleaver, Hesham A Sadek, Sean J Morrison, Ralph J DeBerardinis.
      Mammalian embryogenesis requires rapid growth and proper metabolic regulation1. Midgestation features increasing oxygen and nutrient availability concomitant with fetal organ development2,3. Understanding how metabolism supports development requires approaches to observe metabolism directly in model organisms in utero. Here we used isotope tracing and metabolomics to identify evolving metabolic programmes in the placenta and embryo during midgestation in mice. These tissues differ metabolically throughout midgestation, but we pinpointed gestational days (GD) 10.5-11.5 as a transition period for both placenta and embryo. Isotope tracing revealed differences in carbohydrate metabolism between the tissues and rapid glucose-dependent purine synthesis, especially in the embryo. Glucose's contribution to the tricarboxylic acid (TCA) cycle rises throughout midgestation in the embryo but not in the placenta. By GD12.5, compartmentalized metabolic programmes are apparent within the embryo, including different nutrient contributions to the TCA cycle in different organs. To contextualize developmental anomalies associated with Mendelian metabolic defects, we analysed mice deficient in LIPT1, the enzyme that activates 2-ketoacid dehydrogenases related to the TCA cycle4,5. LIPT1 deficiency suppresses TCA cycle metabolism during the GD10.5-GD11.5 transition, perturbs brain, heart and erythrocyte development and leads to embryonic demise by GD11.5. These data document individualized metabolic programmes in developing organs in utero.
    DOI:  https://doi.org/10.1038/s41586-022-04557-9
  32. Birth Defects Res. 2022 Apr 09.
    Elucidating arrhythmogenic right ventricular cardiomyopathy with stem cells.
    Kenneth R Laurita, Sunil K Vasireddi, Judith A Mackall.
      Human stems cells have sparked many novel strategies for treating heart disease and for elucidating their underlying mechanisms. For example, arrhythmogenic right ventricular cardiomyopathy (ARVC) is an inherited heart muscle disorder that is associated with fatal arrhythmias often occurring in healthy young adults. Fibro-fatty infiltrate, a clinical hallmark, progresses with the disease and can develop across both ventricles. Pathogenic variants in genes have been identified, with most being responsible for encoding cardiac desmosome proteins that reside at myocyte boundaries that are critical for cell-to-cell coupling. Despite some understanding of the molecular signaling mechanisms associated with ARVC mutations, their relationship with arrhythmogenesis is complex and not well understood for a monogenetic disorder. This review article focuses on arrhythmia mechanisms in ARVC based on clinical and animal studies and their relationship with disease causing variants. We also discuss the ways in which stem cells can be leveraged to improve our understanding of the role cardiac myocytes, nonmyocytes, metabolic signals, and inflammatory mediators play in an early onset disease such as ARVC.
    Keywords:  ARVC; arrhythmia; cardiomyopathy; cytokines; desmosomes; gene mutations; stem cells
    DOI:  https://doi.org/10.1002/bdr2.2010
  33. Nat Methods. 2022 Apr 08.
    DiMeLo-seq: a long-read, single-molecule method for mapping protein-DNA interactions genome wide.
    Nicolas Altemose, Annie Maslan, Owen K Smith, Kousik Sundararajan, Rachel R Brown, Reet Mishra, Angela M Detweiler, Norma Neff, Karen H Miga, Aaron F Straight, Aaron Streets.
      Studies of genome regulation routinely use high-throughput DNA sequencing approaches to determine where specific proteins interact with DNA, and they rely on DNA amplification and short-read sequencing, limiting their quantitative application in complex genomic regions. To address these limitations, we developed directed methylation with long-read sequencing (DiMeLo-seq), which uses antibody-tethered enzymes to methylate DNA near a target protein's binding sites in situ. These exogenous methylation marks are then detected simultaneously with endogenous CpG methylation on unamplified DNA using long-read, single-molecule sequencing technologies. We optimized and benchmarked DiMeLo-seq by mapping chromatin-binding proteins and histone modifications across the human genome. Furthermore, we identified where centromere protein A localizes within highly repetitive regions that were unmappable with short sequencing reads, and we estimated the density of centromere protein A molecules along single chromatin fibers. DiMeLo-seq is a versatile method that provides multimodal, genome-wide information for investigating protein-DNA interactions.
