bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2023‒06‒25
forty papers selected by
Catalina Vasilescu
Helmholz Munich
  1. Enhanced mitochondrial G-quadruplex formation impedes replication fork progression leading to mtDNA loss in human cells.
  2. Invasive and noninvasive markers of human skeletal muscle mitochondrial function.
  3. Exercise testing and prescription in patients with inborn errors of muscle energy metabolism.
  4. Structural basis of mitochondrial protein import by the TIM23 complex.
  5. Two-Step Tag-Free Isolation of Mitochondria for Improved Protein Discovery and Quantification.
  6. Editorial: Mitochondrial bioenergetics impairments in genetic and metabolic diseases.
  7. PARK15/FBXO7 is dispensable for PINK1/Parkin mitophagy in iNeurons and HeLa cell systems.
  8. Patch-clamp technique to study mitochondrial membrane biophysics.
  9. The evolution of the mitochondrial disease diagnostic odyssey.
  10. Metabolic inflexibility and unusual catabolism in Leigh-like syndrome due to m.10191T>C.
  11. A spatial map of hepatic mitochondria uncovers functional heterogeneity shaped by nutrient-sensing signaling.
  12. Structural basis for the binding of DNP and purine nucleotides onto UCP1.
  13. Mitochondrial matrix protein LETMD1 maintains thermogenic capacity of brown adipose tissue in male mice.
  14. LonP1 Links Mitochondria-ER Interaction to Regulate Heart Function.
  15. Facioscapulohumeral muscular dystrophy is associated with altered myoblast proteome dynamics.
  16. Real-Time Measurement of the Mitochondrial Bioenergetic Profile of Neutrophils.
  17. NUDT6 and NUDT9, two mitochondrial members of the NUDIX family, have distinct hydrolysis activities.
  18. A DEFECT IN MITOCHONDRIAL COMPLEX III BUT NOT IN COMPLEXES I OR IV CAUSES EARLY BETA CELL DYSFUNCTION AND HYPERGLYCEMIA IN MICE.
  19. Developmental transcriptional control of mitochondrial homeostasis is required for activity-dependent synaptic connectivity.
  20. Proton leak through the UCPs and ANT carriers and beyond: A breath for the electron transport chain.
  21. Intranasal delivery of mitochondrial protein humanin rescues cell death and promotes mitochondrial function in Parkinson's disease.
  22. Analysis of MT-ATP8 gene variants reported in patients by modeling in silico and in yeast model organism.
  23. Cooperative sensing of mitochondrial DNA by ZBP1 and cGAS promotes cardiotoxicity.
  24. Mechanisms of dual modulatory effects of spermine on the mitochondrial calcium uniporter complex.
  25. The impacts of the mitochondrial myopathy-associated G58R mutation on the dynamic structural properties of CHCHD10.
  26. Pancreatic islet protection at the expense of secretory function involves serine-linked mitochondrial one-carbon metabolism.
  27. Mitochondrial aconitase suppresses immunity by modulating oxaloacetate and the mitochondrial unfolded protein response.
  28. Neuroprotection in glaucoma: Mechanisms beyond intraocular pressure lowering.
  29. Splice variants of mitofusin 2 shape the endoplasmic reticulum and tether it to mitochondria.
  30. NAD+ Precursors in Human Health and Disease: Current Status and Future Prospects.
  31. Loss of functional peroxisomes leads to increased mitochondrial biogenesis and reduced autophagy that preserve mitochondrial function.
  32. Expansion spatial transcriptomics.
  33. Large-scale rare variant burden testing in Parkinson's disease.
  34. Who Is Responsible for Promoting Equity in Rare Disease Research?
  35. The NAD salvage pathway in mesenchymal cells is indispensable for skeletal development in mice.
  36. FUNDC1 modulates mitochondrial defects and pancreatic β-cell dysfunction under lipotoxicity.
  37. AutoPrognosis 2.0: Democratizing diagnostic and prognostic modeling in healthcare with automated machine learning.
  38. A systematic review on machine learning approaches in the diagnosis and prognosis of rare genetic diseases.
  39. Mechanisms of readthrough mitigation reveal principles of GCN1-mediated translational quality control.
  40. Investigation of FGF21 mRNA levels and relative mitochondrial DNA copy number levels and their relation in nonalcoholic fatty liver disease: a case-control study.
  1. Nucleic Acids Res. 2023 Jun 23. pii: gkad535. [Epub ahead of print]
    Enhanced mitochondrial G-quadruplex formation impedes replication fork progression leading to mtDNA loss in human cells.
    Mara Doimo, Namrata Chaudhari, Sanna Abrahamsson, Valentin L'Hôte, Tran V H Nguyen, Andreas Berner, Mama Ndi, Alva Abrahamsson, Rabindra Nath Das, Koit Aasumets, Steffi Goffart, Jaakko L O Pohjoismäki, Marcela Dávila López, Erik Chorell, Sjoerd Wanrooij.
      Mitochondrial DNA (mtDNA) replication stalling is considered an initial step in the formation of mtDNA deletions that associate with genetic inherited disorders and aging. However, the molecular details of how stalled replication forks lead to mtDNA deletions accumulation are still unclear. Mitochondrial DNA deletion breakpoints preferentially occur at sequence motifs predicted to form G-quadruplexes (G4s), four-stranded nucleic acid structures that can fold in guanine-rich regions. Whether mtDNA G4s form in vivo and their potential implication for mtDNA instability is still under debate. In here, we developed new tools to map G4s in the mtDNA of living cells. We engineered a G4-binding protein targeted to the mitochondrial matrix of a human cell line and established the mtG4-ChIP method, enabling the determination of mtDNA G4s under different cellular conditions. Our results are indicative of transient mtDNA G4 formation in human cells. We demonstrate that mtDNA-specific replication stalling increases formation of G4s, particularly in the major arc. Moreover, elevated levels of G4 block the progression of the mtDNA replication fork and cause mtDNA loss. We conclude that stalling of the mtDNA replisome enhances mtDNA G4 occurrence, and that G4s not resolved in a timely manner can have a negative impact on mtDNA integrity.
    DOI:  https://doi.org/10.1093/nar/gkad535
  2. Physiol Rep. 2023 06;11(12): e15734
    Invasive and noninvasive markers of human skeletal muscle mitochondrial function.
    Rodrigo Mancilla, Diego Pava-Mejia, Nynke van Polanen, Vera de Wit, Maaike Bergman, Lotte Grevendonk, Johanna Jorgensen, Esther Kornips, Joris Hoeks, Matthijs K C Hesselink, Vera B Schrauwen-Hinderling.
      Mitochondria are organelles that fuel cellular energy requirements by ATP formation via aerobic metabolism. Given the wide variety of methods to assess skeletal muscle mitochondrial capacity, we tested how well different invasive and noninvasive markers of skeletal muscle mitochondrial capacity reflect mitochondrial respiration in permeabilized muscle fibers. Nineteen young men (mean age: 24 ± 4 years) were recruited, and a muscle biopsy was collected to determine mitochondrial respiration from permeabilized muscle fibers and to quantify markers of mitochondrial capacity, content such as citrate synthase (CS) activity, mitochondrial DNA copy number, TOMM20, VDAC, and protein content for complex I-V of the oxidative phosphorylation (OXPHOS) system. Additionally, all participants underwent noninvasive assessments of mitochondrial capacity: PCr recovery postexercise (by 31 P-MRS), maximal aerobic capacity, and gross exercise efficiency by cycling exercise. From the invasive markers, Complex V protein content and CS activity showed the strongest concordance (Rc = 0.50 to 0.72) with ADP-stimulated coupled mitochondrial respiration, fueled by various substrates. Complex V protein content showed the strongest concordance (Rc = 0.72) with maximally uncoupled mitochondrial respiration. From the noninvasive markers, gross exercise efficiency, VO2max , and PCr recovery exhibited concordance values between 0.50 and 0.77 with ADP-stimulated coupled mitochondrial respiration. Gross exercise efficiency showed the strongest concordance with maximally uncoupled mitochondrial respiration (Rc = 0.67). From the invasive markers, Complex V protein content and CS activity are surrogates that best reflect skeletal muscle mitochondrial respiratory capacity. From the noninvasive markers, exercise efficiency and PCr recovery postexercise most closely reflect skeletal muscle mitochondrial respiratory capacity.
    Keywords:  human skeletal muscle; mitochondrial function; skeletal muscle mitochondrial respiration
    DOI:  https://doi.org/10.14814/phy2.15734
  3. J Inherit Metab Dis. 2023 Jun 22.
    Exercise testing and prescription in patients with inborn errors of muscle energy metabolism.
