bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2023–10–29
78 papers selected by
Catalina Vasilescu, Helmholz Munich
  1. Clinical Approaches for Mitochondrial Diseases.
  2. High-throughput single-cell analysis reveals progressive mitochondrial DNA mosaicism throughout life.
  3. A novel mouse model of mitochondrial disease exhibits juvenile-onset severe neurological impairment due to parvalbumin cell mitochondrial dysfunction.
  4. CRISPR Screening in Tandem with Targeted mtDNA Damage Reveals WRNIP1 Essentiality.
  5. The germline coordinates mitokine signaling.
  6. Defective function of α-ketoglutarate dehydrogenase exacerbates mitochondrial ATP deficits during complex I deficiency.
  7. Excessive BNIP3- and BNIP3L-dependent mitophagy underlies the pathogenesis of FBXL4-mutated mitochondrial DNA depletion syndrome.
  8. Role of Mitochondrial Dynamics in Heart Diseases.
  9. Phenotypic heterogeneity of the mitochondrial DNA A8344G variant presenting with dorsal midbrain syndrome.
  10. Mitochondrial complex I ROS production and redox signaling in hypoxia.
  11. Lipocalin 2 regulates mitochondrial phospholipidome remodeling, dynamics, and function in brown adipose tissue in male mice.
  12. The mitochondrial fusion protein OPA1 is dispensable in the liver and its absence induces mitohormesis to protect liver from drug-induced injury.
  13. Loss of UCP2 causes mitochondrial fragmentation by OMA1-dependent proteolytic processing of OPA1 in podocytes.
  14. The functional impact of rare variation across the regulatory cascade.
  15. L-Isoleucine reverses hyperammonemia-induced myotube mitochondrial dysfunction and post-mitotic senescence: L-isoleucine reverses ammonia induced perturbations.
  16. Misregulation of mitochondria-lysosome contact dynamics in Charcot-Marie-Tooth Type 2B disease Rab7 mutant sensory peripheral neurons.
  17. Mitochondrial sAC-cAMP-PKA Axis Modulates the ΔΨm-Dependent Control Coefficients of the Respiratory Chain Complexes: Evidence of Respirasome Plasticity.
  18. Mitochondrial gene expression is required for platelet function and blood clotting.
  19. Beyond gene-disease validity: capturing structured data on inheritance, allelic requirement, disease-relevant variant classes, and disease mechanism for inherited cardiac conditions.
  20. Dual roles of myocardial mitochondrial AKT on diabetic cardiomyopathy and whole body metabolism.
  21. A DRP-like pseudoenzyme coordinates with MICOS to promote cristae architecture.
  22. Mitochondrial matrix RTN4IP1/OPA10 is an oxidoreductase for coenzyme Q synthesis.
  23. Modulation of Mitochondrial Function as a Therapeutic Strategy for Neurodegenerative Diseases.
  24. Call to action to properly utilize electron microscopy to measure organelles to monitor disease.
  25. Mitochondrial DNA Release Is Induced by Apoptotic Stress and Drives the SASP.
  26. Mitochondrial Dysfunction in Dopaminergic Neurons Derived from Patients with LRRK2- and SNCA-Associated Genetic Forms of Parkinson's Disease.
  27. Disrupted brain mitochondrial morphology after in vivo hydrogen sulfide exposure.
  28. Lactate activates the mitochondrial electron transport chain independently of its metabolism.
  29. Deep Mutational Scanning in Rare Disease-related Genes with Saturation Mutagenesis-Reinforced Functional Assays (SMuRF).
  30. The biological function of cytoplasm-translocated ENDOG (endonuclease G).
  31. Blocking AMPKαS496 phosphorylation improves mitochondrial dynamics and hyperglycemia in aging and obesity.
  32. lesSDRF is more: maximizing the value of proteomics data through streamlined metadata annotation.
  33. Anti-mitochondrial antibody-positive myositis.
  34. Editorial: Mitochondrial control of cell fate.
  35. Mitochondrial heteroplasmy as a cause of cell-to-cell phenotypic heterogeneity in clonal populations.
  36. Very-Long-Chain Acyl-CoA Dehydrogenase Deficiency: Family Impact and Perspectives.
  37. Mitophagy in Astrocytes Is Required for the Health of Optic Nerve.
  38. Manganese regulation of COPII condensation controls circulating lipid homeostasis.
  39. Reducing mitochondrial mysteries.
  40. Selective Mitochondrial Respiratory Complex I Subunit Deficiency Causes Tumor Immunogenicity.
  41. Cadmium promotes nonalcoholic fatty liver disease by inhibiting intercellular mitochondrial transfer.
  42. Leber Hereditary Optic Neuropathy (LHON) in Patients with Presumed Childhood Monocular Amblyopia.
  43. The NLRX1-SLC39A7 complex orchestrates mitochondrial dynamics and mitophagy to rejuvenate intervertebral disc by modulating mitochondrial Zn2+ trafficking.
  44. AI for drug discovery is booming, but who owns the patents?
  45. Exome copy number variant detection, analysis and classification in a large cohort of families with undiagnosed rare genetic disease.
  46. Mitochondria and telomeres: hand in glove.
  47. PPA2 Deficiency in 2 Sisters: A Rare Cause of Sudden Cardiac Death.
  48. Augmenting Mitochondrial Respiration in Immature Smooth Muscle Cells with an ACTA2 Pathogenic Variant Mitigates Moyamoya-like Cerebrovascular Disease.
  49. TMEM65 regulates NCLX-dependent mitochondrial calcium efflux.
  50. How defective mitochondrial electrical activity leads to inherited blindness.
  51. A rapid whole-genome sequencing service for infants with rare diseases in the United Arab Emirates.
  52. GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction.
  53. Sexually dimorphic mechanisms of VGLUT-mediated protection from dopaminergic neurodegeneration.
  54. A molecular simulation study of the clinical G409V mutant in PINK1 associated with early-onset Parkinson's disease.
  55. A genetically encoded tool to increase cellular NADH/NAD+ ratio in living cells.
  56. Genome-wide screen reveals Rab12 GTPase as a critical activator of Parkinson's disease-linked LRRK2 kinase.
  57. Challenges facing repeat expansion identification, characterisation, and the pathway to discovery.
  58. Notch Signaling Regulates Mouse Perivascular Adipose Tissue Function via Mitochondrial Pathways.
  59. METTL14 Regulates the m6A Modification of TRAF6 to Suppress Mitochondrial Dysfunction and Ferroptosis in Dopaminergic Neurons via the cGAS-STING Pathway.
  60. Longitudinal Changes in Mitochondrial DNA Copy Number and Telomere Length in Patients with Parkinson's Disease.
  61. Advance in Genomics of Rare Genetic Diseases.
  62. Low Arginine Suggesting the Diagnosis of Mitochondrial Cardiomyopathy.
  63. Microcirculation and Mitochondria: The Critical Unit.
  64. Systematic analysis of paralogous regions in 41,755 exomes uncovers clinically relevant variation.
  65. CCDC127 regulates lipid droplet homeostasis by enhancing mitochondria-ER contacts.
  66. Identification of a robust DNA methylation signature for Fanconi anemia.
  67. Benchmark dataset for training machine learning models to predict the pathway involvement of metabolites.
  68. Divergence in aerobic capacity and energy expenditure influence metabolic tissue mitochondrial protein synthesis rates in aged rats.
  69. Metabolic regulation of proteome stability via N-terminal acetylation controls male germline stem cell differentiation and reproduction.
  70. HALL: a comprehensive database for human aging and longevity studies.
  71. Cell autonomous role of leucine-rich repeat kinase in protection of dopaminergic neuron survival.
  72. Evaluation of fisetin as a potential inducer of mitochondrial biogenesis in SH-SY5Y neuronal cells.
  73. Introducing the South African Rare Diseases Access Initiative.
  74. DNA language models are powerful predictors of genome-wide variant effects.
  75. Lactate biosensors for spectrally and spatially multiplexed fluorescence imaging.
  76. Localization of PPM1H phosphatase tunes Parkinson's disease-linked LRRK2 kinase-mediated Rab GTPase phosphorylation and ciliogenesis.
  77. Large-scale characterization of gender differences in diagnosis prevalence and time to diagnosis.
  78. Screening for new inhibitors of the human Mitochondrial Pyruvate Carrier and their effects on hepatic glucose production and diabetes.
  1. Cells. 2023 Oct 20. pii: 2494. [Epub ahead of print]12(20):
    Clinical Approaches for Mitochondrial Diseases.
    Seongho Hong, Sanghun Kim, Kyoungmi Kim, Hyunji Lee.
      Mitochondria are subcontractors dedicated to energy production within cells. In human mitochondria, almost all mitochondrial proteins originate from the nucleus, except for 13 subunit proteins that make up the crucial system required to perform 'oxidative phosphorylation (OX PHOS)', which are expressed by the mitochondria's self-contained DNA. Mitochondrial DNA (mtDNA) also encodes 2 rRNA and 22 tRNA species. Mitochondrial DNA replicates almost autonomously, independent of the nucleus, and its heredity follows a non-Mendelian pattern, exclusively passing from mother to children. Numerous studies have identified mtDNA mutation-related genetic diseases. The consequences of various types of mtDNA mutations, including insertions, deletions, and single base-pair mutations, are studied to reveal their relationship to mitochondrial diseases. Most mitochondrial diseases exhibit fatal symptoms, leading to ongoing therapeutic research with diverse approaches such as stimulating the defective OXPHOS system, mitochondrial replacement, and allotropic expression of defective enzymes. This review provides detailed information on two topics: (1) mitochondrial diseases caused by mtDNA mutations, and (2) the mechanisms of current treatments for mitochondrial diseases and clinical trials.
    Keywords:  clinical trials; mitochondrial diseases; mitochondrial therapy
    DOI:  https://doi.org/10.3390/cells12202494
  2. Sci Adv. 2023 Oct 27. 9(43): eadi4038
    High-throughput single-cell analysis reveals progressive mitochondrial DNA mosaicism throughout life.
    Angelos Glynos, Lyuba V Bozhilova, Michele Frison, Stephen Burr, James B Stewart, Patrick F Chinnery.
      Heteroplasmic mitochondrial DNA (mtDNA) mutations are a major cause of inherited disease and contribute to common late-onset human disorders. The late onset and clinical progression of mtDNA-associated disease is thought to be due to changing heteroplasmy levels, but it is not known how and when this occurs. Performing high-throughput single-cell genotyping in two mouse models of human mtDNA disease, we saw unanticipated cell-to-cell differences in mtDNA heteroplasmy levels that emerged prenatally and progressively increased throughout life. Proliferating spleen cells and nondividing brain cells had a similar single-cell heteroplasmy variance, implicating mtDNA or organelle turnover as the major force determining cell heteroplasmy levels. The two different mtDNA mutations segregated at different rates with no evidence of selection, consistent with different rates of random genetic drift in vivo, leading to the accumulation of cells with a very high mutation burden at different rates. This provides an explanation for differences in severity seen in human diseases caused by similar mtDNA mutations.
    DOI:  https://doi.org/10.1126/sciadv.adi4038
  3. Commun Biol. 2023 Oct 23. 6(1): 1078
    A novel mouse model of mitochondrial disease exhibits juvenile-onset severe neurological impairment due to parvalbumin cell mitochondrial dysfunction.
    Elizaveta A Olkhova, Carla Bradshaw, Alasdair Blain, Debora Alvim, Doug M Turnbull, Fiona E N LeBeau, Yi Shiau Ng, Gráinne S Gorman, Nichola Z Lax.
      Mitochondrial diseases comprise a common group of neurometabolic disorders resulting from OXPHOS defects, that may manifest with neurological impairments, for which there are currently no disease-modifying therapies. Previous studies suggest inhibitory interneuron susceptibility to mitochondrial impairment, especially of parvalbumin-expressing interneurons (PV+). We have developed a mouse model of mitochondrial dysfunction specifically in PV+ cells via conditional Tfam knockout, that exhibited a juvenile-onset progressive phenotype characterised by cognitive deficits, anxiety-like behaviour, head-nodding, stargazing, ataxia, and reduced lifespan. A brain region-dependent decrease of OXPHOS complexes I and IV in PV+ neurons was detected, with Purkinje neurons being most affected. We validated these findings in a neuropathological study of patients with pathogenic mtDNA and POLG variants showing PV+ interneuron loss and deficiencies in complexes I and IV. This mouse model offers a drug screening platform to propel the discovery of therapeutics to treat severe neurological impairment due to mitochondrial dysfunction.
    DOI:  https://doi.org/10.1038/s42003-023-05238-7
  4. bioRxiv. 2023 Oct 03. pii: 2023.10.03.560559. [Epub ahead of print]
    CRISPR Screening in Tandem with Targeted mtDNA Damage Reveals WRNIP1 Essentiality.