    DOI:  https://doi.org/10.1038/s41592-022-01475-6
  34. Chem Sci. 2022 Mar 09. 13(10): 2965-2970
    Precise and long-term tracking of mitochondria in neurons using a bioconjugatable and photostable AIE luminogen.
    Hojeong Park, Guangle Niu, Chao Wu, Chungwon Park, Haixiang Liu, Hyokeun Park, Ryan T K Kwok, Jing Zhang, Benzhao He, Ben Zhong Tang.
      Tracking mitochondrial movement in neurons is an attractive but challenging research field as dysregulation of mitochondrial motion is associated with multiple neurological diseases. To realize accurate and long-term tracking of mitochondria in neurons, we elaborately designed a novel aggregation-induced emission (AIE)-active luminogen, TPAP-C5-yne, where we selected a cationic pyridinium moiety to target mitochondria and employed an activated alkyne terminus to achieve long-term tracking through bioconjugation with amines on mitochondria. For the first time, we successfully achieved the accurate analysis of the motion of a single mitochondrion in live primary hippocampal neurons and the long-term tracking of mitochondria for up to a week in live neurons. Therefore, this new AIEgen can be used as a potential tool to study the transport of mitochondria in live neurons.
    DOI:  https://doi.org/10.1039/d1sc06336g
  35. JCI Insight. 2022 Apr 08. pii: e155640. [Epub ahead of print]7(7):
    Mutant ANP induces mitochondrial and ion channel remodeling in a human iPSC-derived atrial fibrillation model.
    Olivia T Ly, Hanna Chen, Grace E Brown, Liang Hong, Xinge Wang, Yong Duk Han, Mahmud Arif Pavel, Arvind Sridhar, Mark Maienschein-Cline, Brandon Chalazan, Sang-Ging Ong, Khaled Abdelhady, Malek Massad, Lona Ernst Rizkallah, Jalees Rehman, Salman R Khetani, Dawood Darbar.
      Human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) can model heritable arrhythmias to personalize therapies for individual patients. Although atrial fibrillation (AF) is a leading cause of cardiovascular morbidity and mortality, current platforms to generate iPSC-atrial (a) CMs are inadequate for modeling AF. We applied a combinatorial engineering approach, which integrated multiple physiological cues, including metabolic conditioning and electrical stimulation, to generate mature iPSC-aCMs. Using the patient's own atrial tissue as a gold standard benchmark, we assessed the electrophysiological, structural, metabolic, and molecular maturation of iPSC-aCMs. Unbiased transcriptomic analysis and inference from gene regulatory networks identified key gene expression pathways and transcription factors mediating atrial development and maturation. Only mature iPSC-aCMs generated from patients with heritable AF carrying the non-ion channel gene (NPPA) mutation showed enhanced expression and function of a cardiac potassium channel and revealed mitochondrial electron transport chain dysfunction. Collectively, we propose that ion channel remodeling in conjunction with metabolic defects created an electrophysiological substrate for AF. Overall, our electro-metabolic approach generated mature human iPSC-aCMs that unmasked the underlying mechanism of the first non-ion channel gene, NPPA, that causes AF. Our maturation approach will allow for the investigation of the molecular underpinnings of heritable AF and the development of personalized therapies.
    Keywords:  Arrhythmias; Cardiology; Genetic diseases; Genetics; iPS cells
    DOI:  https://doi.org/10.1172/jci.insight.155640
  36. NPJ Genom Med. 2022 Apr 08. 7(1): 27
    Best practices for the interpretation and reporting of clinical whole genome sequencing.
    Medical Genome Initiative*
      Whole genome sequencing (WGS) shows promise as a first-tier diagnostic test for patients with rare genetic disorders. However, standards addressing the definition and deployment practice of a best-in-class test are lacking. To address these gaps, the Medical Genome Initiative, a consortium of leading health care and research organizations in the US and Canada, was formed to expand access to high quality clinical WGS by convening experts and publishing best practices. Here, we present best practice recommendations for the interpretation and reporting of clinical diagnostic WGS, including discussion of challenges and emerging approaches that will be critical to harness the full potential of this comprehensive test.