    Kiera Batten, Kaustuv Bhattacharya, David Simar, Carolyn Broderick.
      Skeletal muscle is a dynamic organ requiring tight regulation of energy metabolism in order to provide bursts of energy for effective function. Several inborn errors of muscle energy metabolism (IEMEM) affect skeletal muscle function and therefore the ability to initiate and sustain physical activity. Exercise testing can be valuable in supporting diagnosis, however its use remains limited due to the inconsistency in data to inform its application in IEMEM populations. While exercise testing is often used in adults with IEMEM, its use in children is far more limited. Once a physiological limitation has been identified and the aetiology defined, habitual exercise can assist with improving functional capacity, with reports supporting favourable adaptations in adult patients with IEMEM. Despite the potential benefits of structured exercise programs, data in paediatric populations remain limited. This review will focus on the utilisation and limitations of exercise testing and prescription for both adults and children, in the management of McArdle Disease, long chain fatty acid oxidation disorders, and myopathic mitochondrial respiratory chain disorders. This article is protected by copyright. All rights reserved.
    Keywords:  McArdle disease; cardiopulmonary exercise test; exercise; fatty acid oxidation disorder; inborn errors of metabolism; mitochondrial myopathy
    DOI:  https://doi.org/10.1002/jimd.12644
  4. Nature. 2023 Jun 21.
    Structural basis of mitochondrial protein import by the TIM23 complex.
    Sue Im Sim, Yuanyuan Chen, Diane L Lynch, James C Gumbart, Eunyong Park.
      Mitochondria import nearly all of their approximately 1,000-2,000 constituent proteins from the cytosol across their double-membrane envelope1-5. Genetic and biochemical studies have shown that the conserved protein translocase, termed the TIM23 complex, mediates import of presequence-containing proteins (preproteins) into the mitochondrial matrix and inner membrane. Among about ten different subunits of the TIM23 complex, the essential multipass membrane protein Tim23, together with the evolutionarily related protein Tim17, has long been postulated to form a protein-conducting channel6-11. However, the mechanism by which these subunits form a translocation path in the membrane and enable the import process remains unclear due to a lack of structural information. Here we determined the cryo-electron microscopy structure of the core TIM23 complex (heterotrimeric Tim17-Tim23-Tim44) from Saccharomyces cerevisiae. Contrary to the prevailing model, Tim23 and Tim17 themselves do not form a water-filled channel, but instead have separate, lipid-exposed concave cavities that face in opposite directions. Our structural and biochemical analyses show that the cavity of Tim17, but not Tim23, forms the protein translocation path, whereas Tim23 probably has a structural role. The results further suggest that, during translocation of substrate polypeptides, the nonessential subunit Mgr2 seals the lateral opening of the Tim17 cavity to facilitate the translocation process. We propose a new model for the TIM23-mediated protein import and sorting mechanism, a central pathway in mitochondrial biogenesis.
    DOI:  https://doi.org/10.1038/s41586-023-06239-6
  5. J Vis Exp. 2023 Jun 02.
    Two-Step Tag-Free Isolation of Mitochondria for Improved Protein Discovery and Quantification.
    Joan Blanco-Fernandez, Alexis A Jourdain.
      Most physiological and disease processes, from central metabolism to immune response to neurodegeneration, involve mitochondria. The mitochondrial proteome is composed of more than 1,000 proteins, and the abundance of each can vary dynamically in response to external stimuli or during disease progression. Here, we describe a protocol for isolating high-quality mitochondria from primary cells and tissues. The two-step procedure comprises (1) mechanical homogenization and differential centrifugation to isolate crude mitochondria, and (2) tag-free immune capture of mitochondria to isolate pure organelles and eliminate contaminants. Mitochondrial proteins from each purification stage are analyzed by quantitative mass spectrometry, and enrichment yields are calculated, allowing the discovery of novel mitochondrial proteins by subtractive proteomics. Our protocol provides a sensitive and comprehensive approach to studying mitochondrial content in cell lines, primary cells, and tissues.
    DOI:  https://doi.org/10.3791/65252
  6. Front Physiol. 2023 ;14 1228926
    Editorial: Mitochondrial bioenergetics impairments in genetic and metabolic diseases.
    Christian Bergamini, Elena Bonora, Noah Moruzzi.
      
    Keywords:  bioenergetics; inherited human disorders; metabolic impairment; mitochondria; mitochondrial dysfunction
    DOI:  https://doi.org/10.3389/fphys.2023.1228926
  7. EMBO Rep. 2023 Jun 19. e56399
    PARK15/FBXO7 is dispensable for PINK1/Parkin mitophagy in iNeurons and HeLa cell systems.
    Felix Kraus, Ellen A Goodall, Ian R Smith, Yizhi Jiang, Julia C Paoli, Frank Adolf, Jiuchun Zhang, Joao A Paulo, Brenda A Schulman, J Wade Harper.
      The protein kinase PINK1 and ubiquitin ligase Parkin promote removal of damaged mitochondria via a feed-forward mechanism involving ubiquitin (Ub) phosphorylation (pUb), Parkin activation, and ubiquitylation of mitochondrial outer membrane proteins to support the recruitment of mitophagy receptors. The ubiquitin ligase substrate receptor FBXO7/PARK15 is mutated in an early-onset parkinsonian-pyramidal syndrome. Previous studies have proposed a role for FBXO7 in promoting Parkin-dependent mitophagy. Here, we systematically examine the involvement of FBXO7 in depolarization and mt UPR-dependent mitophagy in the well-established HeLa and induced-neurons cell systems. We find that FBXO7-/- cells have no demonstrable defect in: (i) kinetics of pUb accumulation, (ii) pUb puncta on mitochondria by super-resolution imaging, (iii) recruitment of Parkin and autophagy machinery to damaged mitochondria, (iv) mitophagic flux, and (v) mitochondrial clearance as quantified by global proteomics. Moreover, global proteomics of neurogenesis in the absence of FBXO7 reveals no obvious alterations in mitochondria or other organelles. These results argue against a general role for FBXO7 in Parkin-dependent mitophagy and point to the need for additional studies to define how FBXO7 mutations promote parkinsonian-pyramidal syndrome.
    Keywords:  FBXO7; iNeurons; mitophagy; proteomics; ubiquitin ligase
    DOI:  https://doi.org/10.15252/embr.202256399
  8. J Gen Physiol. 2023 Aug 07. pii: e202313347. [Epub ahead of print]155(8):
    Patch-clamp technique to study mitochondrial membrane biophysics.
    Anshu Kumari, Dung M Nguyen, Vivek Garg.
      Mitochondria are double-membrane organelles crucial for oxidative phosphorylation, enabling efficient ATP synthesis by eukaryotic cells. Both of the membranes, the highly selective inner mitochondrial membrane (IMM) and a relatively porous outer membrane (OMM), harbor a number of integral membrane proteins that help in the transport of biological molecules. These transporters are especially enriched in the IMM, where they help maintain transmembrane gradients for H+, K+, Ca2+, PO43-, and metabolites like ADP/ATP, citrate, etc. Impaired activity of these transporters can affect the efficiency of energy-transducing processes and can alter cellular redox state, leading to activation of cell-death pathways or metabolic syndromes in vivo. Although several methodologies are available to study ion flux through membrane proteins, the patch-clamp technique remains the gold standard for quantitatively analyzing electrogenic ion exchange across membranes. Direct patch-clamp recordings of mitoplasts (mitochondria devoid of outer membrane) in different modes, such as whole-mitoplast or excised-patch mode, allow researchers the opportunity to study the biophysics of mitochondrial transporters in the native membrane, in real time, in isolation from other fluxes or confounding factors due to changes in ion gradients, pH, or mitochondrial potential (ΔΨ). Here, we summarize the use of patch clamp to investigate several membrane proteins of mitochondria. We demonstrate how this technique can be reliably applied to record whole-mitoplast Ca2+ currents mediated via mitochondrial calcium uniporter or H+ currents mediated by uncoupling protein 1 and discuss critical considerations while recording currents from these small vesicles of the IMM (mitoplast diameter = 2-5 µm).
    DOI:  https://doi.org/10.1085/jgp.202313347
  9. Orphanet J Rare Dis. 2023 Jun 22. 18(1): 157
    The evolution of the mitochondrial disease diagnostic odyssey.
    John L P Thompson, Amel Karaa, Hung Pham, Philip Yeske, Jeffrey Krischer, Yi Xiao, Yuelin Long, Amanda Kramer, David Dimmock, Amy Holbert, Cliff Gorski, Kristin M Engelstad, Richard Buchsbaum, Xiomara Q Rosales, Michio Hirano.