    Tanja Sack, Piriththiv Dhavarasa, Daniel Szames, Siobhan O'Brien, Stephane Angers, Shana O Kelley.
      A major impediment to the characterization of mtDNA repair mechanisms, in comparison to nuclear DNA repair mechanisms, is the difficulty of specifically addressing mitochondrial damage. Using a mitochondria-penetrating peptide, we can deliver DNA-damaging agents directly to mitochondria, bypassing the nuclear compartment. Here, we describe the use of a mtDNA-damaging agent in tandem with CRISPR/Cas9 screening for the genome-wide discovery of factors essential for mtDNA damage response. Using mitochondria-targeted doxorubicin (mtDox) we generate mtDNA double-strand breaks (mtDSBs) specifically in this organelle. Combined with an untargeted Dox screen, we identify genes with significantly greater essentiality during mitochondrial versus nuclear DNA damage. We characterize the essentially of our top hit - WRNIP1 - observed here for the first time to respond to mtDNA damage. We further investigate the mitochondrial role of WRNIP1 in innate immune signaling and nuclear genome maintenance, outlining a model that experimentally supports mitochondrial turnover in response to mtDSBs.
    DOI:  https://doi.org/10.1101/2023.10.03.560559
  5. bioRxiv. 2023 Oct 04. pii: 2023.08.21.554217. [Epub ahead of print]
    The germline coordinates mitokine signaling.
    Koning Shen, Jenni Durieux, Cesar G Mena, Brant M Webster, C Kimberly Tsui, Hanlin Zhang, Lawrence Joe, Kristen Berendzen, Andrew Dillin.
      The ability of mitochondria to coordinate stress responses across tissues is critical for health. In C. elegans , neurons experiencing mitochondrial stress elicit an inter-tissue signaling pathway through the release of mitokine signals, such as serotonin or the WNT ligand EGL-20, which activate the mitochondrial unfolded protein response (UPR MT ) in the periphery to promote organismal health and lifespan. We find that germline mitochondria play a surprising role in neuron-to-peripheral UPR MT signaling. Specifically, we find that germline mitochondria signal downstream of neuronal mitokines, like WNT and serotonin, and upstream of lipid metabolic pathways in the periphery to regulate UPR MT activation. We also find that the germline tissue itself is essential in UPR MT signaling. We propose that the germline has a central signaling role in coordinating mitochondrial stress responses across tissues, and germline mitochondria play a defining role in this coordination because of their inherent roles in germline integrity and inter-tissue signaling.
    DOI:  https://doi.org/10.1101/2023.08.21.554217
  6. Redox Biol. 2023 Oct 17. pii: S2213-2317(23)00333-6. [Epub ahead of print]67 102932
    Defective function of α-ketoglutarate dehydrogenase exacerbates mitochondrial ATP deficits during complex I deficiency.
    Gerardo G Piroli, Allison M Manuel, Richard S McCain, Holland H Smith, Oliver Ozohanics, Sara Mellid, J Hunter Cox, William E Cotham, Michael D Walla, Alberto Cascón, Attila Ambrus, Norma Frizzell.
      The NDUFS4 knockout (KO) mouse phenotype resembles the human Complex I deficiency Leigh Syndrome. The irreversible succination of protein thiols by fumarate is increased in select regions of the NDUFS4 KO brain affected by neurodegeneration. We report that dihydrolipoyllysine-residue succinyltransferase (DLST), a component of the α-ketoglutarate dehydrogenase complex (KGDHC) of the tricarboxylic acid (TCA) cycle, is succinated in the affected regions of the NDUFS4 KO brain. Succination of DLST reduced KGDHC activity in the brainstem (BS) and olfactory bulb (OB) of KO mice. The defective production of KGDHC derived succinyl-CoA resulted in decreased mitochondrial substrate level phosphorylation (SLP), further aggravating the existing oxidative phosphorylation (OXPHOS) ATP deficit. Protein succinylation, an acylation modification that requires succinyl-CoA, was reduced in the KO mice. Modeling succination of a cysteine in the spatial vicinity of the DLST active site or introduction of succinomimetic mutations recapitulates these metabolic deficits. Our data demonstrate that the biochemical deficit extends beyond impaired Complex I assembly and OXPHOS deficiency, functionally impairing select components of the TCA cycle to drive metabolic perturbations in affected neurons.
    Keywords:  Alpha-ketoglutarate dehydrogenase; Complex I; Fumarate; Leigh syndrome; Protein succination; Substrate level phosphorylation
    DOI:  https://doi.org/10.1016/j.redox.2023.102932
  7. Autophagy. 2023 Oct 24.
    Excessive BNIP3- and BNIP3L-dependent mitophagy underlies the pathogenesis of FBXL4-mutated mitochondrial DNA depletion syndrome.
    Kun Gao, Yingji Chen, Ren Mo, Chenji Wang.
      Mitophagy, the process of removing damaged mitochondria to promote cell survival, plays a crucial role in cellular functionality. However, excessive, or uncontrolled mitophagy can lead to reduced mitochondrial content that burdens the remaining organelles, triggering mitophagy-mediated cell death. FBXL4 mutations, which affect the substrate-binding adaptor of the CUL1 (cullin 1)-RING ubiquitin ligase complex (CRL1), have been linked to mitochondrial DNA depletion syndrome type 13 (MTDPS13) characterized by reduced mtDNA content and impaired energy production in affected organs. However, the mechanism behind FBXL4 mutation-driven MTDPS13 remain poorly understood. In a recent study, we demonstrate that the CRL1-FBXL4 complex promotes the degradation of BNIP3 and BNIP3L, two key mitophagy cargo receptors. Deficiency of FBXL4 results in a strong accumulation of BNIP3 and BNIP3L proteins and triggers high levels of BNIP3- and BNIP3L-dependent mitophagy. Patient-derived FBXL4 mutations do not affect its interaction with BNIP3 and BNIP3L but impair the assembly of an active CRL1-FBXL4 complex. Furthermore, excessive mitophagy is observed in knockin mice carrying a patient-derived FBXL4 mutation, and in cortical neurons generated from human patient induced pluripotent stem cells (hiPSCs). These findings support the model that the CRL1-FBXL4 complex tightly restricts basal mitophagy, and its dysregulation leads to severe symptoms of MTDPS13.
    Keywords:  Lysosome; mitochondria; mitophagy; multi-system disorder; ubiquitination
    DOI:  https://doi.org/10.1080/15548627.2023.2274260
  8. Genes (Basel). 2023 Sep 26. pii: 1876. [Epub ahead of print]14(10):
    Role of Mitochondrial Dynamics in Heart Diseases.
    Takeshi Tokuyama, Shigeru Yanagi.
      Mitochondrial dynamics, including fission and fusion processes, are essential for heart health. Mitochondria, the powerhouses of cells, maintain their integrity through continuous cycles of biogenesis, fission, fusion, and degradation. Mitochondria are relatively immobile in the adult heart, but their morphological changes due to mitochondrial morphology factors are critical for cellular functions such as energy production, organelle integrity, and stress response. Mitochondrial fusion proteins, particularly Mfn1/2 and Opa1, play multiple roles beyond their pro-fusion effects, such as endoplasmic reticulum tethering, mitophagy, cristae remodeling, and apoptosis regulation. On the other hand, the fission process, regulated by proteins such as Drp1, Fis1, Mff and MiD49/51, is essential to eliminate damaged mitochondria via mitophagy and to ensure proper cell division. In the cardiac system, dysregulation of mitochondrial dynamics has been shown to cause cardiac hypertrophy, heart failure, ischemia/reperfusion injury, and various cardiac diseases, including metabolic and inherited cardiomyopathies. In addition, mitochondrial dysfunction associated with oxidative stress has been implicated in atherosclerosis, hypertension and pulmonary hypertension. Therefore, understanding and regulating mitochondrial dynamics is a promising therapeutic tool in cardiac diseases. This review summarizes the role of mitochondrial morphology in heart diseases for each mitochondrial morphology regulatory gene, and their potential as therapeutic targets to heart diseases.
    Keywords:  Drp1; Mfn1; Mfn2; Opa1; cardiovascular diseases; fission and fusion; heart failure; mitochondrial dynamics
    DOI:  https://doi.org/10.3390/genes14101876
  9. Am J Ophthalmol Case Rep. 2023 Dec;32 101938
    Phenotypic heterogeneity of the mitochondrial DNA A8344G variant presenting with dorsal midbrain syndrome.
    Megan Kasetty, Michael Altman.
       Purpose: To describe a neuro-ophthalmic presentation of a phenotypically heterogeneous mitochondrial DNA variant.
    Observations: A 10-year-old female with gross motor developmental delay, absence seizures and ataxia subacutely developed poor near acuity and asthenopia. She was found to have accommodative insufficiency, impaired supraduction and convergence retraction nystagmus leading to a diagnosis of dorsal midbrain syndrome. Brain MRI showed highly symmetrical lesions involving the dorsal pons. Genetic testing revealed a previously undiagnosed mitochondrial DNA (mtDNA) pathogenic variant, adenine to guanine at nucleopeptide pair 8344 (A8344G).
    Conclusion and importance: The authors describe a unique, neuro-ophthalmic manifestation of mitochondrial disease in a pediatric patient. This report discusses the phenotypic heterogeneity of the mtDNA A8344G variant, which may include 'stroke-like episodes' involving the brainstem, thus presenting with ophthalmic manifestations.
    Keywords:  Dorsal midbrain syndrome; Metabolic stroke; Mitochondrial disorder; Pediatric neuro-ophthalmology; Pediatric stroke
    DOI:  https://doi.org/10.1016/j.ajoc.2023.101938
  10. Redox Biol. 2023 Oct 16. pii: S2213-2317(23)00327-0. [Epub ahead of print]67 102926
    Mitochondrial complex I ROS production and redox signaling in hypoxia.
    Chidozie N Okoye, Shon A Koren, Andrew P Wojtovich.
      Mitochondria are a main source of cellular energy. Oxidative phosphorylation (OXPHOS) is the major process of aerobic respiration. Enzyme complexes of the electron transport chain (ETC) pump protons to generate a protonmotive force (Δp) that drives OXPHOS. Complex I is an electron entry point into the ETC. Complex I oxidizes nicotinamide adenine dinucleotide (NADH) and transfers electrons to ubiquinone in a reaction coupled with proton pumping. Complex I also produces reactive oxygen species (ROS) under various conditions. The enzymatic activities of complex I can be regulated by metabolic conditions and serves as a regulatory node of the ETC. Complex I ROS plays diverse roles in cell metabolism ranging from physiologic to pathologic conditions. Progress in our understanding indicates that ROS release from complex I serves important signaling functions. Increasing evidence suggests that complex I ROS is important in signaling a mismatch in energy production and demand. In this article, we review the role of ROS from complex I in sensing acute hypoxia.
    Keywords:  Acute hypoxia; Mitochondrial complex I; Oxygen sensing; ROS signaling
    DOI:  https://doi.org/10.1016/j.redox.2023.102926
  11. Nat Commun. 2023 Oct 23. 14(1): 6729
    Lipocalin 2 regulates mitochondrial phospholipidome remodeling, dynamics, and function in brown adipose tissue in male mice.
    Hongming Su, Hong Guo, Xiaoxue Qiu, Te-Yueh Lin, Chao Qin, Gail Celio, Peter Yong, Mark Senders, Xianlin Han, David A Bernlohr, Xiaoli Chen.
      Mitochondrial function is vital for energy metabolism in thermogenic adipocytes. Impaired mitochondrial bioenergetics in brown adipocytes are linked to disrupted thermogenesis and energy balance in obesity and aging. Phospholipid cardiolipin (CL) and phosphatidic acid (PA) jointly regulate mitochondrial membrane architecture and dynamics, with mitochondria-associated endoplasmic reticulum membranes (MAMs) serving as the platform for phospholipid biosynthesis and metabolism. However, little is known about the regulators of MAM phospholipid metabolism and their connection to mitochondrial function. We discover that LCN2 is a PA binding protein recruited to the MAM during inflammation and metabolic stimulation. Lcn2 deficiency disrupts mitochondrial fusion-fission balance and alters the acyl-chain composition of mitochondrial phospholipids in brown adipose tissue (BAT) of male mice. Lcn2 KO male mice exhibit an increase in the levels of CLs containing long-chain polyunsaturated fatty acids (LC-PUFA), a decrease in CLs containing monounsaturated fatty acids, resulting in mitochondrial dysfunction. This dysfunction triggers compensatory activation of peroxisomal function and the biosynthesis of LC-PUFA-containing plasmalogens in BAT. Additionally, Lcn2 deficiency alters PA production, correlating with changes in PA-regulated phospholipid-metabolizing enzymes and the mTOR signaling pathway. In conclusion, LCN2 plays a critical role in the acyl-chain remodeling of phospholipids and mitochondrial bioenergetics by regulating PA production and its function in activating signaling pathways.