    DOI:  https://doi.org/10.1038/s41525-022-00295-z
  37. Cell Stem Cell. 2022 Apr 07. pii: S1934-5909(22)00101-1. [Epub ahead of print]
    Uncompensated mitochondrial oxidative stress underlies heart failure in an iPSC-derived model of congenital heart disease.
    Xinxiu Xu, Kang Jin, Abha S Bais, Wenjuan Zhu, Hisato Yagi, Timothy N Feinstein, Phong K Nguyen, Joseph D Criscione, Xiaoqin Liu, Gisela Beutner, Kalyani B Karunakaran, Krithika S Rao, Haoting He, Phillip Adams, Catherine K Kuo, Dennis Kostka, Gloria S Pryhuber, Sruti Shiva, Madhavi K Ganapathiraju, George A Porter, Jiuann-Huey Ivy Lin, Bruce Aronow, Cecilia W Lo.
      Hypoplastic left heart syndrome (HLHS) is a severe congenital heart disease with 30% mortality from heart failure (HF) in the first year of life, but the cause of early HF remains unknown. Induced pluripotent stem-cell-derived cardiomyocytes (iPSC-CM) from patients with HLHS showed that early HF is associated with increased apoptosis, mitochondrial respiration defects, and redox stress from abnormal mitochondrial permeability transition pore (mPTP) opening and failed antioxidant response. In contrast, iPSC-CM from patients without early HF showed normal respiration with elevated antioxidant response. Single-cell transcriptomics confirmed that early HF is associated with mitochondrial dysfunction accompanied with endoplasmic reticulum (ER) stress. These findings indicate that uncompensated oxidative stress underlies early HF in HLHS. Importantly, mitochondrial respiration defects, oxidative stress, and apoptosis were rescued by treatment with sildenafil to inhibit mPTP opening or TUDCA to suppress ER stress. Together these findings point to the potential use of patient iPSC-CM for modeling clinical heart failure and the development of therapeutics.
    Keywords:  TUDCA; antioxidant response; congenital heart disease; endoplasmic reticulum stress; heart failure; hypoplastic left heart syndrome; i; induced pluripotent stem-cell-derived cardiomyocytes; mitochondrial permeability transition pore; oxidative stress; sildenafil
    DOI:  https://doi.org/10.1016/j.stem.2022.03.003
  38. Front Mol Neurosci. 2022 ;15 852181
    Mitochondrial Reactive Oxygen Species Mediate Activation of TRPV1 and Calcium Entry Following Peripheral Sensory Axotomy.
    Bradley Kievit, Aaron D Johnstone, Julien Gibon, Philip A Barker.
      Axons that are physically separated from their soma activate a series of signaling events that results in axonal self-destruction. A critical element of this signaling pathway is an intra-axonal calcium rise that occurs just prior to axonal fragmentation. Previous studies have shown that preventing this calcium rise delays the onset of axon fragmentation, yet the ion channels responsible for the influx, and the mechanisms by which they are activated, are largely unknown. Axonal injury can be modeled in vitro by transecting murine dorsal root ganglia (DRG) sensory axons. We coupled transections with intra-axonal calcium imaging and found that Ca2+ influx is sharply reduced in axons lacking trpv1 (for transient receptor potential cation channel vanilloid 1) and in axons treated with capsazepine (CPZ), a TRPV1 antagonist. Sensory neurons from trpv1 -/- mice were partially rescued from degeneration after transection, indicating that TRPV1 normally plays a pro-degenerative role after axonal injury. TRPV1 activity can be regulated by direct post-translational modification induced by reactive oxygen species (ROS). Here, we tested the hypothesis that mitochondrial ROS production induced by axotomy is required for TRPV1 activity and subsequent axonal degeneration. We found that reducing mitochondrial depolarization with NAD+ supplementation or scavenging ROS using NAC or MitoQ sharply attenuates TRPV1-dependent calcium influx induced by axotomy. This study shows that ROS-dependent TRPV1 activation is required for Ca2+ entry after axotomy.
    Keywords:  ROS; TRPV1; axotomy; degeneration; mitochondria
    DOI:  https://doi.org/10.3389/fnmol.2022.852181
  39. Mol Metab. 2022 Apr 01. pii: S2212-8778(22)00056-4. [Epub ahead of print] 101487
    Hepatocyte-specific activity of TSC22D4 triggers progressive NAFLD by impairing mitochondrial function.