      BACKGROUND: Mitochondrial diseases often require multiple years and clinicians to diagnose. We lack knowledge of the stages of this diagnostic odyssey, and factors that affect it. Our goals are to report the results of the 2018 Odyssey2 (OD2) survey of patients with a medical diagnosis of mitochondrial disease; and to propose steps to reduce the odyssey going forward, and procedures to evaluate them.METHODS: Data are from the NIH-funded NAMDC-RDCRN-UMDF OD2 survey (N = 215). The main outcomes are Time from symptom Onset to mitochondrial disease Diagnosis (TOD) and Number of Doctors Seen during this diagnostic process (NDOCS).
    RESULTS: Expert recoding increased analyzable responses by 34% for final mitochondrial diagnosis and 39% for prior non-mitochondrial diagnosis. Only one of 122 patients who initially saw a primary care physician (PCP) received a mitochondrial diagnosis, compared to 26 of 86 (30%) who initially saw a specialist (p < 0.001). Mean TOD overall was 9.9 ± 13.0 years, and mean NDOCS 6.7 ± 5.2. Mitochondrial diagnosis brings extensive benefits through treatment changes and increased membership in and support of advocacy groups.
    CONCLUSIONS: Because TOD is long and NDOCS high, there is great potential for shortening the mitochondrial odyssey. Although prompt patient contact with primary mitochondrial disease specialists, or early implementation of appropriate tests, may shorten the diagnostic odyssey, specific proposals for improvement require testing and confirmation with adequately complete, unbiased data across all its stages, and appropriate methods. Electronic Health Record (EHRs) may help by accessing diagnostic codes early, but their reliability and diagnostic utility have not been established for this group of diseases.
    DOI:  https://doi.org/10.1186/s13023-023-02754-x
  10. Clin Nutr ESPEN. 2023 08;pii: S2405-4577(23)00131-6. [Epub ahead of print]56 149-151
    Metabolic inflexibility and unusual catabolism in Leigh-like syndrome due to m.10191T>C.
    Shaundra M Newstead, Josef Finsterer.
      BACKGROUND AND AIMS: Hypercatabolism is a well-known feature of mitochondrial diseases but some patients may present with hypometabolism, as the following case.METHODS: Case report using standard investigation methods.
    RESULTS: The patient is a 32 years-old female with a Leigh-like syndrome due to the mtDNA variant m.10191 T > C in MT-ND3. Leigh-like syndrome is characterized by symmetric basal ganglia or brainstem lesions plus involvement of organs other than the brain. The patient presented with hypometabolism, which did not respond to ketogenic diet but responded to fasting. The patient showed a Warburg-like effect, which resulted in reliance on glucose due to the exclusion of oxidative phosphorylation with an extremely low VO2max. The patient only entered substantial ketosis when all gluconeogenic substrates were removed. Prolonged survival in the index patient may have possibly resulted from this previously unreported protective mechanism to reduce oxidative stress. The unusual Warburg-like phenomenon was interpreted as a possible mechanism of patients with a mitochondrial disease to survive into adulthood.
    CONCLUSIONS: This case shows that mitochondrial disease can manifest with hypometabolism and that an unusual Warburg-like effect may be responsible in some patients with mitochondrial disease to survive into adulthood.
    Keywords:  Ketogenic diet; Leigh-like syndrome; Mitochondrial disease; Respiratory chain; Warburg effect
    DOI:  https://doi.org/10.1016/j.clnesp.2023.05.007
  11. bioRxiv. 2023 Apr 13. pii: 2023.04.13.536717. [Epub ahead of print]
    A spatial map of hepatic mitochondria uncovers functional heterogeneity shaped by nutrient-sensing signaling.
    Sun Woo Sophie Kang, Rory P Cunningham, Colin B Miller, Constance M Cultraro, Jonathan Hernandez, Lisa M Jenkins, Alexei Lobanov, Maggie Cam, Natalie Porat-Shliom.
      In the liver, mitochondria are exposed to different concentrations of nutrients due to their spatial positioning across the periportal (PP) and pericentral (PC) axis. How these mitochondria sense and integrate these signals to respond and maintain homeostasis is not known. Here, we combined intravital microscopy, spatial proteomics, and functional assessment to investigate mitochondrial heterogeneity in the context of liver zonation. We found that PP and PC mitochondria are morphologically and functionally distinct; beta-oxidation and mitophagy were elevated in PP regions, while lipid synthesis was predominant in the PC mitochondria. In addition, comparative phosphoproteomics revealed that mitophagy and lipid synthesis are regulated by phosphorylation in a zonated manner. Furthermore, we demonstrated that acute pharmacological modulation of nutrient sensing through AMPK and mTOR shifted mitochondrial phenotypes in the PP and PC regions of the intact liver. This study highlights the role of protein phosphorylation in mitochondrial structure, function, and overall homeostasis in hepatic metabolic zonation. The findings have important implications for liver physiology and disease.
    DOI:  https://doi.org/10.1101/2023.04.13.536717
  12. Nature. 2023 Jun 19.
    Structural basis for the binding of DNP and purine nucleotides onto UCP1.
    Yunlu Kang, Lei Chen.
      Uncoupling protein 1 (UCP1) conducts protons through the inner mitochondrial membrane to uncouple mitochondrial respiration from ATP production, thereby converting the electrochemical gradient of protons into heat1,2. The activity of UCP1 is activated by endogenous fatty acids and synthetic small molecules, such as 2,4-dinitrophenol (DNP), and is inhibited by purine nucleotides, such as ATP3-5. However, the mechanism by which UCP1 binds these ligands remains elusive. Here, we present the structures of human UCP1 in the nucleotide-free state, the DNP-bound state, and the ATP-bound state. The structures show that the central cavity of UCP1 is open to the cytosolic side. DNP binds inside the cavity, making contact with TM2 and TM6. ATP also binds inside the same cavity and induces conformational changes in TM2, together with the inward bending of TM1, TM4, TM5, and TM6 of UCP1, resulting in a more compact structure of UCP1. The binding site of ATP overlaps with that of DNP, suggesting that ATP competitively blocks the functional engagement of DNP, resulting in the inhibition of the proton-conducting activity of UCP1.
    DOI:  https://doi.org/10.1038/s41586-023-06332-w
  13. Nat Commun. 2023 Jun 23. 14(1): 3746
    Mitochondrial matrix protein LETMD1 maintains thermogenic capacity of brown adipose tissue in male mice.
    Anna Park, Kwang-Eun Kim, Isaac Park, Sang Heon Lee, Kun-Young Park, Minkyo Jung, Xiaoxu Li, Maroun Bou Sleiman, Su Jeong Lee, Dae-Soo Kim, Jaehoon Kim, Dae-Sik Lim, Eui-Jeon Woo, Eun Woo Lee, Baek Soo Han, Kyoung-Jin Oh, Sang Chul Lee, Johan Auwerx, Ji Young Mun, Hyun-Woo Rhee, Won Kon Kim, Kwang-Hee Bae, Jae Myoung Suh.
      Brown adipose tissue (BAT) has abundant mitochondria with the unique capability of generating heat via uncoupled respiration. Mitochondrial uncoupling protein 1 (UCP1) is activated in BAT during cold stress and dissipates mitochondrial proton motive force generated by the electron transport chain to generate heat. However, other mitochondrial factors required for brown adipocyte respiration and thermogenesis under cold stress are largely unknown. Here, we show LETM1 domain-containing protein 1 (LETMD1) is a BAT-enriched and cold-induced protein required for cold-stimulated respiration and thermogenesis of BAT. Proximity labeling studies reveal that LETMD1 is a mitochondrial matrix protein. Letmd1 knockout male mice display aberrant BAT mitochondria and fail to carry out adaptive thermogenesis under cold stress. Letmd1 knockout BAT is deficient in oxidative phosphorylation (OXPHOS) complex proteins and has impaired mitochondrial respiration. In addition, BAT-specific Letmd1 deficient mice exhibit phenotypes identical to those observed in Letmd1 knockout mice. Collectively, we demonstrate that the BAT-enriched mitochondrial matrix protein LETMD1 plays a tissue-autonomous role that is essential for BAT mitochondrial function and thermogenesis.
    DOI:  https://doi.org/10.1038/s41467-023-39106-z
  14. Research (Wash D C). 2023 ;6 0175
    LonP1 Links Mitochondria-ER Interaction to Regulate Heart Function.