    DOI:  https://doi.org/10.1038/s41467-023-42473-2
  12. Nat Commun. 2023 Oct 23. 14(1): 6721
    The mitochondrial fusion protein OPA1 is dispensable in the liver and its absence induces mitohormesis to protect liver from drug-induced injury.
    Hakjoo Lee, Tae Jin Lee, Chad A Galloway, Wenbo Zhi, Wei Xiao, Karen L de Mesy Bentley, Ashok Sharma, Yong Teng, Hiromi Sesaki, Yisang Yoon.
      Mitochondria are critical for metabolic homeostasis of the liver, and their dysfunction is a major cause of liver diseases. Optic atrophy 1 (OPA1) is a mitochondrial fusion protein with a role in cristae shaping. Disruption of OPA1 causes mitochondrial dysfunction. However, the role of OPA1 in liver function is poorly understood. In this study, we delete OPA1 in the fully developed liver of male mice. Unexpectedly, OPA1 liver knockout (LKO) mice are healthy with unaffected mitochondrial respiration, despite disrupted cristae morphology. OPA1 LKO induces a stress response that establishes a new homeostatic state for sustained liver function. Our data show that OPA1 is required for proper complex V assembly and that OPA1 LKO protects the liver from drug toxicity. Mechanistically, OPA1 LKO decreases toxic drug metabolism and confers resistance to the mitochondrial permeability transition. This study demonstrates that OPA1 is dispensable in the liver, and that the mitohormesis induced by OPA1 LKO prevents liver injury and contributes to liver resiliency.
    DOI:  https://doi.org/10.1038/s41467-023-42564-0
  13. FASEB J. 2023 11;37(11): e23265
    Loss of UCP2 causes mitochondrial fragmentation by OMA1-dependent proteolytic processing of OPA1 in podocytes.
    Qianqian Yang, Lulu Wang, Yuehong Liang, Qingyu He, Qi Sun, Jing Luo, Hongdi Cao, Yi Fang, Yang Zhou, Junwei Yang, Ping Wen, Lei Jiang.
      Mitochondrial dysfunction plays an important role in the onset and progression of podocyte injury and proteinuria. However, the process by which the change in the podocyte mitochondria occurs is not well understood. Uncoupling protein 2 (UCP2) is a mitochondrial anion carrier protein, which is located in the mitochondrial inner membrane. Here, we reported that mice with podocyte-specific Ucp2 deficiency developed podocytopathy with proteinuria with aging. Furthermore, those mice exhibited increased proteinuria in experimental models evoked by Adriamycin. Our findings suggest that UCP2 mediates mitochondrial dysfunction by regulating mitochondrial dynamic balance. Ucp2-deleted podocytes exhibited increased mitochondrial fission and deficient in ATP production. Mechanistically, opacity protein 1 (OPA1), a key protein in fusion of mitochondrial inner membrane, was regulated by UCP2. Ucp2 deficiency promoted proteolysis of OPA1 by activation OMA1 which belongs to mitochondrial inner membrane zinc metalloprotease. Those finding demonstrate the role of UCP2 in mitochondrial dynamics in podocytes and provide new insights into pathogenesis associated with podocyte injury and proteinuria.
    Keywords:  OMA1; OPA1; UCP2; mitochondria; podocyte injury
    DOI:  https://doi.org/10.1096/fj.202301055R
  14. Cell Genom. 2023 Oct 11. 3(10): 100401
    The functional impact of rare variation across the regulatory cascade.
    Taibo Li, Nicole Ferraro, Benjamin J Strober, Francois Aguet, Silva Kasela, Marios Arvanitis, Bohan Ni, Laurens Wiel, Elliot Hershberg, Kristin Ardlie, Dan E Arking, Rebecca L Beer, Jennifer Brody, Thomas W Blackwell, Clary Clish, Stacey Gabriel, Robert Gerszten, Xiuqing Guo, Namrata Gupta, W Craig Johnson, Tuuli Lappalainen, Henry J Lin, Yongmei Liu, Deborah A Nickerson, George Papanicolaou, Jonathan K Pritchard, Pankaj Qasba, Ali Shojaie, Josh Smith, Nona Sotoodehnia, Kent D Taylor, Russell P Tracy, David Van Den Berg, Matthew T Wheeler, Stephen S Rich, Jerome I Rotter, Alexis Battle, Stephen B Montgomery.
      Each human genome has tens of thousands of rare genetic variants; however, identifying impactful rare variants remains a major challenge. We demonstrate how use of personal multi-omics can enable identification of impactful rare variants by using the Multi-Ethnic Study of Atherosclerosis, which included several hundred individuals, with whole-genome sequencing, transcriptomes, methylomes, and proteomes collected across two time points, 10 years apart. We evaluated each multi-omics phenotype's ability to separately and jointly inform functional rare variation. By combining expression and protein data, we observed rare stop variants 62 times and rare frameshift variants 216 times as frequently as controls, compared to 13-27 times as frequently for expression or protein effects alone. We extended a Bayesian hierarchical model, "Watershed," to prioritize specific rare variants underlying multi-omics signals across the regulatory cascade. With this approach, we identified rare variants that exhibited large effect sizes on multiple complex traits including height, schizophrenia, and Alzheimer's disease.
    Keywords:  functional genomics; machine learning; methylome; multi-omics; proteome; rare variants; transcriptome
    DOI:  https://doi.org/10.1016/j.xgen.2023.100401
  15. J Nutr Biochem. 2023 Oct 21. pii: S0955-2863(23)00231-0. [Epub ahead of print] 109498
    L-Isoleucine reverses hyperammonemia-induced myotube mitochondrial dysfunction and post-mitotic senescence: L-isoleucine reverses ammonia induced perturbations.
    Avinash Kumar, Annette Bellar, Saurabh Mishra, Jinendiran Sekar, Nicole Welch.
      Perturbations in the metabolism of ammonia, a cytotoxic endogenous metabolite, occur in a number of chronic diseases, with consequent hyperammonemia. Increased skeletal muscle ammonia uptake causes metabolic, molecular and phenotype alterations including cataplerosis of (loss of tricarboxylic acid cycle (TCA) cycle intermediate) α-ketoglutarate (αKG), mitochondrial oxidative dysfunction, and a senescence associated molecular phenotype (SAMP). L-Isoleucine (Ile) is an essential, branched-chain amino acid (BCAA) that simultaneously provides acetyl-CoA as an oxidative substrate and succinyl-CoA for anaplerosis (providing TCA cycle intermediates). Our multiomics analyses in myotubes and skeletal muscle from hyperammonemic mice and human patients with cirrhosis showed perturbations in BCAA transporters and catabolism. We therefore determined if Ile reverses hyperammonemia-induced impaired mitochondrial oxidative function and SAMP. Studies were performed in differentiated murine C2C12 myotubes that were early passage, late passage (senescent), or those depleted of LAT1/SLC7A5 and human induced pluripotent stem cell-derived myotubes (hiPSCM). Ile reverses hyperammonemia-induced reduction in maximum respiratory capacity, complex I,II and III function in early passage murine myotubes and hiPSCM. Consistently, low ATP content and impaired global protein synthesis (high energy requiring cellular process) during hyperammonemia are reversed by Ile in murine myotubes and hiPSCM. Lower abundance of critical regulators of protein synthesis in mTORC1 signaling, and increased phosphorylation of eukaryotic initiation factor 2α are also reversed by Ile. Genetic depletion studies showed that Ile responses are independent of the amino acid transporter LAT1/SLC7A5. Our studies show that Ile reverses the hyperammonemia-induced impaired mitochondrial oxidative function, cataplerosis and SAMP in a LAT1/SLC7A5 transporter-independent manner.
    Keywords:  L-isoleucine; anaplerosis; cataplerosis; hyperammonemia; mitochondrial oxidation; myotube
    DOI:  https://doi.org/10.1016/j.jnutbio.2023.109498
  16. Proc Natl Acad Sci U S A. 2023 Oct 31. 120(44): e2313010120
    Misregulation of mitochondria-lysosome contact dynamics in Charcot-Marie-Tooth Type 2B disease Rab7 mutant sensory peripheral neurons.
    Yvette C Wong, Nirupa D Jayaraj, Tayler B Belton, George C Shum, Hannah E Ball, Dongjun Ren, Abigail L D Tadenev, Dimitri Krainc, Robert W Burgess, Daniela M Menichella.
      Inter-organelle contact sites between mitochondria and lysosomes mediate the crosstalk and bidirectional regulation of their dynamics in health and disease. However, mitochondria-lysosome contact sites and their misregulation have not been investigated in peripheral sensory neurons. Charcot-Marie-Tooth type 2B disease is an autosomal dominant axonal neuropathy affecting peripheral sensory neurons caused by mutations in the GTPase Rab7. Using live super-resolution and confocal time-lapse microscopy, we showed that mitochondria-lysosome contact sites dynamically form in the soma and axons of peripheral sensory neurons. Interestingly, Charcot-Marie-Tooth type 2B mutant Rab7 led to prolonged mitochondria-lysosome contact site tethering preferentially in the axons of peripheral sensory neurons, due to impaired Rab7 GTP hydrolysis-mediated contact site untethering. We further generated a Charcot-Marie-Tooth type 2B mutant Rab7 knock-in mouse model which exhibited prolonged axonal mitochondria-lysosome contact site tethering and defective downstream axonal mitochondrial dynamics due to impaired Rab7 GTP hydrolysis as well as fragmented mitochondria in the axon of the sciatic nerve. Importantly, mutant Rab7 mice further demonstrated preferential sensory behavioral abnormalities and neuropathy, highlighting an important role for mutant Rab7 in driving degeneration of peripheral sensory neurons. Together, this study identifies an important role for mitochondria-lysosome contact sites in the pathogenesis of peripheral neuropathy.
    Keywords:  Charcot–Marie–Tooth disease; inter-organelle contact site; lysosome; mitochondria; peripheral neuropathy
    DOI:  https://doi.org/10.1073/pnas.2313010120
  17. Int J Mol Sci. 2023 Oct 13. pii: 15144. [Epub ahead of print]24(20):
    Mitochondrial sAC-cAMP-PKA Axis Modulates the ΔΨm-Dependent Control Coefficients of the Respiratory Chain Complexes: Evidence of Respirasome Plasticity.
    Rosella Scrima, Olga Cela, Michela Rosiello, Ari Qadir Nabi, Claudia Piccoli, Giuseppe Capitanio, Francesco Antonio Tucci, Aldo Leone, Giovanni Quarato, Nazzareno Capitanio.
      The current view of the mitochondrial respiratory chain complexes I, III and IV foresees the occurrence of their assembly in supercomplexes, providing additional functional properties when compared with randomly colliding isolated complexes. According to the plasticity model, the two structural states of the respiratory chain may interconvert, influenced by the intracellular prevailing conditions. In previous studies, we suggested the mitochondrial membrane potential as a factor for controlling their dynamic balance. Here, we investigated if and how the cAMP/PKA-mediated signalling influences the aggregation state of the respiratory complexes. An analysis of the inhibitory titration profiles of the endogenous oxygen consumption rates in intact HepG2 cells with specific inhibitors of the respiratory complexes was performed to quantify, in the framework of the metabolic flux theory, the corresponding control coefficients. The attained results, pharmacologically inhibiting either PKA or sAC, indicated that the reversible phosphorylation of the respiratory chain complexes/supercomplexes influenced their assembly state in response to the membrane potential. This conclusion was supported by the scrutiny of the available structure of the CI/CIII2/CIV respirasome, enabling us to map several PKA-targeted serine residues exposed to the matrix side of the complexes I, III and IV at the contact interfaces of the three complexes.
    Keywords:  cAMP/PKA signaling pathway; metabolic flux theory; mitochondrial membrane potential; mitochondrial respiratory chain complexes; soluble adenylate cyclase; supercomplexes
    DOI:  https://doi.org/10.3390/ijms242015144
  18. Cell Rep. 2023 Oct 25. pii: S2211-1247(23)01324-4. [Epub ahead of print]42(11): 113312
    Mitochondrial gene expression is required for platelet function and blood clotting.
    Tara R Richman, Judith A Ermer, Jessica Baker, Stefan J Siira, Benjamin T Kile, Matthew D Linden, Oliver Rackham, Aleksandra Filipovska.