    Gretchen Wolff, Minako Sakurai, Amit Mhamane, Maria Troullinaki, Adriano Maida, Ioannis K Deligiannis, Kelvin Yin, Peter Weber, Jakob Morgenstern, Annika Wieder, Yun Kwon, Revathi Sekar, Anja Zeigerer, Michael Roden, Matthias Blüher, Nadine Volk, Tanja Poth, Thilo Hackert, Lena Wiedmann, Francesca De Angelis Rigotti, Juan Rodriguez-Vita, Andreas Fischer, Rajesh Mukthavaram, Pattraranee Limphong, Kiyoshi Tachikawa, Priya Karmali, Joseph Payne, Padmanabh Chivukula, Bilgen Ekim-Üstünel, Celia P Martinez-Jimenez, Julia Szendrödi, Peter Nawroth, Stephan Herzig.
      OBJECTIVE: Fibrotic organ responses have recently been identified as long-term complications in diabetes. Indeed, insulin resistance and aberrant hepatic lipid accumulation represent driving features of progressive non-alcoholic fatty liver disease (NAFLD), ranging from simple steatosis and non-alcoholic steatohepatitis (NASH) to fibrosis. Effective pharmacological regimens to stop progressive liver disease are still lacking to-date.METHODS: Based on our previous discovery of transforming growth factor beta-like stimulated clone (TSC)22D4 as a key driver of insulin resistance and glucose intolerance in obesity and type 2 diabetes, we generated a TSC22D4-hepatocyte specific knockout line (TSC22D4-HepaKO) and exposed mice to control or NASH diet models. Mechanistic insights were generated by metabolic phenotyping and single-nuclei RNA sequencing.
    RESULTS: Hepatic TSC22D4 expression was significantly correlated with markers of liver disease progression and fibrosis in both murine and human livers. Indeed, hepatic TSC22D4 levels were elevated in human NASH patients as well as in several murine NASH models. Specific genetic deletion of TSC22D4 in hepatocytes led to reduced liver lipid accumulation, improvements in steatosis and inflammation scores and decreased apoptosis in mice fed a lipogenic MCD diet. Single-nuclei RNA sequencing revealed a distinct TSC22D4-dependent gene signature identifying an upregulation of mitochondrial-related processes in hepatocytes upon loss of TSC22D4. An enrichment of genes involved in the TCA cycle, mitochondrial organization, and triglyceride metabolism underscored the hepatocyte-protective phenotype and overall decreased liver damage as seen in mouse models of hepatocyte-selective TSC22D4 loss-of-function.
    CONCLUSIONS: Together, our data uncover a new connection between targeted depletion of TSC22D4 and intrinsic metabolic processes in progressive liver disease. Hepatocyte-specific reduction of TSC22D4 improves hepatic steatosis and promotes hepatocyte survival via mitochondrial-related mechanisms thus paving the way for targeted therapies.
    Keywords:  Fibrosis; Hepatocyte-specific; NAFLD; NASH; TSC22D4
    DOI:  https://doi.org/10.1016/j.molmet.2022.101487
  40. iScience. 2022 Apr 15. 25(4): 104097
    High-resolution Slide-seqV2 spatial transcriptomics enables discovery of disease-specific cell neighborhoods and pathways.
    Jamie L Marshall, Teia Noel, Qingbo S Wang, Haiqi Chen, Evan Murray, Ayshwarya Subramanian, Katherine A Vernon, Silvana Bazua-Valenti, Katie Liguori, Keith Keller, Robert R Stickels, Breanna McBean, Rowan M Heneghan, Astrid Weins, Evan Z Macosko, Fei Chen, Anna Greka.
      High-resolution spatial transcriptomics enables mapping of RNA expression directly from intact tissue sections; however, its utility for the elucidation of disease processes and therapeutically actionable pathways remains unexplored. We applied Slide-seqV2 to mouse and human kidneys, in healthy and distinct disease paradigms. First, we established the feasibility of Slide-seqV2 in tissue from nine distinct human kidneys, which revealed a cell neighborhood centered around a population of LYVE1+ macrophages. Second, in a mouse model of diabetic kidney disease, we detected changes in the cellular organization of the spatially restricted kidney filter and blood-flow-regulating apparatus. Third, in a mouse model of a toxic proteinopathy, we identified previously unknown, disease-specific cell neighborhoods centered around macrophages. In a spatially restricted subpopulation of epithelial cells, we discovered perturbations in 77 genes associated with the unfolded protein response. Our studies illustrate and experimentally validate the utility of Slide-seqV2 for the discovery of disease-specific cell neighborhoods.