    Yujie Li, Dawei Huang, Lianqun Jia, Fugen Shangguan, Shiwei Gong, Linhua Lan, Zhiyin Song, Juan Xu, Chaojun Yan, Tongke Chen, Yin Tan, Yongzhang Liu, Xingxu Huang, Carolyn K Suzuki, Zhongzhou Yang, Guanlin Yang, Bin Lu.
      Interorganelle contacts and communications are increasingly recognized to play a vital role in cellular function and homeostasis. In particular, the mitochondria-endoplasmic reticulum (ER) membrane contact site (MAM) is known to regulate ion and lipid transfer, as well as signaling and organelle dynamics. However, the regulatory mechanisms of MAM formation and their function are still elusive. Here, we identify mitochondrial Lon protease (LonP1), a highly conserved mitochondrial matrix protease, as a new MAM tethering protein. The removal of LonP1 substantially reduces MAM formation and causes mitochondrial fragmentation. Furthermore, deletion of LonP1 in the cardiomyocytes of mouse heart impairs MAM integrity and mitochondrial fusion and activates the unfolded protein response within the ER (UPRER). Consequently, cardiac-specific LonP1 deficiency causes aberrant metabolic reprogramming and pathological heart remodeling. These findings demonstrate that LonP1 is a novel MAM-localized protein orchestrating MAM integrity, mitochondrial dynamics, and UPRER, offering exciting new insights into the potential therapeutic strategy for heart failure.
    DOI:  https://doi.org/10.34133/research.0175
  15. Mol Cell Proteomics. 2023 Jun 21. pii: S1535-9476(23)00116-0. [Epub ahead of print] 100605
    Facioscapulohumeral muscular dystrophy is associated with altered myoblast proteome dynamics.
    Yusuke Nishimura, Adam J Bittel, Connor A Stead, Yi-Wen Chen, Jatin G Burniston.
      Proteomic studies in facioscapulohumeral muscular dystrophy (FSHD) could offer new insight to disease mechanisms underpinned by post-transcriptional processes. We used stable isotope (deuterium oxide; D2O) labelling and peptide mass spectrometry to investigate the abundance and turnover rates of proteins in cultured muscle cells from 2 individuals affected by FSHD and their unaffected siblings (UASb). We measured the abundance of 4420 proteins and the turnover rate of 2324 proteins in each (n = 4) myoblast sample. FSHD myoblasts exhibited a greater abundance but slower turnover rate of subunits of mitochondrial respiratory complexes and mitochondrial ribosomal proteins, which may indicate an accumulation of 'older' less viable mitochondrial proteins in myoblasts from individuals affected by FSHD. Treatment with a 2'-O-methoxyethyl modified antisense oligonucleotide targeting exon 3 of the double homeobox 4 (DUX4) transcript tended to reverse mitochondrial protein dysregulation in FSHD myoblasts, indicating the effect on mitochondrial proteins may be a DUX4-dependent mechanism. Our results highlight the importance of post-transcriptional processes and protein turnover in FSHD pathology and provide a resource for the FSHD research community to explore this burgeoning aspect of FSHD.
    Keywords:  FSHD; biosynthetic labelling; deuterium oxide; fractional synthesis rate; heavy water; mitochondria; mitochondrial ribosome; protein turnover; proteome dynamics; skeletal muscle
    DOI:  https://doi.org/10.1016/j.mcpro.2023.100605
  16. J Vis Exp. 2023 Jun 02.
    Real-Time Measurement of the Mitochondrial Bioenergetic Profile of Neutrophils.
    Sunitha Pulikkot, Meng Zhao, Zhichao Fan.
      Neutrophils are the first line of defense and the most abundant leukocytes in humans. These effector cells perform functions such as phagocytosis and oxidative burst, and create neutrophil extracellular traps (NETs) for microbial clearance. New insights into the metabolic activities of neutrophils challenge the early concept that they primarily rely on glycolysis. Precise measurement of metabolic activities can unfold different metabolic requirements of neutrophils, including the tricarboxylic acid (TCA) cycle (also known as the Krebs cycle), oxidative phosphorylation (OXPHOS), pentose phosphate pathway (PPP), and fatty acid oxidation (FAO) under physiological conditions and in disease states. This paper describes a step-by-step protocol and prerequirements to measure oxygen consumption rate (OCR) as an indicator of mitochondrial respiration on mouse bone marrow-derived neutrophils, human blood-derived neutrophils, and the neutrophil-like HL60 cell line, using metabolic flux analysis on a metabolic extracellular flux analyzer. This method can be used for quantifying the mitochondrial functions of neutrophils under normal and disease conditions.
    DOI:  https://doi.org/10.3791/64971
  17. Mitochondrion. 2023 Jun 19. pii: S1567-7249(23)00054-5. [Epub ahead of print]
    NUDT6 and NUDT9, two mitochondrial members of the NUDIX family, have distinct hydrolysis activities.
    Louis Debar, Layal Ishak, Amandine Moretton, Saber Anoosheh, Frederic Morel, Louise Jenninger, Isabelle Balandier, Patrick Vernet, Anders Hofer, Siet van den Wildenberg, Geraldine Farge.
      The 22 members of the NUDIX (NUcleoside DIphosphate linked to another moiety, X) hydrolase superfamily can hydrolyze a variety of phosphorylated molecules including (d)NTPs and their oxidized forms, nucleotide sugars, capped mRNAs and dinucleotide coenzymes such as NADH and FADH. Beside this broad range of enzymatic substrates, the NUDIX proteins can also be found in different cellular compartments, mainly in the nucleus and in the cytosol, but also in the peroxisome and in the mitochondria. Here we studied two members of the family, NUDT6 and NUDT9. We showed that NUDT6 is expressed in human cells and localizes exclusively to mitochondria and we confirmed that NUDT9 has a mitochondrial localization. To elucidate their potential role within this organelle, we investigated the functional consequences at the mitochondrial level of NUDT6- and NUDT9-deficiency and found that the depletion of either of the two proteins results in an increased activity of the respiratory chain and an alteration of the mitochondrial respiratory chain complexes expression. We demonstrated that NUDT6 and NUDT9 have distinct substrate specificity in vitro, which is dependent on the cofactor used. They can both hydrolyze a large range of low molecular weight compounds such as NAD+(H), FAD and ADPR, but NUDT6 is mainly active towards NADH, while NUDT9 displays a higher activity towards ADPR.
    Keywords:  ADP-ribose; FAD; NADH; NUDIX; NUDT6; NUDT9; mitochondria
    DOI:  https://doi.org/10.1016/j.mito.2023.06.003
  18. Diabetes. 2023 Jun 21. pii: db220728. [Epub ahead of print]
    A DEFECT IN MITOCHONDRIAL COMPLEX III BUT NOT IN COMPLEXES I OR IV CAUSES EARLY BETA CELL DYSFUNCTION AND HYPERGLYCEMIA IN MICE.
    Anna L Lang, Nadee Nissanka, Ruy A Louzada, Alejandro Tamayo, Elizabeth Pereira, Carlos T Moraes, Alejandro Caicedo.
      Mitochondrial metabolism and oxidative respiration are crucial for pancreatic beta cell function and stimulus secretion coupling. Oxidative phosphorylation (OxPhos) produces ATP and other metabolites that potentiate insulin secretion. However, the contribution of individual OxPhos complexes to beta cell function is unknown. We generated beta cell specific, inducible OxPhos complex KO mouse models to investigate the effects of disrupting Complex I, Complex III, or Complex IV on beta cell function. Although all KO models had similar mitochondrial respiratory defects, Complex III caused early hyperglycemia, glucose intolerance, and loss of glucose-stimulated insulin secretion in vivo. However, ex vivo insulin secretion did not change. Complex I and IV KO models showed diabetic phenotypes much later. Mitochondrial Ca2+ responses to glucose stimulation 3 weeks after gene deletion ranged from not affected to severely disrupted depending on the complex targeted, supporting the unique roles of each complex in beta cell signaling. Mitochondrial antioxidant enzyme immunostaining increased in islets from Complex III KO, but not from Complex I or IV KO mice, indicating that severe diabetic phenotype in the Complex III deficient mice is causing alterations in cellular redox status. The current study highlights that defects in individual OxPhos complexes lead to different pathogenic outcomes.
    DOI:  https://doi.org/10.2337/db22-0728
  19. bioRxiv. 2023 Jun 11. pii: 2023.06.11.544500. [Epub ahead of print]
    Developmental transcriptional control of mitochondrial homeostasis is required for activity-dependent synaptic connectivity.