      Platelets are anucleate blood cells that contain mitochondria and regulate blood clotting in response to injury. Mitochondria contain their own gene expression machinery that relies on nuclear-encoded factors for the biogenesis of the oxidative phosphorylation system to produce energy required for thrombosis. The autonomy of the mitochondrial gene expression machinery from the nucleus is unclear, and platelets provide a valuable model to understand its importance in anucleate cells. Here, we conditionally delete Elac2, Ptcd1, or Mtif3 in platelets, which are essential for mitochondrial gene expression at the level of RNA processing, stability, or translation, respectively. Loss of ELAC2, PTCD1, or MTIF3 leads to increased megakaryocyte ploidy, elevated circulating levels of reticulated platelets, thrombocytopenia, and consequent extended bleeding time. Impaired mitochondrial gene expression reduces agonist-induced platelet activation. Transcriptomic and proteomic analyses show that mitochondrial gene expression is required for fibrinolysis, hemostasis, and blood coagulation in response to injury.
    Keywords:  CP: Immunology; megakaryocytes; mitochondria; mitochondrial gene expression; platelets; translation
    DOI:  https://doi.org/10.1016/j.celrep.2023.113312
  19. Genome Med. 2023 Oct 23. 15(1): 86
    Beyond gene-disease validity: capturing structured data on inheritance, allelic requirement, disease-relevant variant classes, and disease mechanism for inherited cardiac conditions.
    Katherine S Josephs, Angharad M Roberts, Pantazis Theotokis, Roddy Walsh, Philip J Ostrowski, Matthew Edwards, Andrew Fleming, Courtney Thaxton, Jason D Roberts, Melanie Care, Wojciech Zareba, Arnon Adler, Amy C Sturm, Rafik Tadros, Valeria Novelli, Emma Owens, Lucas Bronicki, Olga Jarinova, Bert Callewaert, Stacey Peters, Tom Lumbers, Elizabeth Jordan, Babken Asatryan, Neesha Krishnan, Ray E Hershberger, C Anwar A Chahal, Andrew P Landstrom, Cynthia James, Elizabeth M McNally, Daniel P Judge, Peter van Tintelen, Arthur Wilde, Michael Gollob, Jodie Ingles, James S Ware.
       BACKGROUND: As the availability of genomic testing grows, variant interpretation will increasingly be performed by genomic generalists, rather than domain-specific experts. Demand is rising for laboratories to accurately classify variants in inherited cardiac condition (ICC) genes, including secondary findings.
    METHODS: We analyse evidence for inheritance patterns, allelic requirement, disease mechanism and disease-relevant variant classes for 65 ClinGen-curated ICC gene-disease pairs. We present this information for the first time in a structured dataset, CardiacG2P, and assess application in genomic variant filtering.
    RESULTS: For 36/65 gene-disease pairs, loss of function is not an established disease mechanism, and protein truncating variants are not known to be pathogenic. Using the CardiacG2P dataset as an initial variant filter allows for efficient variant prioritisation whilst maintaining a high sensitivity for retaining pathogenic variants compared with two other variant filtering approaches.
    CONCLUSIONS: Access to evidence-based structured data representing disease mechanism and allelic requirement aids variant filtering and analysis and is a pre-requisite for scalable genomic testing.
    Keywords:  Allelic requirement; Disease mechanism; Gene curation; Genomic variant filtering; Inheritance; Inherited cardiac conditions; Variant classification; Variant interpretation
    DOI:  https://doi.org/10.1186/s13073-023-01246-8
  20. Cardiovasc Diabetol. 2023 Oct 27. 22(1): 294
    Dual roles of myocardial mitochondrial AKT on diabetic cardiomyopathy and whole body metabolism.
    Yu-Han Chen, Albert P Ta, Yumay Chen, Hsiao-Chen Lee, Wenjun Fan, Phang-Lang Chen, Maria C Jordan, Kenneth P Roos, Grant R MacGregor, Qin Yang, Robert A Edwards, Junfeng Li, Ping H Wang.
       BACKGROUND: The PI3K/AKT pathway transduces the majority of the metabolic actions of insulin. In addition to cytosolic targets, insulin-stimulated phospho-AKT also translocates to mitochondria in the myocardium. Mouse models of diabetes exhibit impaired mitochondrial AKT signaling but the implications of this on cardiac structure and function is unknown. We hypothesized that loss of mitochondrial AKT signaling is a critical step in cardiomyopathy and reduces cardiac oxidative phosphorylation.
    METHODS: To focus our investigation on the pathophysiological consequences of this mitochondrial signaling pathway, we generated transgenic mouse models of cardiac-specific, mitochondria-targeting, dominant negative AKT1 (CAMDAKT) and constitutively active AKT1 expression (CAMCAKT). Myocardial structure and function were examined using echocardiography, histology, and biochemical assays. We further investigated the underlying effects of mitochondrial AKT1 on mitochondrial structure and function, its interaction with ATP synthase, and explored in vivo metabolism beyond the heart.
    RESULTS: Upon induction of dominant negative mitochondrial AKT1, CAMDAKT mice developed cardiac fibrosis accompanied by left ventricular hypertrophy and dysfunction. Cardiac mitochondrial oxidative phosphorylation efficiency and ATP content were reduced, mitochondrial cristae structure was lost, and ATP synthase structure was compromised. Conversely, CAMCAKT mice were protected against development of diabetic cardiomyopathy when challenged with a high calorie diet. Activation of mitochondrial AKT1 protected cardiac function and increased fatty acid uptake in myocardium. In addition, total energy expenditure was increased in CAMCAKT mice, accompanied by reduced adiposity and reduced development of fatty liver.
    CONCLUSION: CAMDAKT mice modeled the effects of impaired mitochondrial signaling which occurs in the diabetic myocardium. Disruption of this pathway is a key step in the development of cardiomyopathy. Activation of mitochondrial AKT1 in CAMCAKT had a protective role against diabetic cardiomyopathy as well as improved metabolism beyond the heart.
    Keywords:  ATP synthase; Diabetic cardiomyopathy; Fatty liver; Heart failure; Mitochondria dysfunction; Mitochondrial AKT; Obesity
    DOI:  https://doi.org/10.1186/s12933-023-02020-1
  21. bioRxiv. 2023 Oct 04. pii: 2023.10.03.560745. [Epub ahead of print]
    A DRP-like pseudoenzyme coordinates with MICOS to promote cristae architecture.
    Abhishek Kumar, Mehmet Oguz Gok, Kailey N Nguyen, Michael L Reese, Jeremy G Wideman, Sergio A Muñoz-Gómez, Jonathan R Friedman.
      Mitochondrial cristae architecture is crucial for optimal respiratory function of the organelle. Cristae shape is maintained in part by the mitochondrial inner membrane-localized MICOS complex. While MICOS is required for normal cristae morphology, the precise mechanistic role of each of the seven human MICOS subunits, and how the complex coordinates with other cristae shaping factors, has not been fully determined. Here, we examine the MICOS complex in Schizosaccharomyces pombe , a minimal model whose genome only encodes for four core subunits. Using an unbiased proteomics approach, we identify a poorly characterized inner mitochondrial membrane protein that interacts with MICOS and is required to maintain cristae morphology, which we name Mmc1. We demonstrate that Mmc1 works in concert with MICOS complexes to promote normal mitochondrial morphology and respiratory function. Bioinformatic analyses reveal that Mmc1 is a distant relative of the Dynamin-Related Protein (DRP) family of GTPases, which are well established to shape and remodel membranes. We find that, like DRPs, Mmc1 self-associates and forms high molecular weight assemblies. Interestingly, however, Mmc1 is a pseudoenzyme that lacks key residues required for GTP binding and hydrolysis, suggesting it does not dynamically remodel membranes. These data are consistent with a model in which Mmc1 stabilizes cristae architecture by acting as a scaffold to support cristae ultrastructure on the matrix side of the inner membrane. Our study reveals a new class of proteins that evolved early in fungal phylogeny and is required for the maintenance of cristae architecture. This highlights the possibility that functionally analogous proteins work with MICOS to establish cristae morphology in metazoans.
    DOI:  https://doi.org/10.1101/2023.10.03.560745
  22. Nat Chem Biol. 2023 Oct 26.
    Mitochondrial matrix RTN4IP1/OPA10 is an oxidoreductase for coenzyme Q synthesis.
    Isaac Park, Kwang-Eun Kim, Jeesoo Kim, Ae-Kyeong Kim, Subin Bae, Minkyo Jung, Jinhyuk Choi, Pratyush Kumar Mishra, Taek-Min Kim, Chulhwan Kwak, Myeong-Gyun Kang, Chang-Mo Yoo, Ji Young Mun, Kwang-Hyeon Liu, Kyu-Sun Lee, Jong-Seo Kim, Jae Myoung Suh, Hyun-Woo Rhee.
      Targeting proximity-labeling enzymes to specific cellular locations is a viable strategy for profiling subcellular proteomes. Here, we generated transgenic mice (MAX-Tg) expressing a mitochondrial matrix-targeted ascorbate peroxidase. Comparative analysis of matrix proteomes from the muscle tissues showed differential enrichment of mitochondrial proteins. We found that reticulon 4-interacting protein 1 (RTN4IP1), also known as optic atrophy-10, is enriched in the mitochondrial matrix of muscle tissues and is an NADPH oxidoreductase. Interactome analysis and in vitro enzymatic assays revealed an essential role for RTN4IP1 in coenzyme Q (CoQ) biosynthesis by regulating the O-methylation activity of COQ3. Rtn4ip1-knockout myoblasts had markedly decreased CoQ9 levels and impaired cellular respiration. Furthermore, muscle-specific knockdown of dRtn4ip1 in flies resulted in impaired muscle function, which was reversed by dietary supplementation with soluble CoQ. Collectively, these results demonstrate that RTN4IP1 is a mitochondrial NAD(P)H oxidoreductase essential for supporting mitochondrial respiration activity in the muscle tissue.
    DOI:  https://doi.org/10.1038/s41589-023-01452-w
  23. J Prev Alzheimers Dis. 2023 ;10(4): 675-685
    Modulation of Mitochondrial Function as a Therapeutic Strategy for Neurodegenerative Diseases.
    E Trushina, T K O Nguyen, S Trushin.
      Despite recent FDA approval of anti-amyloid antibodies for Alzheimer's Disease, strategies that target early molecular mechanisms and could delay or change the disease trajectory are still needed. Mitochondria emerge as a signaling organelle that could modulate multiple molecular mechanisms to enhance cellular bioenergetics and promote neuronal survival. Approaches to enhance mitochondrial function could promote healthy aging delaying the onset of age-related diseases such as Alzheimer's Disease. Some of these strategies have been recently tested in clinical trials. Emerging evidence demonstrates that in response to mild energetic stress, mitochondria could orchestrate a robust adaptive stress response activating multiple neuroprotective mechanism. The objective of this review is to highlight recent development of mitochondria-targeting therapeutics for neurodegenerative diseases, mitochondria complex I inhibitors in particular.
    Keywords:  Alzheimer’s Disease; Mitochondria; complex I inhibitors; mitochondria targeting therapeutics; mitochondrial signaling; neurodegenerative diseases of aging; neuroprotection
    DOI:  https://doi.org/10.14283/jpad.2023.108
  24. Eur J Cell Biol. 2023 Oct 16. pii: S0171-9335(23)00080-8. [Epub ahead of print]102(4): 151365
    Call to action to properly utilize electron microscopy to measure organelles to monitor disease.
    Kit Neikirk, Edgar-Garza Lopez, Andrea G Marshall, Ahmad Alghanem, Evan Krystofiak, Bartosz Kula, Nathan Smith, Jianqiang Shao, Prasanna Katti, Antentor Hinton.
      This review provides an overview of the current methods for quantifying mitochondrial ultrastructure, including cristae morphology, mitochondrial contact sites, and recycling machinery and a guide to utilizing electron microscopy to effectively measure these organelles. Quantitative analysis of mitochondrial ultrastructure is essential for understanding mitochondrial biology and developing therapeutic strategies for mitochondrial-related diseases. Techniques such as transmission electron microscopy (TEM) and serial block face-scanning electron microscopy, as well as how they can be combined with other techniques including confocal microscopy, super-resolution microscopy, and correlative light and electron microscopy are discussed. Beyond their limitations and challenges, we also offer specific magnifications that may be best suited for TEM analysis of mitochondrial, endoplasmic reticulum, and recycling machinery. Finally, perspectives on future quantification methods are offered.
    Keywords:  3D EM; MERCs; Mitochondria; Quantification; TEM
    DOI:  https://doi.org/10.1016/j.ejcb.2023.151365
  25. Cancer Discov. 2023 Oct 27. OF1
    Mitochondrial DNA Release Is Induced by Apoptotic Stress and Drives the SASP.
      Minority mitochondrial outer membrane permeabilization (miMOMP) during senescence drives the SASP.
    DOI:  https://doi.org/10.1158/2159-8290.CD-RW2023-169
  26. Curr Issues Mol Biol. 2023 Oct 17. 45(10): 8395-8411
    Mitochondrial Dysfunction in Dopaminergic Neurons Derived from Patients with LRRK2- and SNCA-Associated Genetic Forms of Parkinson's Disease.