    Keywords:  Cell biology; Pathophysiology; Transcriptomics
    DOI:  https://doi.org/10.1016/j.isci.2022.104097
  41. Trends Genet. 2022 Mar 30. pii: S0168-9525(22)00039-7. [Epub ahead of print]
    Genetic disorders of cellular trafficking.
    Angeles García-Cazorla, Alfonso Oyarzábal, Jean-Marie Saudubray, Diego Martinelli, Carlo Dionisi-Vici.
      Cellular trafficking is essential to maintain critical biological functions. Mutations in 346 genes, most of them described in the last 5 years, are associated with disorders of cellular trafficking. Whereas initially restricted to membrane trafficking, the recent detection of many diseases has contributed to the discovery of new biological pathways. Accordingly, we propose to redesign this rapidly growing group of diseases combining biological mechanisms and clinical presentation into the following categories: (i) membrane trafficking (including organelle-related); (ii) membrane contact sites; (iii) autophagy; (iv) cytoskeleton-related. We present the most recently described pathophysiological findings, disorders and phenotypes. Although all tissues and organs are affected, the nervous system is especially vulnerable.
    Keywords:  autophagy; cellular trafficking; inherited metabolic diseases; membrane contact sites; vesicular trafficking
    DOI:  https://doi.org/10.1016/j.tig.2022.02.012
  42. Cell Rep. 2022 Apr 05. pii: S2211-1247(22)00395-3. [Epub ahead of print]39(1): 110643
    Population-based high-throughput toxicity screen of human iPSC-derived cardiomyocytes and neurons.
    Ching Ying Huang, Martin W Nicholson, Jyun Yuan Wang, Chien Yu Ting, Ming Heng Tsai, Yu Che Cheng, Chun Lin Liu, Darien Z H Chan, Yi Chan Lee, Ching Chuan Hsu, Yu Hung Hsu, Chiou Fong Yang, Cindy M C Chang, Shu Chian Ruan, Po Ju Lin, Jen Hao Lin, Li Lun Chen, Marvin L Hsieh, Yuan Yuan Cheng, Wan Tseng Hsu, Yi Ling Lin, Chien Hsiun Chen, Yu Hsiang Hsu, Ying Ta Wu, Timothy A Hacker, Joseph C Wu, Timothy J Kamp, Patrick C H Hsieh.
      In this study, we establish a population-based human induced pluripotent stem cell (hiPSC) drug screening platform for toxicity assessment. After recruiting 1,000 healthy donors and screening for high-frequency human leukocyte antigen (HLA) haplotypes, we identify 13 HLA-homozygous "super donors" to represent the population. These "super donors" are also expected to represent at least 477,611,135 of the global population. By differentiating these representative hiPSCs into cardiomyocytes and neurons we show their utility in a high-throughput toxicity screen. To validate hit compounds, we demonstrate dose-dependent toxicity of the hit compounds and assess functional modulation. We also show reproducible in vivo drug toxicity results using mouse models with select hit compounds. This study shows the feasibility of using a population-based hiPSC drug screening platform to assess cytotoxicity, which can be used as an innovative tool to study inter-population differences in drug toxicity and adverse drug reactions in drug discovery applications.
    Keywords:  CP: Stem cell research; cardiomyocyte; drug screening; human leukocyte antigen; human-induced pluripotent stem cell; neuron; toxicity
    DOI:  https://doi.org/10.1016/j.celrep.2022.110643
  43. Curr Pediatr Rev. 2022 Apr 04.
    Inborn errors of metabolism screening in neonates: current perspective with diagnosis and therapy.
    Sukhes Mukherjee, Suman Kumar Ray.