    Iryna Mohylyak, Mercedes Bengochea, Carlos Pascual-Caro, Noemi Asfogo, Sara Fonseca-Topp, Natasha Danda, Zeynep Kalender Atak, Maxime De Waegeneer, Pierre-Yves Plaçais, Thomas Preat, Stein Aerts, Olga Corti, Jaime de Juan-Sanz, Bassem A Hassan.
      During neuronal circuit formation, local control of axonal organelles ensures proper synaptic connectivity. Whether this process is genetically encoded is unclear and if so, its developmental regulatory mechanisms remain to be identified. We hypothesized that developmental transcription factors regulate critical parameters of organelle homeostasis that contribute to circuit wiring. We combined cell type-specific transcriptomics with a genetic screen to discover such factors. We identified Telomeric Zinc finger-Associated Protein (TZAP) as a temporal developmental regulator of neuronal mitochondrial homeostasis genes, including Pink1 . In Drosophila , loss of dTzap function during visual circuit development leads to loss of activity-dependent synaptic connectivity, that can be rescued by Pink1 expression. At the cellular level, loss of dTzap/TZAP leads to defects in mitochondrial morphology, attenuated calcium uptake and reduced synaptic vesicle release in fly and mammalian neurons. Our findings highlight developmental transcriptional regulation of mitochondrial homeostasis as a key factor in activity-dependent synaptic connectivity.
    DOI:  https://doi.org/10.1101/2023.06.11.544500
  20. Biochimie. 2023 Jun 17. pii: S0300-9084(23)00146-3. [Epub ahead of print]214(Pt B): 77-85
    Proton leak through the UCPs and ANT carriers and beyond: A breath for the electron transport chain.
    Salvatore Nesci.
      Mitochondria produce heat as a result of an ineffective H+ cycling of mitochondria respiration across the inner mitochondrial membrane (IMM). This event present in all mitochondria, known as proton leak, can decrease protonmotive force (Δp) and restore mitochondrial respiration by partially uncoupling the substrate oxidation from the ADP phosphorylation. During impaired conditions of ATP generation with F1FO-ATPase, the Δp increases and IMM is hyperpolarized. In this bioenergetic state, the respiratory complexes support H+ transport until the membrane potential stops the H+ pump activity. Consequently, the electron transfer is stalled and the reduced form of electron carriers of the respiratory chain can generate O2∙¯ triggering the cascade of ROS formation and oxidative stress. The physiological function to attenuate the production of O2∙¯ by Δp dissipation can be attributed to the proton leak supported by the translocases of IMM.
    Keywords:  Electron transport chain; Mitochondria; Proton conductance; Proton leak; Proton-motive force; Reactive oxygen species
    DOI:  https://doi.org/10.1016/j.biochi.2023.06.008
  21. Theranostics. 2023 ;13(10): 3330-3345
    Intranasal delivery of mitochondrial protein humanin rescues cell death and promotes mitochondrial function in Parkinson's disease.
    Kyung Hwa Kim.
      Rationale: Mitochondrial dysfunction is a key factor in the pathogenesis of Parkinson's disease (PD). Accordingly, many aspects of mitochondrial function have been studied as a putative therapeutic target. Here we present a novel strategy to promote mitochondrial function and protect against Parkinson's disease by the peptide encoded within mitochondrial genome, mitochondria-derived peptide (MDP) humanin (HN). Methods: To test humanin as a potential biomarker in PD, we measured protein levels of circulating humanin from the plasma of PD patients and transgenic or neurotoxic mouse models of PD. Next, we aimed to identify whether HN peptide treatment can regulate its activity or expression. Using mouse models of PD, we assessed HN delivery to the brain via the nasal route of administration. We further revealed a possible mechanism underlying the therapeutic effectiveness of HN peptide for PD using in vitro and ex vivo model of PD. Results: Although the expression of intracellular HN was not correlated with PD, HN treatment itself could induce intracellular HN expression and enhance mitochondrial biogenesis inducing mitochondrial gene expression. After intranasal administration, HN peptide resulted in neuroprotection and behavioral recovery in an animal model of PD. Interestingly, HN peptide following intranasal delivery was found within the brain, mainly via the trigeminal pathways. Mechanistically, HN treatment induced activation of phosphatidylinositol-3-kinase/protein kinase B (PI3K/AKT) signaling pathway which led to enhanced mitochondrial biogenesis resulting in upregulation of mitochondrial gene including humanin. Conclusion: These data support a novel role of mitochondrial protein humanin in mitochondrial function and neuronal survival against Parkinson's disease, in which humanin treatment is sufficient for stimulating mitochondrial gene expression.
    Keywords:  Parkinson's disease; autoinduction; humanin; mitochondria-derived peptide; mitochondrial biogenesis
    DOI:  https://doi.org/10.7150/thno.84165
  22. Sci Rep. 2023 Jun 20. 13(1): 9972
    Analysis of MT-ATP8 gene variants reported in patients by modeling in silico and in yeast model organism.
    Chiranjit Panja, Katarzyna Niedzwiecka, Emilia Baranowska, Jaroslaw Poznanski, Roza Kucharczyk.
      Defects in ATP synthase functioning due to the substitutions in its two mitochondrially encoded subunits a and 8 lead to untreatable mitochondrial diseases. Defining the character of variants in genes encoding these subunits is challenging due to their low frequency, heteroplasmy of mitochondrial DNA in patients' cells and polymorphisms of mitochondrial genome. We successfully used yeast S. cerevisiae as a model to study the effects of variants in MT-ATP6 gene and our research led to understand how eight amino acid residues substitutions impact the proton translocation through the channel formed by subunit a and c-ring of ATP synthase at the molecular level. Here we applied this approach to study the effects of the m.8403T>C variant in MT-ATP8 gene. The biochemical data from yeast mitochondria indicate that equivalent mutation is not detrimental for the yeast enzyme functioning. The structural analysis of substitutions in subunit 8 introduced by m.8403T>C and five other variants in MT-ATP8 provides indications about the role of subunit 8 in the membrane domain of ATP synthase and potential structural consequences of substitutions in this subunit.
    DOI:  https://doi.org/10.1038/s41598-023-36637-9
  23. Cell. 2023 Jun 19. pii: S0092-8674(23)00591-3. [Epub ahead of print]
    Cooperative sensing of mitochondrial DNA by ZBP1 and cGAS promotes cardiotoxicity.
    Yuanjiu Lei, Jordyn J VanPortfliet, Yi-Fan Chen, Joshua D Bryant, Ying Li, Danielle Fails, Sylvia Torres-Odio, Katherine B Ragan, Jingti Deng, Armaan Mohan, Bing Wang, Olivia N Brahms, Shawn D Yates, Michael Spencer, Carl W Tong, Marcus W Bosenberg, Laura Ciaccia West, Gerald S Shadel, Timothy E Shutt, Jason W Upton, Pingwei Li, A Phillip West.
      Mitochondrial DNA (mtDNA) is a potent agonist of the innate immune system; however, the exact immunostimulatory features of mtDNA and the kinetics of detection by cytosolic nucleic acid sensors remain poorly defined. Here, we show that mitochondrial genome instability promotes Z-form DNA accumulation. Z-DNA binding protein 1 (ZBP1) stabilizes Z-form mtDNA and nucleates a cytosolic complex containing cGAS, RIPK1, and RIPK3 to sustain STAT1 phosphorylation and type I interferon (IFN-I) signaling. Elevated Z-form mtDNA, ZBP1 expression, and IFN-I signaling are observed in cardiomyocytes after exposure to Doxorubicin, a first-line chemotherapeutic agent that induces frequent cardiotoxicity in cancer patients. Strikingly, mice lacking ZBP1 or IFN-I signaling are protected from Doxorubicin-induced cardiotoxicity. Our findings reveal ZBP1 as a cooperative partner for cGAS that sustains IFN-I responses to mitochondrial genome instability and highlight ZBP1 as a potential target in heart failure and other disorders where mtDNA stress contributes to interferon-related pathology.
    Keywords:  STING; Z-DNA; ZBP1; cGAS; cardiotoxicity; heart failure; mitochondrial DNA; type I interferon
    DOI:  https://doi.org/10.1016/j.cell.2023.05.039
  24. bioRxiv. 2023 Jun 06. pii: 2023.06.06.543936. [Epub ahead of print]
    Mechanisms of dual modulatory effects of spermine on the mitochondrial calcium uniporter complex.
    Yung-Chi Tu, Fan-Yi Chao, Ming-Feng Tsai.