    Anna S Vetchinova, Marina R Kapkaeva, Mikhail V Ivanov, Kristina A Kutukova, Natalia M Mudzhiri, Lydia E Frumkina, Anatoly V Brydun, Vladimir S Sukhorukov, Sergey N Illarioshkin.
      Parkinson's disease (PD) is the second most common neurodegenerative disease. Some cases of PD may be caused by genetic factors, among which mutations in the LRRK2 and SNCA genes play an important role. To develop effective neuroprotective strategies for PD, it is important to diagnose the disease at the earliest stages of the neurodegenerative process. Therefore, the detection of diagnostic and prognostic markers of Parkinson's disease (PD) is an urgent medical need. Advances in induced pluripotent stem cell (iPSC) culture technology provide new opportunities for the search for new biomarkers of PD and its modeling in vitro. In our work, we used a new technology for multiplex profiling of gene expression using barcoding on the Nanostring platform to assess the activity of mitochondrial genes on iPSC-derived cultures of dopaminergic neurons obtained from patients with LRRK2- and SNCA-associated genetic forms PD and a healthy donor. Electron microscopy revealed ultrastructural changes in mitochondria in both LRRK2 and SNCA mutant cells, whereas mitochondria in cells from a healthy donor were normal. In a culture with the SNCA gene mutation, the ratio of the area occupied by mitochondria to the total area of the cytoplasm was significantly lower than in the control and in the line with the LRRK2 gene mutation. Transcriptome analysis of 105 mitochondria proteome genes using the Nanostring platform revealed differences between the diseased and normal cells in the activity of genes involved in respiratory complex function, the tricarboxylic acid cycle, ATP production, mitochondria-endoplasmic reticulum interaction, mitophagy, regulation of calcium concentration, and mitochondrial DNA replication.
    Keywords:  LRRK2; Parkinson’s disease; SCNA; alpha-synuclein; dardarin; dopaminergic neurons; induced pluripotent stem cells; mitochondria; transcriptomics
    DOI:  https://doi.org/10.3390/cimb45100529
  27. Sci Rep. 2023 10 24. 13(1): 18129
    Disrupted brain mitochondrial morphology after in vivo hydrogen sulfide exposure.
    Wilson K Rumbeiha, Dong-Suk Kim, Angela Min, Maya Nair, Cecilia Giulivi.
      Changes in mitochondrial dynamics are often associated with dietary patterns, medical treatments, xenobiotics, and diseases. Toxic exposures to hydrogen sulfide (H2S) harm mitochondria by inhibiting Complex IV and via other mechanisms. However, changes in mitochondrial dynamics, including morphology following acute exposure to H2S, are not yet fully understood. This study followed mitochondrial morphology changes over time after a single acute LCt50 dose of H2S by examining electron microscopy thalami images of surviving mice. Our findings revealed that within the initial 48 h after H2S exposure, mitochondrial morphology was impaired by H2S, supported by the disruption and scarcity of the cristae, which are required to enhance the surface area for ATP production. At the 72-h mark point, a spectrum of morphological cellular changes was observed, and the disordered mitochondrial network, accompanied by the probable disruption of mitophagy, was tied to changes in mitochondrial shape. In summary, this study sheds light on how acute exposure to high levels of H2S triggers alterations in mitochondrial shape and structure as early as 24 h that become more evident at 72 h post-exposure. These findings underscore the impact of H2S on mitochondrial function and overall cellular health.
    DOI:  https://doi.org/10.1038/s41598-023-44807-y
  28. Mol Cell. 2023 Oct 20. pii: S1097-2765(23)00800-6. [Epub ahead of print]
    Lactate activates the mitochondrial electron transport chain independently of its metabolism.
    Xin Cai, Charles P Ng, Olivia Jones, Tak Shun Fung, Keun Woo Ryu, Dayi Li, Craig B Thompson.
      Lactate has long been considered a cellular waste product. However, we found that as extracellular lactate accumulates, it also enters the mitochondrial matrix and stimulates mitochondrial electron transport chain (ETC) activity. The resulting increase in mitochondrial ATP synthesis suppresses glycolysis and increases the utilization of pyruvate and/or alternative respiratory substrates. The ability of lactate to increase oxidative phosphorylation does not depend on its metabolism. Both L- and D-lactate are effective at enhancing ETC activity and suppressing glycolysis. Furthermore, the selective induction of mitochondrial oxidative phosphorylation by unmetabolized D-lactate reversibly suppressed aerobic glycolysis in both cancer cell lines and proliferating primary cells in an ATP-dependent manner and enabled cell growth on respiratory-dependent bioenergetic substrates. In primary T cells, D-lactate enhanced cell proliferation and effector function. Together, these findings demonstrate that lactate is a critical regulator of the ability of mitochondrial oxidative phosphorylation to suppress glucose fermentation.
    Keywords:  TCA cycle; electron transport chain; glycolysis; lactate; mitochondria; oxidative phosphorylation
    DOI:  https://doi.org/10.1016/j.molcel.2023.09.034
  29. bioRxiv. 2023 Oct 13. pii: 2023.07.12.548370. [Epub ahead of print]
    Deep Mutational Scanning in Rare Disease-related Genes with Saturation Mutagenesis-Reinforced Functional Assays (SMuRF).
    Kaiyue Ma, Kenneth K Ng, Shushu Huang, Nicole J Lake, Jenny Xu, Lin Ge, Keryn G Woodman, Katherine E Koczwara, Angela Lek, Monkol Lek.
      Interpretation of disease-causing genetic variants remains a challenge in the field of human genetics and rare disease. Current costs and complexity of performing deep mutational scanning for charting variant effects hampers crowd-sourcing approaches toward genome-wide resolution of variants in all disease-related genes. Our framework, Saturation Mutagenesis-Reinforced Functional assays (SMuRF), addresses these issues by modularizing DMS components, offering simple and cost-effective saturation mutagenesis, as well as streamlining functional assays to enhance interpretation of unresolved variants. Applying SMuRF to neuromuscular disease genes FKRP and LARGE1 , we have generated functional scores for over 99.8% of all possible coding single nucleotide variants (SNVs), providing an additional line of evidence for clinical variant interpretation in dystroglycanopathies. Data generated from SMuRF enables severity prediction, resolve critical protein structural regions susceptible to missense disruptions, and provide training datasets for development of computational predictors. In summary, our approach provides a framework for enabling variant-to-function insights for disease genes in a manner that is accessible for crowd-sourcing implementation across standard research laboratories.
    DOI:  https://doi.org/10.1101/2023.07.12.548370
  30. Autophagy. 2023 Oct 27. 1-3
    The biological function of cytoplasm-translocated ENDOG (endonuclease G).
    Wenjun Wang, Jianshuang Li, Qinghua Zhou.
      ENDOG, a mitochondrial intermembrane space located endonuclease, participates in DNA fragmentation and apoptosis by translocating to the nucleus. ENDOG can also relocate to the mitochondrial matrix, where it regulates mitochondrial genome cleavage. However, the biological function of cytoplasm-translocated ENDOG remains unclear. Our previous study reported that starvation induces the release of ENDOG from mitochondria to the cytoplasm, promoting macroautophagy/autophagy in a process conserved across species. We demonstrate that ENDOG can be phosphorylated by GSK3B, which enhances ENDOG binding to YWHAG/14-3-3γ, and leads to the release of TSC2 and PIK3C3/VPS34 from YWHAG/14-3-3γ, followed by MTORC1 pathway suppression and autophagy initiation. Additionally, we recently reported that ENDOG can also activate the MTORC2-AKT-ACLY signaling axis by promoting the release of RICTOR and TSC2 from YWHAG/14-3-3γ, resulting in acetyl-CoA production. Furthermore, cytoplasmic ENDOG can translocate to the endoplasmic reticulum, where it binds with HSPA5/BIP to release ERN1/IRE1a-EIF2AK3/PERK to activate the endoplasmic reticulum stress response, eventually promoting lipid synthesis. Collectively, ENDOG will be released from the mitochondrial intermembrane space, and translocated to the mitochondrial matrix, cytoplasm, and nucleus during different stress stimulation, where it digests DNA or interacts with crucial proteins to regulate different biological functions, including apoptosis, autophagy, mitophagy, and lipid synthesis.
    Keywords:  Autophagy; ENDOG; MTORC1; MTORC2; endoplasmic reticulum
    DOI:  https://doi.org/10.1080/15548627.2023.2271750
  31. Cell Chem Biol. 2023 Oct 26. pii: S2451-9456(23)00336-7. [Epub ahead of print]
    Blocking AMPKαS496 phosphorylation improves mitochondrial dynamics and hyperglycemia in aging and obesity.
    Alexia Pearah, Balamurugan Ramatchandirin, Ting Liu, Risa M Wolf, Arisa Ikeda, Sally Radovick, Hiromi Sesaki, Fredric E Wondisford, Brian O'Rourke, Ling He.
      Impaired mitochondrial dynamics causes aging-related or metabolic diseases. Yet, the molecular mechanism responsible for the impairment of mitochondrial dynamics is still not well understood. Here, we report that elevated blood insulin and/or glucagon levels downregulate mitochondrial fission through directly phosphorylating AMPKα at S496 by AKT or PKA, resulting in the impairment of AMPK-MFF-DRP1 signaling and mitochondrial dynamics and activity. Since there are significantly increased AMPKα1 phosphorylation at S496 in the liver of elderly mice, obese mice, and obese patients, we, therefore, designed AMPK-specific targeting peptides (Pa496m and Pa496h) to block AMPKα1S496 phosphorylation and found that these targeting peptides can increase AMPK kinase activity, augment mitochondrial fission and oxidation, and reduce ROS, leading to the rejuvenation of mitochondria. Furthermore, these AMPK targeting peptides robustly suppress liver glucose production in obese mice. Our data suggest these targeting peptides are promising therapeutic agents for improving mitochondrial dynamics and activity and alleviating hyperglycemia in elderly and obese patients.
    Keywords:  AKT; AMPK targeting peptides; AMPKαS496 phosphorylation; PKA; hyperglycemia; liver gluconeogenesis; mitochondrial fission
    DOI:  https://doi.org/10.1016/j.chembiol.2023.09.017
  32. Nat Commun. 2023 Oct 24. 14(1): 6743
    lesSDRF is more: maximizing the value of proteomics data through streamlined metadata annotation.
    Tine Claeys, Tim Van Den Bossche, Yasset Perez-Riverol, Kris Gevaert, Juan Antonio Vizcaíno, Lennart Martens.
      Public proteomics data often lack essential metadata, limiting its potential. To address this, we present lesSDRF, a tool to simplify the process of metadata annotation, thereby ensuring that data leave a lasting, impactful legacy well beyond its initial publication.
    DOI:  https://doi.org/10.1038/s41467-023-42543-5
  33. Am J Med. 2023 Oct 21. pii: S0002-9343(23)00666-6. [Epub ahead of print]
    Anti-mitochondrial antibody-positive myositis.
    Kosuke Ishizuka, Yoshiyuki Ohira.
      
    Keywords:  Anti-mitochondrial M2 antibody; Anti-mitochondrial antibody-positive myositis; Primary biliary cholangitis
    DOI:  https://doi.org/10.1016/j.amjmed.2023.10.009
  34. Front Cell Dev Biol. 2023 ;11 1302075
    Editorial: Mitochondrial control of cell fate.
    Guohua Gong, Huiliang Zhang, Stephen C Kolwicz.
      
    Keywords:  cell fate; dynamics; homeostasis; mitochondrial biogenesis; mitophagy
    DOI:  https://doi.org/10.3389/fcell.2023.1302075
  35. Front Cell Dev Biol. 2023 ;11 1276629
    Mitochondrial heteroplasmy as a cause of cell-to-cell phenotypic heterogeneity in clonal populations.
    Dmitry A Knorre.
      
    Keywords:  heterogeneity; heteroplasmy; mitochondrial dysfuncion; mtDNA; pathogenicity threshold; retrograde signaling; yeast
    DOI:  https://doi.org/10.3389/fcell.2023.1276629
  36. Int J Neonatal Screen. 2023 Oct 06. pii: 53. [Epub ahead of print]9(4):
    Very-Long-Chain Acyl-CoA Dehydrogenase Deficiency: Family Impact and Perspectives.
    Sarah Crawford, Elizabeth Sablon, Nadia Ali, Ami R Rosen, Patricia L Hall, Juanita Neira Fresneda.