      Inborn errors of metabolism (IEMs) are rare hereditary or acquired disorders resulting from an enzymatic deformity in biochemical and metabolic pathways influencing proteins, fats, carbohydrate metabolism, or hampered some organelle function. Even though individual IEMs are uncommon, together, they represent a diverse class of genetic diseases, with new issues and disease mechanisms being portrayed consistently. IEM includes the extraordinary multifaceted nature of the fundamental pathophysiology, biochemical diagnosis, molecular level investigation, and complex therapeutic choices. However, due to the molecular, biochemical, and clinical heterogeneity of IEM, screening alone will not detect and diagnose all illnesses included in newborn screening programs. Early diagnosis prevents the emergence of severe clinical symptoms in the majority of IEM cases, lowering morbidity and death. The appearance of IEM disease can vary from neonates to adult people, with the more serious conditions showing up in juvenile stages along with significant morbidity as well as mortality. Advances in understanding the physiological, biochemical, and molecular etiologies of numerous IEMs by means of modalities, for instance, the latest molecular-genetic technologies, genome engineering knowledge, entire exome sequencing, and metabolomics, have prompted remarkable advancement in detection and treatment in modern times. In this review, we analyze the biochemical basis of IEMs, clinical manifestations, the present status of screening, ongoing advances, and efficiency of diagnosis in treatment for IEMs, along with prospects for further exploration as well as innovation.
    Keywords:  Inborn errors of metabolism; biochemical diagnosis; clinical manifestations; metabolomics; molecular level investigation; neonatal screening
    DOI:  https://doi.org/10.2174/1573396318666220404194452
  44. Cell Death Dis. 2022 Apr 08. 13(4): 321
    Ischemia-induced cleavage of OPA1 at S1 site aggravates mitochondrial fragmentation and reperfusion injury in neurons.
    Xiang Li, Haiying Li, Zhongmou Xu, Cheng Ma, Tianyi Wang, Wanchun You, Zhengquan Yu, Haitao Shen, Gang Chen.
      Neuronal mitochondrial dynamics are disturbed after ischemic stroke. Optic atrophy 1 (OPA1) and its GTPase activity are involved in maintaining mitochondrial cristae and inner membrane fusion. This study aimed to explore the role of OMA1-mediated OPA1 cleavage (S1-OPA1) in neurons exposed to cerebral ischemia and reperfusion. After oxygen-glucose deprivation (OGD) for 60 min, we found that mitochondrial fragmentation occurred successively in the axon and soma of neurons, accompanied by an increase in S1-OPA1. In addition, S1-OPA1 overexpression significantly aggravated mitochondrial damage in neurons exposed to OGD for 60 min and 24 h after OGD/R, characterized by mitochondrial fragmentation, decreased mitochondrial membrane potential, mitochondrial cristae ultrastructural damage, increased superoxide production, decreased ATP production and increased mitochondrial apoptosis, which was inhibited by the lysine 301 to alanine mutation (K301A). Furthermore, we performed neuron-specific overexpression of S1-OPA1 in the cerebral cortex around ischemia of middle cerebral artery occlusion/reperfusion (MCAO/R) mice. The results further demonstrated in vivo that S1-OPA1 exacerbated neuronal mitochondrial ultrastructural destruction and injury induced by cerebral ischemia-reperfusion, while S1-OPA1-K301 overexpression had no effect. In conclusion, ischemia induced neuronal OMA1-mediated cleavage of OPA1 at the S1 site. S1-OPA1 aggravated neuronal mitochondrial fragmentation and damage in a GTPase-dependent manner, and participated in neuronal ischemia-reperfusion injury.
    DOI:  https://doi.org/10.1038/s41419-022-04782-0
  45. Nat Methods. 2022 Apr 08.
    Searching thousands of genomes to classify somatic and novel structural variants using STIX.
    Murad Chowdhury, Brent S Pedersen, Fritz J Sedlazeck, Aaron R Quinlan, Ryan M Layer.
      Structural variants are associated with cancers and developmental disorders, but challenges with estimating population frequency remain a barrier to prioritizing mutations over inherited variants. In particular, variability in variant calling heuristics and filtering limits the use of current structural variant catalogs. We present STIX, a method that, instead of relying on variant calls, indexes and searches the raw alignments from thousands of samples to enable more comprehensive allele frequency estimation.