      The mitochondrial Ca 2+ uniporter mediates the crucial cellular process of mitochondrial Ca 2+ uptake, which regulates cell bioenergetics, intracellular Ca 2+ signaling, and cell death initiation. The uniporter contains the pore-forming MCU subunit, an EMRE protein that binds to MCU, and the regulatory MICU1 subunit, which can dimerize with MICU1 or MICU2 and under resting cellular [Ca 2+ ] occludes the MCU pore. It has been known for decades that spermine, which is ubiquitously present in animal cells, can enhance mitochondrial Ca 2+ uptake, but the underlying mechanisms remain unclear. Here, we show that spermine exerts dual modulatory effects on the uniporter. In physiological concentrations of spermine, it enhances uniporter activity by breaking the physical interactions between MCU and the MICU1-containing dimers to allow the uniporter to constitutively take up Ca 2+ even in low [Ca 2+ ] conditions. This potentiation effect does not require MICU2 or the EF-hand motifs in MICU1. When [spermine] rises to millimolar levels, it inhibits the uniporter by targeting the pore region in a MICU-independent manner. The MICU1-dependent spermine potentiation mechanism proposed here, along with our previous finding that cardiac mitochondria have very low MICU1, can explain the puzzling observation in the literature that mitochondria in the heart show no response to spermine.
    DOI:  https://doi.org/10.1101/2023.06.06.543936
  25. J Biomol Struct Dyn. 2023 Jun 22. 1-10
    The impacts of the mitochondrial myopathy-associated G58R mutation on the dynamic structural properties of CHCHD10.
    Hakan Alici, Vladimir N Uversky, David E Kang, Junga Alexa Woo, Orkid Coskuner-Weber.
      The mitochondria are responsible for producing energy within the cell, and in mitochondrial myopathy, there is a defect in the energy production process. The CHCHD10 gene codes for a protein called coiled-coil-helix-coiled-coil-helix domain-containing protein 10 (CHCHD10), which is found in the mitochondria and is involved in the regulation of mitochondrial function. G58R mutation has been shown to disrupt the normal function of CHCHD10, leading to mitochondrial dysfunction and ultimately to the development of mitochondrial myopathy. The structures of G58R mutant CHCHD10 and how G58R mutation impacts the wild-type CHCHD10 protein at the monomeric level are unknown. To address this problem, we conducted homology modeling, multiple run molecular dynamics simulations and bioinformatics calculations. We represent herein the structural ensemble properties of the G58R mutant CHCHD10 (CHCHD10G58R) in aqueous solution. Moreover, we describe the impacts of G58R mutation on the structural ensembles of wild-type CHCHD10 (CHCHD10WT) in aqueous solution. The dynamics properties as well as structural properties of CHCHD10WT are impacted by the mitochondrial myopathy-related G58R mutation. Specifically, the secondary and tertiary structure properties, root mean square fluctuations, Ramachandran diagrams and results from principal component analysis demonstrate that the CHCHD10WT and CHCHD10G58R proteins possess different structural ensemble characteristics and describe the impacts of G58R mutation on CHCHD10WT. These findings may be helpful for designing new treatments for mitochondrial myopathy.Communicated by Ramaswamy H. Sarma.
    Keywords:  CHCHD10; G58R mutation; genetics; mitochondrial myopathy
    DOI:  https://doi.org/10.1080/07391102.2023.2227713
  26. Cell Rep. 2023 Jun 22. pii: S2211-1247(23)00714-3. [Epub ahead of print]42(7): 112703
    Pancreatic islet protection at the expense of secretory function involves serine-linked mitochondrial one-carbon metabolism.
    Angela Pelligra, Jessica Mrugala, Kerstin Griess, Philip Kirschner, Oliver Nortmann, Barbara Bartosinska, Andrea Köster, Natalia I Krupenko, Dominik Gebel, Philipp Westhoff, Bodo Steckel, Daniel Eberhard, Diran Herebian, Bengt-Frederik Belgardt, Jürgen Schrader, Andreas P M Weber, Sergey A Krupenko, Eckhard Lammert.
      
    DOI:  https://doi.org/10.1016/j.celrep.2023.112703
  27. Nat Commun. 2023 Jun 22. 14(1): 3716
    Mitochondrial aconitase suppresses immunity by modulating oxaloacetate and the mitochondrial unfolded protein response.
    Eunah Kim, Andrea Annibal, Yujin Lee, Hae-Eun H Park, Seokjin Ham, Dae-Eun Jeong, Younghun Kim, Sangsoon Park, Sujeong Kwon, Yoonji Jung, JiSoo Park, Sieun S Kim, Adam Antebi, Seung-Jae V Lee.
      Accumulating evidence indicates that mitochondria play crucial roles in immunity. However, the role of the mitochondrial Krebs cycle in immunity remains largely unknown, in particular at the organism level. Here we show that mitochondrial aconitase, ACO-2, a Krebs cycle enzyme that catalyzes the conversion of citrate to isocitrate, inhibits immunity against pathogenic bacteria in C. elegans. We find that the genetic inhibition of aco-2 decreases the level of oxaloacetate. This increases the mitochondrial unfolded protein response, subsequently upregulating the transcription factor ATFS-1, which contributes to enhanced immunity against pathogenic bacteria. We show that the genetic inhibition of mammalian ACO2 increases immunity against pathogenic bacteria by modulating the mitochondrial unfolded protein response and oxaloacetate levels in cultured cells. Because mitochondrial aconitase is highly conserved across phyla, a therapeutic strategy targeting ACO2 may eventually help properly control immunity in humans.
    DOI:  https://doi.org/10.1038/s41467-023-39393-6
  28. Mol Aspects Med. 2023 Jun 16. pii: S0098-2997(23)00033-X. [Epub ahead of print]92 101193
    Neuroprotection in glaucoma: Mechanisms beyond intraocular pressure lowering.
    James R Tribble, Flora Hui, Heberto Quintero, Sana El Hajji, Katharina Bell, Adriana Di Polo, Pete A Williams.
      Glaucoma is a common, complex, multifactorial neurodegenerative disease characterized by progressive dysfunction and then loss of retinal ganglion cells, the output neurons of the retina. Glaucoma is the most common cause of irreversible blindness and affects ∼80 million people worldwide with many more undiagnosed. The major risk factors for glaucoma are genetics, age, and elevated intraocular pressure. Current strategies only target intraocular pressure management and do not directly target the neurodegenerative processes occurring at the level of the retinal ganglion cell. Despite strategies to manage intraocular pressure, as many as 40% of glaucoma patients progress to blindness in at least one eye during their lifetime. As such, neuroprotective strategies that target the retinal ganglion cell and these neurodegenerative processes directly are of great therapeutic need. This review will cover the recent advances from basic biology to on-going clinical trials for neuroprotection in glaucoma covering degenerative mechanisms, metabolism, insulin signaling, mTOR, axon transport, apoptosis, autophagy, and neuroinflammation. With an increased understanding of both the basic and clinical mechanisms of the disease, we are closer than ever to a neuroprotective strategy for glaucoma.
    Keywords:  Apoptosis; Autophagy; Axon degeneration; Axon transport; Calcium signaling; Glaucoma; Insulin; Metabolism; Mitochondria; Neurodegeneration; Neuroinflammation; Neuroprotection; Optic nerve; Retinal ganglion cell; mTOR
    DOI:  https://doi.org/10.1016/j.mam.2023.101193
  29. Science. 2023 Jun 23. 380(6651): eadh9351
    Splice variants of mitofusin 2 shape the endoplasmic reticulum and tether it to mitochondria.
    Déborah Naón, María Isabel Hernández-Alvarez, Satoko Shinjo, Milosz Wieczor, Saska Ivanova, Olga Martins de Brito, Albert Quintana, Juan Hidalgo, Manuel Palacín, Pilar Aparicio, Juan Castellanos, Luis Lores, David Sebastián, Sonia Fernández-Veledo, Joan Vendrell, Jorge Joven, Modesto Orozco, Antonio Zorzano, Luca Scorrano.
      In eukaryotic cells, different organelles interact at membrane contact sites stabilized by tethers. Mitochondrial mitofusin 2 (MFN2) acts as a membrane tether that interacts with an unknown partner on the endoplasmic reticulum (ER). In this work, we identified the MFN2 splice variant ERMIT2 as the ER tethering partner of MFN2. Splicing of MFN2 produced ERMIT2 and ERMIN2, two ER-specific variants. ERMIN2 regulated ER morphology, whereas ERMIT2 localized at the ER-mitochondria interface and interacted with mitochondrial mitofusins to tether ER and mitochondria. This tethering allowed efficient mitochondrial calcium ion uptake and phospholipid transfer. Expression of ERMIT2 ameliorated the ER stress, inflammation, and fibrosis typical of liver-specific Mfn2 knockout mice. Thus, ER-specific MFN2 variants display entirely extramitochondrial MFN2 functions involved in interorganellar tethering and liver metabolic activities.