      Very-Long-Chain Acyl-CoA Dehydrogenase Deficiency (VLCADD) is a fatty acid oxidation disorder characterized by the decreased ability of the enzyme very-long-chain acyl-CoA dehydrogenase to break down fatty acids with 14 to 20-long carbon chains. The resulting clinical manifestations are variable in severity and include hypoketotic hypoglycemia, rhabdomyolysis, and cardiomyopathy. Treatment can consist of limiting the dietary intake of long-chain fatty acids, the prevention of fasting, and the supplementation of medium-chain fats. This study, conducted in the context of a 5-year long-term follow-up on VLCADD, evaluates how the diagnosis of this fatty acid disorder impacts the family, specifically as it relates to the medical diet and barriers to care. Caregivers (n = 10) of individuals with VLCADD responded to a survey about how VLCADD potentially impacts their family. The review included the clinical outcomes of the patients (n = 11), covering instances of rhabdomyolysis, cardiomyopathy, and hospitalizations related to VLCADD. Families affected by VLCADD experience barriers to care, including difficulties with finances, ability to work, and access to nutrition.
    Keywords:  VLCADD; barriers; cardiomyopathy; caregiver; medical diet; metabolism; rhabdomyolysis
    DOI:  https://doi.org/10.3390/ijns9040053
  37. Cells. 2023 Oct 20. pii: 2496. [Epub ahead of print]12(20):
    Mitophagy in Astrocytes Is Required for the Health of Optic Nerve.
    Meysam Yazdankhah, Sayan Ghosh, Haitao Liu, Stacey Hose, J Samuel Zigler, Debasish Sinha.
      Mitochondrial dysfunction in astrocytes has been implicated in the development of various neurological disorders. Mitophagy, mitochondrial autophagy, is required for proper mitochondrial function by preventing the accumulation of damaged mitochondria. The importance of mitophagy, specifically in the astrocytes of the optic nerve (ON), has been little studied. We introduce an animal model in which two separate mutations act synergistically to produce severe ON degeneration. The first mutation is in Cryba1, which encodes βA3/A1-crystallin, a lens protein also expressed in astrocytes, where it regulates lysosomal pH. The second mutation is in Bckdk, which encodes branched-chain ketoacid dehydrogenase kinase, which is ubiquitously expressed in the mitochondrial matrix and involved in the catabolism of the branched-chain amino acids. BCKDK is essential for mitochondrial function and the amelioration of oxidative stress. Neither of the mutations in isolation has a significant effect on the ON, but animals homozygous for both mutations (DM) exhibit very serious ON degeneration. ON astrocytes from these double-mutant (DM) animals have lysosomal defects, including impaired mitophagy, and dysfunctional mitochondria. Urolithin A can rescue the mitophagy impairment in DM astrocytes and reduce ON degeneration. These data demonstrate that efficient mitophagy in astrocytes is required for ON health and functional integrity.
    Keywords:  BCKDK; astrocytes; autophagy; lysosome; mitochondria; mitophagy; optic nerve; βA3/A1-crystallin
    DOI:  https://doi.org/10.3390/cells12202496
  38. Nat Cell Biol. 2023 Oct 26.
    Manganese regulation of COPII condensation controls circulating lipid homeostasis.
    Xiao Wang, Runze Huang, Yawei Wang, Wenjing Zhou, Yating Hu, Yuanhang Yao, Kunlun Cheng, Xin Li, Bolin Xu, Jie Zhang, Yaowen Xu, Fanxin Zeng, Yuangang Zhu, Xiao-Wei Chen.
      Precise control of circulating lipids is instrumental in health and disease. Bulk lipids, carried by specialized lipoproteins, are secreted into the circulation, initially via the coat protein complex II (COPII). How the universal COPII machinery accommodates the abundant yet unconventional lipoproteins remains unclear, let alone its therapeutic translation. Here we report that COPII uses manganese-tuning, self-constrained condensation to selectively drive lipoprotein delivery and set lipid homeostasis in vivo. Serendipitously, adenovirus hijacks the condensation-based transport mechanism, thus enabling the identification of cytosolic manganese as an unexpected control signal. Manganese directly binds the inner COPII coat and enhances its condensation, thereby shifting the assembly-versus-dynamics balance of the transport machinery. Manganese can be mobilized from mitochondria stores to signal COPII, and selectively controls lipoprotein secretion with a distinctive, bell-shaped function. Consequently, dietary titration of manganese enables tailored lipid management that counters pathological dyslipidaemia and atherosclerosis, implicating a condensation-targeting strategy with broad therapeutic potential for cardio-metabolic health.
    DOI:  https://doi.org/10.1038/s41556-023-01260-3
  39. Nat Chem Biol. 2023 Oct 26.
    Reducing mitochondrial mysteries.
    Rachel M Guerra, David J Pagliarini.
      
    DOI:  https://doi.org/10.1038/s41589-023-01435-x
  40. bioRxiv. 2023 Oct 03. pii: 2023.10.02.560316. [Epub ahead of print]
    Selective Mitochondrial Respiratory Complex I Subunit Deficiency Causes Tumor Immunogenicity.
    Jiaxin Liang, Tevis Vitale, Xixi Zhang, Thomas D Jackson, Deyang Yu, Mark Jedrychowski, Steve P Gygi, Hans R Widlund, Kai W Wucherpfennig, Pere Puigserver.
      Targeting of specific metabolic pathways in tumor cells has the potential to sensitize them to immune-mediated attack. Here we provide evidence for a specific means of mitochondrial respiratory Complex I (CI) inhibition that improves tumor immunogenicity and sensitivity to immune checkpoint blockade (ICB). Targeted genetic deletion of the CI subunits Ndufs4 and Ndufs6 , but not other subunits, induces an immune-dependent tumor growth attenuation in mouse melanoma models. We show that deletion of Ndufs4 induces expression of the transcription factor Nlrc5 and genes in the MHC class I antigen presentation and processing pathway. This induction of MHC-related genes is driven by an accumulation of pyruvate dehydrogenase-dependent mitochondrial acetyl-CoA downstream of CI subunit deletion. This work provides a novel functional modality by which selective CI inhibition restricts tumor growth, suggesting that specific targeting of Ndufs4 , or related CI subunits, increases T-cell mediated immunity and sensitivity to ICB.
    DOI:  https://doi.org/10.1101/2023.10.02.560316
  41. Cell Mol Biol Lett. 2023 Oct 27. 28(1): 87
    Cadmium promotes nonalcoholic fatty liver disease by inhibiting intercellular mitochondrial transfer.
    Jian Sun, Yan Chen, Tao Wang, Waseem Ali, Yonggang Ma, Yan Yuan, Jianhong Gu, Jianchun Bian, Zongping Liu, Hui Zou.
      Mitochondrial transfer regulates intercellular communication, and mitochondria regulate cell metabolism and cell survival. However, the role and mechanism of mitochondrial transfer in Cd-induced nonalcoholic fatty liver disease (NAFLD) are unclear. The present study shows that mitochondria can be transferred between hepatocytes via microtubule-dependent tunneling nanotubes. After Cd treatment, mitochondria exhibit perinuclear aggregation in hepatocytes and blocked intercellular mitochondrial transfer. The different movement directions of mitochondria depend on their interaction with different motor proteins. The results show that Cd destroys the mitochondria-kinesin interaction, thus inhibiting mitochondrial transfer. Moreover, Cd increases the interaction of P62 with Dynactin1, promotes negative mitochondrial transport, and increases intracellular lipid accumulation. Mitochondria and hepatocyte co-culture significantly reduced Cd damage to hepatocytes and lipid accumulation. Thus, Cd blocks intercellular mitochondrial transfer by disrupting the microtubule system, inhibiting mitochondrial positive transport, and promoting their negative transport, thereby promoting the development of NAFLD.
    Keywords:  Cadmium; Intercellular mitochondrial transfer; Nonalcoholic fatty liver disease; Tunneling nanotubes
    DOI:  https://doi.org/10.1186/s11658-023-00498-x
  42. J Clin Med. 2023 Oct 22. pii: 6669. [Epub ahead of print]12(20):
    Leber Hereditary Optic Neuropathy (LHON) in Patients with Presumed Childhood Monocular Amblyopia.
    Sanja Petrovic Pajic, Ana Fakin, Maja Sustar Habjan, Martina Jarc-Vidmar, Marko Hawlina.
       BACKGROUND: Most Leber hereditary optic neuropathy (LHON) cases are bilateral and sequential; however, there are rare unilateral examples, or those in which the delay of onset of vision loss between one and the other eye is longer. In the case of presumed childhood amblyopia in one eye, vision loss in the good eye may be the only symptom of bilateral disease, which was unnoticed in the previously amblyopic eye, or a preexisting episode of LHON in the "amblyopic" eye. The clinical decision in such cases may be difficult and suggestive of other forms of atypical optic neuropathy until confirmed by genetic testing.
    CASE SERIES: We present three genetically confirmed (MT-ND1:m.3700G>A, MT-ND6:m14484 T>C, and MT-ND4:m.11778G>A) patients with subacute vision loss in the previously good eye, with the other eye believed to be amblyopic from childhood and their features different from what would be expected in true amblyopia. In all, electrophysiology testing showed a bilaterally reduced amplitude of PERG with low VEP P100 wave amplitudes and prolonged peak time in both eyes, also unusual for amblyopia. During follow-up, the pallor of the optic discs progressed in all eyes. Significant thinning of the peripapillary retinal nerve fiber layer (pRNFL; retinal nerve fiber layer around the optic disc) and ganglion cell complex (GCC) in the macular region was present. All three patients had a peculiar history. The first patient was treated for presumed hyperopic amblyopia that did not improve since childhood, experienced visual loss in the good eye at the age of 17, and was negative for the three typical LHON mutations. Extended testing confirmed an atypical pathogenic variant MT-ND1:m.3700G>A in homoplasmy. The second patient with presumed strabismic amblyopia had an unusual presentation of vision loss only at the age of 61, and after the exclusion of other causes, a typical MT-ND4:m.11778G>A pathogenic variant was found in homoplasmy. The third case was peculiar as he had presumed strabismic amblyopia since childhood and had some degree of disc pallor in the amblyopic eye upon presenting with loss of vision in the good eye at the age of 21, and a typical pathogenic variant m14484 T>C, p.Met64Val was subsequently confirmed. However, one year after disease onset, he started to experience significant spontaneous functional improvement in the non-amblyopic up to 1.0 Snellen whilst improvement in the presumed amblyopic eye was modest, suggesting preexisting amblyopia. This interestingly extensive improvement was carefully followed by electrophysiology as well as visual acuity and fields.
    CONCLUSIONS: This report shows three different scenarios of presentation of LHON in patients with presumed uniocular amblyopia from childhood. In such cases, the diagnosis may be difficult, and detailed structural and functional evaluation of the optic nerve head is necessary to assess whether an earlier LHON episode was misdiagnosed as amblyopia or whether LHON presented bilaterally on both eyes whilst only being noticed in the previously good eye.
    Keywords:  LHON; amblyopia; low visual acuity; retinal thickness; segmentation analysis; visual acuity improvement
    DOI:  https://doi.org/10.3390/jcm12206669
  43. Autophagy. 2023 Oct 24.
    The NLRX1-SLC39A7 complex orchestrates mitochondrial dynamics and mitophagy to rejuvenate intervertebral disc by modulating mitochondrial Zn2+ trafficking.
    Yu Song, Huaizhen Liang, Gaocai Li, Liang Ma, Dingchao Zhu, Weifeng Zhang, Bide Tong, Shuai Li, Yong Gao, Xinghuo Wu, Yukun Zhang, Xiaobo Feng, Kun Wang, Cao Yang.
      Intervertebral disc degeneration (IDD) is the most critical pathological factor in the development of low back pain. The maintenance of nucleus pulposus (NP) cell and intervertebral disc integrity benefits largely from well-controlled mitochondrial quality, surveilled by mitochondrial dynamics (fission and fusion) and mitophagy, but the outcome is cellular context-dependent that remain to be clarified. Our studies revealed that the loss of NLRX1 is correlated with NP cell senescence and IDD progression, which involve disordered mitochondrial quality. Further using animal and in vitro tissue and cell models, we demonstrated that NLRX1 could facilitate mitochondrial quality by coupling mitochondrial dynamic factors (p-DNM1L, L-OPA1:S-OPA1, OMA1) and mitophagy activity. Conversely, mitochondrial collapse occurred in NLRX1-defective NP cells and switched on the compensatory PINK1-PRKN pathway that led to excessive mitophagy and aggressive NP cell senescence. Mechanistically, NLRX1 was originally shown to interact with zinc transporter SLC39A7 and modulate mitochondrial Zn2+ trafficking via the formation of an NLRX1-SLC39A7 complex on the mitochondrial membrane of NP cells, subsequently orchestrating mitochondrial dynamics and mitophagy. The restoration of NLRX1 function by gene overexpression or pharmacological agonist (NX-13) treatment showed great potential for regulating mitochondrial fission with synchronous fusion and mitophagy, thus sustaining mitochondrial homeostasis, ameliorating NP cell senescence and rejuvenating intervertebral discs. Collectively, our findings highlight a working model whereby the NLRX1-SLC39A7 complex coupled mitochondrial dynamics and mitophagy activity to surveil and target damaged mitochondria for degradation, which determines the beneficial function of the mitochondrial surveillance system and ultimately rejuvenates intervertebral discs.