    DOI:  https://doi.org/10.1038/s41592-022-01423-4
  46. Hum Mutat. 2022 Apr 07.
    Phenotype-driven approaches to enhance variant prioritization and diagnosis of rare disease.
    Julius O Jacobsen, Catherine Kelly, Valentina Cipriani, Genomics England Research Consortium, Christopher J Mungall, Justin Reese, Daniel Danis, Peter N Robinson, Damian Smedley.
      Rare disease diagnostics and disease gene discovery have been revolutionized by whole exome and genome sequencing but identifying the causative variant(s) from the millions in each individual remains challenging. Use of deep phenotyping of patients and reference genotype-phenotype knowledge, alongside variant data such as allele frequency, segregation and predicted pathogenicity, has proved an effective strategy to tackle this issue. Here we review the numerous tools that have been developed to automate this approach and demonstrate the power of such an approach on several thousand diagnosed cases from the 100,000 Genomes Project. Finally, we discuss the challenges that need to be overcome if we are going to improve detection rates and help the majority of patients that still remain without a molecular diagnosis after state of the art genomic interpretation. This article is protected by copyright. All rights reserved.
    Keywords:  Diagnostics; Phenotypes; Rare disease; Variant prioritization
    DOI:  https://doi.org/10.1002/humu.24380
  47. Pediatr Investig. 2022 Mar;6(1): 29-35
    RNA sequencing role and application in clinical diagnostic.
    Fatemeh Peymani, Aiman Farzeen, Holger Prokisch.
      Although whole-exome sequencing and whole-genome sequencing has tremendously improved our understanding of the genetic etiology of human disorders, about half of the patients still do not receive a molecular diagnosis. The high fraction of variants with uncertain significance and the challenges of interpretation of noncoding variants have urged scientists to implement RNA sequencing (RNA-seq) in the diagnostic approach as a high throughput assay to complement genomic data with functional evidence. RNA-seq data can be used to identify aberrantly spliced genes, detect allele-specific expression, and identify gene expression outliers. Amongst eight studies utilizing RNA-seq, a mean diagnostic uplift of 15% has been reported. Here, we provide an overview of how RNA-seq has been implemented to aid in identifying the causal variants of Mendelian disorders.
    Keywords:  Aberrant expression; Clinical diagnosis; Gene expression outliers; Genetics diagnosis; RNA phenotype; RNA sequencing; Transcriptome
    DOI:  https://doi.org/10.1002/ped4.12314
  48. Cell Death Dis. 2022 Apr 02. 13(4): 296
    Ultrastructural and proteomic profiling of mitochondria-associated endoplasmic reticulum membranes reveal aging signatures in striated muscle.
    Xue Lu, Yingchao Gong, Wanyu Hu, Yankai Mao, Ting Wang, Zeyu Sun, Xiaoling Su, Guosheng Fu, Yanpeng Wang, Dongwu Lai.
      Aging is a major risk for developing cardiac and skeletal muscle dysfunction, yet the underlying mechanism remains elusive. Here we demonstrated that the mitochondria-associated endoplasmic reticulum membranes (MAMs) in the rat heart and skeletal muscle were disrupted during aging. Using quantitative morphological analysis, we showed that the mitochondria-endoplasmic reticulum contacts (MERCs) were reduced by half over the lifespan with an early onset of accelerated thickening in the clefts. The ultrastructural changes were further validated by proteomic profiling of the MAM fractions. A combination of subcellular fractionation and quantitative mass spectrometry identified 1306 MAM-enriched proteins in both heart and skeletal muscle, with a catalog of proteins dysregulated with aging. Functional mapping of the MAM proteome suggested several aging signatures to be closely associated with the ER-mitochondria crosstalk, including local metabolic rewiring, calcium homeostasis imbalance, and impaired organelle dynamics and autophagy. Moreover, we identified a subset of highly interconnected proteins in an ER-mitochondria organization network, which were consistently down-regulated with aging. These decreased proteins, including VDAC1, SAMM50, MTX1 and MIC60, were considered as potential contributors to the age-related MAM dysfunction. This study highlights the perturbation in MAM integrity during the striated muscle aging process, and provides a framework for understanding aging biology from the perspective of organelle interactions.
    DOI:  https://doi.org/10.1038/s41419-022-04746-4
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