    DOI:  https://doi.org/10.1126/science.adh9351
  30. Antioxid Redox Signal. 2023 Jun 19.
    NAD+ Precursors in Human Health and Disease: Current Status and Future Prospects.
    Keisuke Yaku, Takashi Nakagawa.
      SIGNIFICANCE: Nicotinamide adenine dinucleotide (NAD+) acts as a cofactor in many important biological processes. The administration of NAD+ precursors increases the intracellular NAD+ pool and has beneficial effects on physiological changes and diseases associated with aging in various organisms, including rodents and humans.RECENT ADVANCES: Evidence from pre-clinical studies demonstrating the beneficial effects of NAD+ precursors has rapidly increased in the last decade. The results of these studies have prompted the development of clinical trials using NAD+ precursors, particularly nicotinamide riboside (NR) and nicotinamide mononucleotide (NMN). Additionally, in vivo studies of NAD+ metabolism have rapidly progressed. Critical issue: Several studies have demonstrated that the oral administration of NAD+ precursors, such as NR and NMN, is safe and significantly increases NAD+ levels in humans. However, the efficacy of these NAD+ precursors is lower than expected from the results of pre-clinical studies. In addition, the identification of the contribution of the host-gut microbiota interactions to NR and NMN metabolism has added to the complexity of NAD+ metabolism.
    FUTURE DIRECTIONS: Further studies are required to determine the efficacy of NAD+ precursors in humans. Further in vivo studies of NAD+ metabolism are required to optimize the effects of NAD+ supplementation. There is also a need for methods of delivering NAD+ precursors to target organs or tissues to increase the outcomes of clinical trials.
    DOI:  https://doi.org/10.1089/ars.2023.0354
  31. Cell Mol Life Sci. 2023 Jun 20. 80(7): 183
    Loss of functional peroxisomes leads to increased mitochondrial biogenesis and reduced autophagy that preserve mitochondrial function.
    Lijun Chi, Dorothy Lee, Sharon Leung, Guanlan Hu, Bijun Wen, Paul Delgado-Olguin, Miluska Vissa, Ren Li, John H Brumell, Peter K Kim, Robert H J Bandsma.
      Peroxisomes are essential for mitochondrial health, as the absence of peroxisomes leads to altered mitochondria. However, it is unclear whether the changes in mitochondria are a function of preserving cellular function or a response to cellular damage caused by the absence of peroxisomes. To address this, we developed conditional hepatocyte-specific Pex16 deficient (Pex16 KO) mice that develop peroxisome loss and subjected them to a low-protein diet to induce metabolic stress. Loss of PEX16 in hepatocytes led to increased biogenesis of small mitochondria and reduced autophagy flux but with preserved capacity for respiration and ATP capacity. Metabolic stress induced by low protein feeding led to mitochondrial dysfunction in Pex16 KO mice and impaired biogenesis. Activation of PPARα partially corrected these mitochondrial disturbances, despite the absence of peroxisomes. The findings of this study demonstrate that the absence of peroxisomes in hepatocytes results in a concerted effort to preserve mitochondrial function, including increased mitochondrial biogenesis, altered morphology, and modified autophagy activity. Our study underscores the relationship between peroxisomes and mitochondria in regulating the hepatic metabolic responses to nutritional stressors.
    Keywords:  Fenofibrate; Malnutrition; Metabolism; Mitophagy; Nuclear hormone receptor; mTOR
    DOI:  https://doi.org/10.1007/s00018-023-04827-3
  32. Nat Methods. 2023 Jun 22.
    Expansion spatial transcriptomics.
    Yuhang Fan, Žaneta Andrusivová, Yunming Wu, Chew Chai, Ludvig Larsson, Mengxiao He, Liqun Luo, Joakim Lundeberg, Bo Wang.
      Capture array-based spatial transcriptomics methods have been widely used to resolve gene expression in tissues; however, their spatial resolution is limited by the density of the array. Here we present expansion spatial transcriptomics to overcome this limitation by clearing and expanding tissue prior to capturing the entire polyadenylated transcriptome with an enhanced protocol. This approach enables us to achieve higher spatial resolution while retaining high library quality, which we demonstrate using mouse brain samples.
    DOI:  https://doi.org/10.1038/s41592-023-01911-1
  33. Brain. 2023 Jun 22. pii: awad214. [Epub ahead of print]
    Large-scale rare variant burden testing in Parkinson's disease.
    UK Brain Expression Consortium (UKBEC)
      Parkinson's disease (PD) has a large heritable component and genome-wide association studies to date have identified over 90 loci with disease-associated common variants, providing deeper insights into the disease biology. However, there have not been large-scale rare variant analyses for PD. To address this gap, we investigated the rare genetic component of PD at minor allele frequencies <1%, using whole genome and whole exome sequencing data from 7,184 PD cases, 6,701 proxy-cases, and 51,650 healthy controls from the Accelerating Medicines Partnership Parkinson's disease (AMP-PD) initiative, the National Institutes of Health, the UK Biobank, and Genentech. We performed burden tests meta-analyses on small indels and single nucleotide protein-altering variants, prioritized based on their predicted functional impact. Our work identified several genes reaching exome-wide significance. Two of these genes, GBA1 and LRRK2, have variants that have been previously implicated as risk factors for PD, with some variants in LRRK2 resulting in monogenic forms of the disease. We identify potential novel risk associations for variants in B3GNT3, AUNIP, ADH5, TUBA1B, OR1G1, CAPN10, and TREML1, but were unable to replicate the observed associations in independent datasets. Of these, B3GNT3 and TREML1 could provide new evidence for the role of neuroinflammation in PD. To date, this is the largest analysis of rare genetic variants in PD.
    Keywords:   GBA1 ; LRRK2 ; Parkinson’s disease; burden; genetics; rare variant
    DOI:  https://doi.org/10.1093/brain/awad214
  34. Am J Bioeth. 2023 07;23(7): 83-85
    Who Is Responsible for Promoting Equity in Rare Disease Research?
    Matthew S McCoy.
      
    DOI:  https://doi.org/10.1080/15265161.2023.2207512
  35. Nat Commun. 2023 Jun 17. 14(1): 3616
    The NAD salvage pathway in mesenchymal cells is indispensable for skeletal development in mice.
    Aaron Warren, Ryan M Porter, Olivia Reyes-Castro, Md Mohsin Ali, Adriana Marques-Carvalho, Ha-Neui Kim, Landon B Gatrell, Ernestina Schipani, Intawat Nookaew, Charles A O'Brien, Roy Morello, Maria Almeida.
      NAD is an essential co-factor for cellular energy metabolism and multiple other processes. Systemic NAD+ deficiency has been implicated in skeletal deformities during development in both humans and mice. NAD levels are maintained by multiple synthetic pathways but which ones are important in bone forming cells is unknown. Here, we generate mice with deletion of Nicotinamide Phosphoribosyltransferase (Nampt), a critical enzyme in the NAD salvage pathway, in all mesenchymal lineage cells of the limbs. At birth, NamptΔPrx1 exhibit dramatic limb shortening due to death of growth plate chondrocytes. Administration of the NAD precursor nicotinamide riboside during pregnancy prevents the majority of in utero defects. Depletion of NAD post-birth also promotes chondrocyte death, preventing further endochondral ossification and joint development. In contrast, osteoblast formation still occurs in knockout mice, in line with distinctly different microenvironments and reliance on redox reactions between chondrocytes and osteoblasts. These findings define a critical role for cell-autonomous NAD homeostasis during endochondral bone formation.
    DOI:  https://doi.org/10.1038/s41467-023-39392-7
  36. Biochem Biophys Res Commun. 2023 Jun 14. pii: S0006-291X(23)00797-0. [Epub ahead of print]672 54-64
    FUNDC1 modulates mitochondrial defects and pancreatic β-cell dysfunction under lipotoxicity.
    Beier Tong, Zhengwei Zhang, Xuefeng Li, Jie Liu, Huawei Wang, Linyang Song, Jieyuan Feng, Zhe Dai, Yancheng Xu.