    Keywords:  Intervertebral disc degeneration; NLRX1; SLC39A7; mitochondrial dynamics; mitophagy; nucleus pulposus
    DOI:  https://doi.org/10.1080/15548627.2023.2274205
  44. Nat Biotechnol. 2023 Oct 23.
    AI for drug discovery is booming, but who owns the patents?
    Matthew Hutson.
      
    DOI:  https://doi.org/10.1038/s41587-023-02029-7
  45. medRxiv. 2023 Oct 05. pii: 2023.10.05.23296595. [Epub ahead of print]
    Exome copy number variant detection, analysis and classification in a large cohort of families with undiagnosed rare genetic disease.
    Gabrielle Lemire, Alba Sanchis-Juan, Kathryn Russell, Samantha Baxter, Katherine R Chao, Moriel Singer-Berk, Emily Groopman, Isaac Wong, Eleina England, Julia Goodrich, Lynn Pais, Christina Austin-Tse, Stephanie DiTroia, Emily O'Heir, Vijay S Ganesh, Monica H Wojcik, Emily Evangelista, Hana Snow, Ikeoluwa Osei-Owusu, Jack Fu, Mugdha Singh, Yulia Mostovoy, Steve Huang, Kiran Garimella, Samantha L Kirkham, Jennifer E Neil, Diane D Shao, Christopher A Walsh, Emanuela Argili, Carolyn Le, Elliott H Sherr, Joseph Gleeson, Shirlee Shril, Ronen Schneider, Friedhelm Hildebrandt, Vijay G Sankaran, Jill A Madden, Casie A Genetti, Alan H Beggs, Pankaj B Agrawal, Kinga M Bujakowska, Emily Place, Eric A Pierce, Sandra Donkervoort, Carsten G Bönnemann, Lyndon Gallacher, Zornitza Stark, Tiong Tan, Susan M White, Ana Töpf, Volker Straub, Mark D Fleming, Martin R Pollak, Katrin Õunap, Sander Pajusalu, Kirsten A Donald, Zandre Bruwer, Gianina Ravenscroft, Nigel G Laing, Daniel G MacArthur, Heidi L Rehm, Michael E Talkowski, Harrison Brand, Anne O'Donnell-Luria.
      Copy number variants (CNVs) are significant contributors to the pathogenicity of rare genetic diseases and with new innovative methods can now reliably be identified from exome sequencing. Challenges still remain in accurate classification of CNV pathogenicity. CNV calling using GATK-gCNV was performed on exomes from a cohort of 6,633 families (15,759 individuals) with heterogeneous phenotypes and variable prior genetic testing collected at the Broad Institute Center for Mendelian Genomics of the GREGoR consortium. Each family's CNV data was analyzed using the seqr platform and candidate CNVs classified using the 2020 ACMG/ClinGen CNV interpretation standards. We developed additional evidence criteria to address situations not covered by the current standards. The addition of CNV calling to exome analysis identified causal CNVs for 173 families (2.6%). The estimated sizes of CNVs ranged from 293 bp to 80 Mb with estimates that 44% would not have been detected by standard chromosomal microarrays. The causal CNVs consisted of 141 deletions, 15 duplications, 4 suspected complex structural variants (SVs), 3 insertions and 10 complex SVs, the latter two groups being identified by orthogonal validation methods. We interpreted 153 CNVs as likely pathogenic/pathogenic and 20 CNVs as high interest variants of uncertain significance. Calling CNVs from existing exome data increases the diagnostic yield for individuals undiagnosed after standard testing approaches, providing a higher resolution alternative to arrays at a fraction of the cost of genome sequencing. Our improvements to the classification approach advances the systematic framework to assess the pathogenicity of CNVs.
    DOI:  https://doi.org/10.1101/2023.10.05.23296595
  46. Biogerontology. 2023 Oct 21.
    Mitochondria and telomeres: hand in glove.
    Mélina Vaurs, Elif Beyza Dolu, Anabelle Decottignies.
      Born as an endosymbiont, the bacteria engulfed by the proto-eukaryotic cell more than 1.45 billion years ago progressively evolved as an important organelle with multiple interactions with the host cell. In particular, strong connections between mitochondria and the chromosome ends, the telomeres, led to propose a new theory of ageing in which dysfunctional telomeres and mitochondria are the main actors of a vicious circle reducing cell fitness and promoting cellular ageing. We review the evidences that oxidative stress and dysfunctional mitochondria damage telomeres and further discuss the interrelationship between telomere biology and mitochondria through the lens of telomerase which shuttles between the nucleus and mitochondria. Finally, we elaborate on the possible role of the mitochondrial genome on the inheritance of human telomere length through the expression of mitochondrial gene variants.
    Keywords:  Mitochondria; Oxidative stress; Telomerase; Telomere
    DOI:  https://doi.org/10.1007/s10522-023-10074-7
  47. JACC Case Rep. 2023 Oct 18. 24 102024
    PPA2 Deficiency in 2 Sisters: A Rare Cause of Sudden Cardiac Death.
    Will Genthe, Colleen Donnelly, David Ezon, Veronica Fettig, Jaya Ganesh, Isaac Marin-Valecia, Bruce D Gelb.
      Inorganic pyrophosphatase 2 (PPA2) deficiency is a genetic cause of sudden cardiac death, often triggered by viral infection or alcohol consumption. Literature on management is limited because most cases are diagnosed post mortem. We report lethal and nonlethal cardiac presentations of PPA2 deficiency in 2 adolescent sisters that resulted from a novel pathogenic PPA2 variant. (Level of Difficulty: Advanced.).
    Keywords:  PPA2; genetics; mitochondrial disease; multidisciplinary care; sudden cardiac death
    DOI:  https://doi.org/10.1016/j.jaccas.2023.102024
  48. Res Sq. 2023 Oct 12. pii: rs.3.rs-3304679. [Epub ahead of print]
    Augmenting Mitochondrial Respiration in Immature Smooth Muscle Cells with an ACTA2 Pathogenic Variant Mitigates Moyamoya-like Cerebrovascular Disease.
    Dianna Milewicz, Anita Kaw, Ting Wu, Zbigniew Starosolski, Zhen Zhou, Albert Pedroza, Suravi Majumder, Xue-Yan Duan, Kaveeta Kaw, Jose Esparza Pinelo, Michael P Fischbein, Philip Lorenzi, Lin Tan, Sara Martinez, Iqbal Mahmud, Laxman Devkota, Heinrich Taegtmeyer, Ketan Ghaghada, Sean Marrelli, Callie Kwartler.
      ACTA2 pathogenic variants altering arginine 179 cause childhood-onset strokes due to moyamoya disease (MMD)-like occlusion of the distal internal carotid arteries. A smooth muscle cell (SMC)-specific knock-in mouse model ( Acta2 SMC-R179C/+ ) inserted the mutation into 67% of aortic SMCs, whereas explanted SMCs were uniformly heterozygous. Acta2 R179C/+ SMCs fail to fully differentiate and maintain stem cell-like features, including high glycolytic flux, and increasing oxidative respiration (OXPHOS) with nicotinamide riboside (NR) drives the mutant SMCs to differentiate and decreases migration. Acta2 SMC-R179C/+ mice have intraluminal MMD-like occlusive lesions and strokes after carotid artery injury, whereas the similarly treated WT mice have no strokes and patent lumens. Treatment with NR prior to the carotid artery injury attenuates the strokes, MMD-like lumen occlusions, and aberrant vascular remodeling in the Acta2 SMC-R179C/+ mice. These data highlight the role of immature SMCs in MMD-associated occlusive disease and demonstrate that altering SMC metabolism to drive quiescence of Acta2 R179C/+ SMCs attenuates strokes and aberrant vascular remodeling in the Acta2 SMC-R179C/+ mice.
    DOI:  https://doi.org/10.21203/rs.3.rs-3304679/v1
  49. bioRxiv. 2023 Oct 09. pii: 2023.10.06.561062. [Epub ahead of print]
    TMEM65 regulates NCLX-dependent mitochondrial calcium efflux.
    Joanne F Garbincius, Oniel Salik, Henry M Cohen, Carmen Choya-Foces, Adam S Mangold, Angelina D Makhoul, Anna E Schmidt, Dima Y Khalil, Joshua J Doolittle, Anya S Wilkinson, Emma K Murray, Michael P Lazaropoulos, Alycia N Hildebrand, Dhanendra Tomar, John W Elrod.
      The balance between mitochondrial calcium ( m Ca 2+ ) uptake and efflux regulates ATP production, but if perturbed causes energy starvation or m Ca 2+ overload and cell death. The mitochondrial sodium-calcium exchanger, NCLX, is a critical route of m Ca 2+ efflux in excitable tissues, such as the heart and brain, and animal models support NCLX as a promising therapeutic target to limit pathogenic m Ca 2+ overload. However, the mechanisms that regulate NCLX activity remain largely unknown. We used proximity biotinylation proteomic screening to identify the NCLX interactome and define novel regulators of NCLX function. Here, we discover the mitochondrial inner membrane protein, TMEM65, as an NCLX-proximal protein that potently enhances sodium (Na + )-dependent m Ca 2+ efflux. Mechanistically, acute pharmacologic NCLX inhibition or genetic deletion of NCLX ablates the TMEM65-dependent increase in m Ca 2+ efflux. Further, loss-of-function studies show that TMEM65 is required for Na + -dependent m Ca 2+ efflux. Co-fractionation and in silico structural modeling of TMEM65 and NCLX suggest these two proteins exist in a common macromolecular complex in which TMEM65 directly stimulates NCLX function. In line with these findings, knockdown of Tmem65 in mice promotes m Ca 2+ overload in the heart and skeletal muscle and impairs both cardiac and neuromuscular function. We further demonstrate that TMEM65 deletion causes excessive mitochondrial permeability transition, whereas TMEM65 overexpression protects against necrotic cell death during cellular Ca 2+ stress. Collectively, our results show that loss of TMEM65 function in excitable tissue disrupts NCLX-dependent m Ca 2+ efflux, causing pathogenic m Ca 2+ overload, cell death and organ-level dysfunction, and that gain of TMEM65 function mitigates these effects. These findings demonstrate the essential role of TMEM65 in regulating NCLX-dependent m Ca 2+ efflux and suggest modulation of TMEM65 as a novel strategy for the therapeutic control of m Ca 2+ homeostasis.
    DOI:  https://doi.org/10.1101/2023.10.06.561062
  50. Proc Natl Acad Sci U S A. 2023 Nov 07. 120(45): e2315649120
    How defective mitochondrial electrical activity leads to inherited blindness.
    Peter J Burke.
      
    DOI:  https://doi.org/10.1073/pnas.2315649120
  51. Nat Med. 2023 Oct 23.
    A rapid whole-genome sequencing service for infants with rare diseases in the United Arab Emirates.
    Ahmad N Abou Tayoun, Alawi Alsheikh-Ali.
      
    DOI:  https://doi.org/10.1038/s41591-023-02596-x
  52. bioRxiv. 2023 Oct 11. pii: 2023.10.10.561776. [Epub ahead of print]
    GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction.
    Gonzalo Benegas, Carlos Albors, Alan J Aw, Chengzhong Ye, Yun S Song.
      Whereas protein language models have demonstrated remarkable efficacy in predicting the effects of missense variants, DNA counterparts have not yet achieved a similar competitive edge for genome-wide variant effect predictions, especially in complex genomes such as that of humans. To address this challenge, we here introduce GPN-MSA, a novel framework for DNA language models that leverages whole-genome sequence alignments across multiple species and takes only a few hours to train. Across several benchmarks on clinical databases (ClinVar, COSMIC, and OMIM) and population genomic data (gnomAD), our model for the human genome achieves outstanding performance on deleteriousness prediction for both coding and non-coding variants.
    DOI:  https://doi.org/10.1101/2023.10.10.561776
  53. bioRxiv. 2023 Oct 03. pii: 2023.10.02.560584. [Epub ahead of print]
    Sexually dimorphic mechanisms of VGLUT-mediated protection from dopaminergic neurodegeneration.
    Silas A Buck, Sophie A Rubin, Tenzin Kunkhyen, Christoph D Treiber, Xiangning Xue, Lief E Fenno, Samuel J Mabry, Varun R Sundar, Zilu Yang, Divia Shah, Kyle D Ketchesin, Darius D Becker-Krail, Iaroslavna Vasylieva, Megan C Smith, Florian J Weisel, Wenjia Wang, M Quincy Erickson-Oberg, Emma I O'Leary, Eshan Aravind, Charu Ramakrishnan, Yoon Seok Kim, Yanying Wu, Matthias Quick, Jonathan A Coleman, William A MacDonald, Rania Elbakri, Briana R De Miranda, Michael J Palladino, Brian D McCabe, Kenneth N Fish, Marianne L Seney, Stephen Rayport, Susana Mingote, Karl Deisseroth, Thomas S Hnasko, Rajeshwar Awatramani, Alan M Watson, Scott Waddell, Claire E J Cheetham, Ryan W Logan, Zachary Freyberg.