      Insulin resistance and many metabolic disorders are causally linked to mitochondrial dysfunction or defective mitochondrial quality control. Mitophagy is a highly selective mechanism that recognizes and removes damaged mitochondria to maintain mitochondrial homeostasis. Here, we addressed the potential role of FUNDC1, a mediator of mitophagy, in pancreatic β-cell dysfunction under lipotoxicity. In pancreatic MIN6 cells, FUNDC1 deficiency aggravated palmitate-induced mitochondrial dysfunction, which led to cell death and insulin insensitivity. Interestingly, FUNDC1 overexpression prevented these cellular harms brought on by palmitate. In mice models, pancreatic-specific FUNDC1 overexpression alleviated high-fat diet (HFD)-induced insulin resistance and obesity. Mechanistically, pancreatic-specific overexpression of FUNDC1 ameliorated mitochondrial defects and endoplasmic reticulum (ER) stress upon HFD. Our research indicates that FUNDC1 plays an essential role in apoptosis and dysfunction of pancreatic β-cells via modulating lipotoxicity-induced mitochondrial defects.
    Keywords:  FUNDC1; Insulin resistance; Mitochondrial dysfunction; Palmitate; Pancreatic β-cell
    DOI:  https://doi.org/10.1016/j.bbrc.2023.06.042
  37. PLOS Digit Health. 2023 Jun;2(6): e0000276
    AutoPrognosis 2.0: Democratizing diagnostic and prognostic modeling in healthcare with automated machine learning.
    Fergus Imrie, Bogdan Cebere, Eoin F McKinney, Mihaela van der Schaar.
      Diagnostic and prognostic models are increasingly important in medicine and inform many clinical decisions. Recently, machine learning approaches have shown improvement over conventional modeling techniques by better capturing complex interactions between patient covariates in a data-driven manner. However, the use of machine learning introduces technical and practical challenges that have thus far restricted widespread adoption of such techniques in clinical settings. To address these challenges and empower healthcare professionals, we present an open-source machine learning framework, AutoPrognosis 2.0, to facilitate the development of diagnostic and prognostic models. AutoPrognosis leverages state-of-the-art advances in automated machine learning to develop optimized machine learning pipelines, incorporates model explainability tools, and enables deployment of clinical demonstrators, without requiring significant technical expertise. To demonstrate AutoPrognosis 2.0, we provide an illustrative application where we construct a prognostic risk score for diabetes using the UK Biobank, a prospective study of 502,467 individuals. The models produced by our automated framework achieve greater discrimination for diabetes than expert clinical risk scores. We have implemented our risk score as a web-based decision support tool, which can be publicly accessed by patients and clinicians. By open-sourcing our framework as a tool for the community, we aim to provide clinicians and other medical practitioners with an accessible resource to develop new risk scores, personalized diagnostics, and prognostics using machine learning techniques. Software: https://github.com/vanderschaarlab/AutoPrognosis.
    DOI:  https://doi.org/10.1371/journal.pdig.0000276
  38. J Biomed Inform. 2023 Jun 21. pii: S1532-0464(23)00150-8. [Epub ahead of print] 104429
    A systematic review on machine learning approaches in the diagnosis and prognosis of rare genetic diseases.
    P Roman-Naranjo, A M Parra-Perez, J A Lopez-Escamez.
      BACKGROUND: The diagnosis of rare genetic diseases is often challenging due to the complexity of the genetic underpinnings of these conditions and the limited availability of diagnostic tools. Machine learning (ML) algorithms have the potential to improve the accuracy and speed of diagnosis by analyzing large amounts of genomic data and identifying complex multiallelic patterns that may be associated with specific diseases. In this systematic review, we aimed to identify the methodological trends and the ML application areas in rare genetic diseases.METHODS: We performed a systematic review of the literature following the PRISMA guidelines to search studies that used ML approaches to enhance the diagnosis of rare genetic diseases. Studies that used DNA-based sequencing data and a variety of ML algorithms were included, summarized, and analyzed using bibliometric methods, visualization tools, and a feature co-occurrence analysis.
    FINDINGS: Our search identified 22 studies that met the inclusion criteria. We found that exome sequencing was the most frequently used sequencing technology (59%), and rare neoplastic diseases were the most prevalent disease scenario (59%). In rare neoplasms, the most frequent applications of ML models were the differential diagnosis or stratification of patients (38.5%) and the identification of somatic mutations (30.8%). In other rare diseases, the most frequent goals were the prioritization of rare variants or genes (55.5%) and the identification of biallelic or digenic inheritance (33.3%). The most employed method was the random forest algorithm (54.5%). In addition, the features of the datasets needed for training these algorithms were distinctive depending on the goal pursued, including the mutational load in each gene for the differential diagnosis of patients, or the combination of genotype features and sequence-derived features (such as GC-content) for the identification of somatic mutations.
    CONCLUSIONS: ML algorithms based on sequencing data are mainly used for the diagnosis of rare neoplastic diseases, with random forest being the most common approach. We identified key features in the datasets used for training these ML models according to the objective pursued. These features can support the development of future ML models in the diagnosis of rare genetic diseases.
    Keywords:  DNA-sequencing; artificial intelligence; genomics; precision medicine; rare diseases; rare variants
    DOI:  https://doi.org/10.1016/j.jbi.2023.104429
  39. Cell. 2023 Jun 13. pii: S0092-8674(23)00587-1. [Epub ahead of print]
    Mechanisms of readthrough mitigation reveal principles of GCN1-mediated translational quality control.
    Martin B D Müller, Prasad Kasturi, Gopal G Jayaraj, F Ulrich Hartl.
      Readthrough into the 3' untranslated region (3' UTR) of the mRNA results in the production of aberrant proteins. Metazoans efficiently clear readthrough proteins, but the underlying mechanisms remain unknown. Here, we show in Caenorhabditis elegans and mammalian cells that readthrough proteins are targeted by a coupled, two-level quality control pathway involving the BAG6 chaperone complex and the ribosome-collision-sensing protein GCN1. Readthrough proteins with hydrophobic C-terminal extensions (CTEs) are recognized by SGTA-BAG6 and ubiquitylated by RNF126 for proteasomal degradation. Additionally, cotranslational mRNA decay initiated by GCN1 and CCR4/NOT limits the accumulation of readthrough products. Unexpectedly, selective ribosome profiling uncovered a general role of GCN1 in regulating translation dynamics when ribosomes collide at nonoptimal codons, enriched in 3' UTRs, transmembrane proteins, and collagens. GCN1 dysfunction increasingly perturbs these protein classes during aging, resulting in mRNA and proteome imbalance. Our results define GCN1 as a key factor acting during translation in maintaining protein homeostasis.
    Keywords:  BAG6 complex; CCR4/NOT; GCN1; aging; codon optimality; collagens; cotranslational mRNA decay; disomes; readthrough mitigation; transmembrane proteins
    DOI:  https://doi.org/10.1016/j.cell.2023.05.035
  40. Front Mol Biosci. 2023 ;10 1203019
    Investigation of FGF21 mRNA levels and relative mitochondrial DNA copy number levels and their relation in nonalcoholic fatty liver disease: a case-control study.
    Massoud Houshmand, Vahide Zeinali, Amirhossein Hosseini, Atena Seifi, Bardia Danaei, Sharareh Kamfar.
      Background: Although the exact mechanisms of nonalcoholic fatty liver disease (NAFLD) are not fully understood, numerous pieces of evidence show that the variations in mitochondrial DNA (mtDNA) level and hepatic Fibroblast growth factor 21 (FGF21) expression may be related to NAFLD susceptibility. Objectives: The main objective of this study was to determine relative levels of mtDNA copy number and hepatic FGF21 expression in a cohort of Iranian NAFLD patients and evaluate the possible relationship. Methods: This study included 27 NAFLD patients (10 with nonalcoholic fatty liver (NAFL) and 17 with non-alcoholic steatohepatitis (NASH)) and ten healthy subjects. Total RNA and genomic DNA were extracted from liver tissue samples, and then mtDNA copy number and FGF21 expression levels were assessed by quantitative real-time PCR. Results: The relative level of hepatic mtDNA copy number was 3.9-fold higher in patients than in controls (p < 0.0001). NAFLD patients showed a 2.9-fold increase in hepatic FGF21 expression compared to controls (p < 0.013). Results showed that hepatic FGF21 expression was positively correlated with BMI, serum ALT, and AST levels (p < 0.05). The level of mitochondrial copy number and hepatic FGF21 expression was not significantly associated with stages of change in hepatic steatosis. Finally, there was a significant correlation between FGF21 expression and mitochondrial copy number in NAFLD patients (p = 0.027). Conclusion: Our findings suggest a considerable rise of hepatic FGF21 mRNA levels and mtDNA-CN and show a positive correlation between them in the liver tissue of NAFLD patients.
    Keywords:  FGF21; NAFLD; fibroblast growth factor 21; mitochondrial DNA; nonalcoholic fatty liver disease
    DOI:  https://doi.org/10.3389/fmolb.2023.1203019
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