      Parkinson's disease (PD) targets some dopamine (DA) neurons more than others. Sex differences offer insights, with females more protected from DA neurodegeneration. The mammalian vesicular glutamate transporter VGLUT2 and Drosophila ortholog dVGLUT have been implicated as modulators of DA neuron resilience. However, the mechanisms by which VGLUT2/dVGLUT protects DA neurons remain unknown. We discovered DA neuron dVGLUT knockdown increased mitochondrial reactive oxygen species in a sexually dimorphic manner in response to depolarization or paraquat-induced stress, males being especially affected. DA neuron dVGLUT also reduced ATP biosynthetic burden during depolarization. RNA sequencing of VGLUT + DA neurons in mice and flies identified candidate genes that we functionally screened to further dissect VGLUT-mediated DA neuron resilience across PD models. We discovered transcription factors modulating dVGLUT-dependent DA neuroprotection and identified dj-1β as a regulator of sex-specific DA neuron dVGLUT expression. Overall, VGLUT protects DA neurons from PD-associated degeneration by maintaining mitochondrial health.
    DOI:  https://doi.org/10.1101/2023.10.02.560584
  54. Int J Biol Macromol. 2023 Oct 19. pii: S0141-8130(23)04463-X. [Epub ahead of print] 127566
    A molecular simulation study of the clinical G409V mutant in PINK1 associated with early-onset Parkinson's disease.
    Hsuan-Hsuan Lo, Ya-Jyun Chen, Cheng-Han Jiang, Chih-Hua Tseng, Chia-Ning Yang.
      The serine/threonine kinase PINK1 is responsible for phosphorylating a ubiquitin (Ub)-like domain in an E3 Ub ligase Parkin protein and a Parkin-bound Ub. PINK1 works as a mitochondrial quality control by phosphorylating and activating the E3 ubiquitin ligase Parkin. Recent medicinal study has reported that mutations of Parkin and PINK1 cause defects in mitophagy and induce early-onset Parkinson's disease (EOPD). In this study, we conducted molecular dynamics simulations to investigate the structural discrepancy caused by a clinical G409V mutation in PINK1 kinase domain's A-loop. The Ub phosphorylation begins with PINK1 D362 deprotonating the hydroxyl group of the substrate Ub's S65' and PINK1's A-loop is responsible for coordinating S65'. On contrary to G409 offering structural plasticity, the replaced, bulky V409 interferes with the alignment of D362-S65', seriously hampering Ub phosphorylation, leading to the accumulation of damaged mitochondria, and ultimately EOPD. In this study, we predicted the hPINK1WT-UbWT binding mode and detected the structural impact brought by G409V replacement. It is expected the concluded remarks to be beneficial for developing cures to alleviate structural interference and restore PINK1 function.
    Keywords:  Early-onset Parkinson's disease; Molecular dynamics simulations; PINK1
    DOI:  https://doi.org/10.1016/j.ijbiomac.2023.127566
  55. Nat Chem Biol. 2023 Oct 26.
    A genetically encoded tool to increase cellular NADH/NAD+ ratio in living cells.
    Xingxiu Pan, Mina L Heacock, Evana N Abdulaziz, Sara Violante, Austin L Zuckerman, Nirajan Shrestha, Canglin Yao, Russell P Goodman, Justin R Cross, Valentin Cracan.
      Impaired redox metabolism is a key contributor to the etiology of many diseases, including primary mitochondrial disorders, cancer, neurodegeneration and aging. However, mechanistic studies of redox imbalance remain challenging due to limited strategies that can perturb redox metabolism in various cellular or organismal backgrounds. Most studies involving impaired redox metabolism have focused on oxidative stress; consequently, less is known about the settings where there is an overabundance of NADH reducing equivalents, termed reductive stress. Here we introduce a soluble transhydrogenase from Escherichia coli (EcSTH) as a novel genetically encoded tool to promote reductive stress in living cells. When expressed in mammalian cells, EcSTH, and a mitochondrially targeted version (mitoEcSTH), robustly elevated the NADH/NAD+ ratio in a compartment-specific manner. Using this tool, we determined that metabolic and transcriptomic signatures of the NADH reductive stress are cellular background specific. Collectively, our novel genetically encoded tool represents an orthogonal strategy to promote reductive stress.
    DOI:  https://doi.org/10.1038/s41589-023-01460-w
  56. Elife. 2023 Oct 24. pii: e87098. [Epub ahead of print]12
    Genome-wide screen reveals Rab12 GTPase as a critical activator of Parkinson's disease-linked LRRK2 kinase.
    Herschel S Dhekne, Francesca Tonelli, Wondwossen M Yeshaw, Claire Y Chiang, Charles Limouse, Ebsy Jaimon, Elena Purlyte, Dario R Alessi, Suzanne R Pfeffer.
      Activating mutations in the Leucine Rich Repeat Kinase 2 (LRRK2) cause Parkinson's disease. LRRK2 phosphorylates a subset of Rab GTPases, particularly Rab10 and Rab8A, and we showed previously that these phosphoRabs play an important role in LRRK2 membrane recruitment and activation (Vides et al., 2022). To learn more about LRRK2 pathway regulation, we carried out an unbiased, CRISPR-based genome-wide screen to identify modifiers of cellular phosphoRab10 levels. A flow cytometry assay was developed to detect changes in phosphoRab10 levels in pools of mouse NIH-3T3 cells harboring unique CRISPR guide sequences. Multiple negative and positive regulators were identified; surprisingly, knockout of the Rab12 gene was especially effective in decreasing phosphoRab10 levels in multiple cell types and knockout mouse tissues. Rab-driven increases in phosphoRab10 were specific for Rab12, LRRK2 dependent and PPM1H phosphatase reversible, and did not require Rab12 phosphorylation; they were seen with wild type and pathogenic G2019S and R1441C LRRK2. As expected for a protein that regulates LRRK2 activity, Rab12 also influenced primary cilia formation. Alphafold modeling revealed a novel Rab12 binding site in the LRRK2 Armadillo domain and we show that residues predicted to be essential for Rab12 interaction at this site influence phosphoRab10 and phosphoRab12 levels in a manner distinct from Rab29 activation of LRRK2. Our data show that Rab12 binding to a new site in the LRRK2 Armadillo domain activates LRRK2 kinase for Rab phosphorylation and could serve as a new therapeutic target for a novel class of LRRK2 inhibitors that do not target the kinase domain.
    Keywords:  cell biology; mouse
    DOI:  https://doi.org/10.7554/eLife.87098
  57. Emerg Top Life Sci. 2023 Oct 27. pii: ETLS20230019. [Epub ahead of print]
    Challenges facing repeat expansion identification, characterisation, and the pathway to discovery.
    Justin L Read, Kayli C Davies, Genevieve C Thompson, Martin B Delatycki, Paul J Lockhart.
      Tandem repeat DNA sequences constitute a significant proportion of the human genome. While previously considered to be functionally inert, these sequences are now broadly accepted as important contributors to genetic diversity. However, the polymorphic nature of these sequences can lead to expansion beyond a gene-specific threshold, causing disease. More than 50 pathogenic repeat expansions have been identified to date, many of which have been discovered in the last decade as a result of advances in sequencing technologies and associated bioinformatic tools. Commonly utilised diagnostic platforms including Sanger sequencing, capillary array electrophoresis, and Southern blot are generally low throughput and are often unable to accurately determine repeat size, composition, and epigenetic signature, which are important when characterising repeat expansions. The rapid advances in bioinformatic tools designed specifically to interrogate short-read sequencing and the development of long-read single molecule sequencing is enabling a new generation of high throughput testing for repeat expansion disorders. In this review, we discuss some of the challenges surrounding the identification and characterisation of disease-causing repeat expansions and the technological advances that are poised to translate the promise of genomic medicine to individuals and families affected by these disorders.
    Keywords:  bioinformatics; cerebellar ataxia; diagnostics; discovery; next-generation sequencing
    DOI:  https://doi.org/10.1042/ETLS20230019
  58. Genes (Basel). 2023 Oct 20. pii: 1964. [Epub ahead of print]14(10):
    Notch Signaling Regulates Mouse Perivascular Adipose Tissue Function via Mitochondrial Pathways.
    Chenhao Yang, Xuehui Yang, Anne Harrington, Christian Potts, Abigail Kaija, Larisa Ryzhova, Lucy Liaw.
      Perivascular adipose tissue (PVAT) regulates vascular function by secreting vasoactive substances. In mice, Notch signaling is activated in the PVAT during diet-induced obesity, and leads to the loss of the thermogenic phenotype and adipocyte whitening due to increased lipid accumulation. We used the Adiponectin-Cre (Adipoq-Cre) strain to activate a ligand-independent Notch1 intracellular domain transgene (N1ICD) to drive constitutive Notch signaling in the adipose tissues (N1ICD;Adipoq-Cre). We previously found that constitutive activation of Notch1 signaling in the PVAT phenocopied the effects of diet-induced obesity. To understand the downstream pathways activated by Notch signaling, we performed a proteomic analysis of the PVAT from control versus N1ICD;Adipoq-Cre mice. This comparison identified prominent changes in the protein signatures related to metabolism, adipocyte homeostasis, mitochondrial function, and ferroptosis. PVAT-derived stromal vascular fraction cells were derived from our mouse strains to study the cellular and molecular phenotypes during adipogenic induction. We found that cells with activated Notch signaling displayed decreased mitochondrial respiration despite similar levels of adipogenesis and mitochondrial number. We observed variable regulation of the proteins related to mitochondrial dynamics and ferroptosis, including PHB3, PINK1, pDRP1, and the phospholipid hydroperoxidase GPX4. Mitochondria regulate some forms of ferroptosis, which is a regulated process of cell death driven by lipid peroxidation. Accordingly, we found that Notch activation promoted lipid peroxidation and ferroptosis in PVAT-derived adipocytes. Because the PVAT phenotype is a regulator of vascular reactivity, we tested the effect of Notch activation in PVAT on vasoreactivity using wire myography. The aortae from the N1ICD;Adipoq-Cre mice had increased vasocontraction and decreased vasorelaxation in a PVAT-dependent and age-dependent manner. Our data provide support for the novel concept that increased Notch signaling in the adipose tissue leads to PVAT whitening, impaired mitochondrial function, increased ferroptosis, and loss of a protective vasodilatory signal. Our study advances our understanding of how Notch signaling in adipocytes affects mitochondrial dynamics, which impacts vascular physiology.
    Keywords:  Notch signaling; mitochondrial dynamics; perivascular adipose tissue
    DOI:  https://doi.org/10.3390/genes14101964
  59. Curr Mol Med. 2023 Oct 20.
    METTL14 Regulates the m6A Modification of TRAF6 to Suppress Mitochondrial Dysfunction and Ferroptosis in Dopaminergic Neurons via the cGAS-STING Pathway.
    Liang Shao, Fan Hu, Renxu Xu, Hongbing Nie, Hong Zhang, Ping Zhang.
       OBJECTIVES: The degeneration of dopaminergic (DA) neurons has emerged as a crucial pathological characteristic in Parkinson's disease (PD). To enrich the related knowledge, we aimed to explore the impact of the METTL14-TRAF6-cGASSTING axis in mitochondrial dysfunction and ferroptosis underlying DA neuron degeneration.
    METHODS: 1-methyl-4-phenylpyridinium ion (MPP+) was used to treat DA neuron MN9D to develop the PD cell models. Afterward, a cell counting kit, flow cytometer, DCFH-DA fluorescent probe, and Dipyrromethene Boron Difluoride staining were utilized to measure the cell viability, iron concentration, ROS level, and lipid peroxidation, respectively. Meanwhile, the mitochondrial ultrastructure, the activity of mitochondrial respiratory chain complexes, and levels of malondialdehyde and glutathione were monitored. In addition, reverse transcription-quantitative polymerase chain reaction and western blot assays were adopted to measure the expression of related genes. cGAS ubiquitylation and TRAF6 messenger RNA (mRNA) N6-methyladenosine (m6A) levels, the linkages among METTL14, TRAF6, and the cGAS-STING pathway were also evaluated.
    RESULTS: METTL14 expression was low, and TRAF6 expression was high after MPP+ treatment. In MPP+-treated MN9D cells, METTL14 overexpression reduced ferroptosis, ROS generation, mitochondrial injury, and oxidative stress (OS) and enhanced mitochondrial membrane potentials. TRAF6 overexpression had promoting impacts on mitochondrial dysfunction and ferroptosis in MPP+-treated MN9D cells, which was reversed by further overexpression of METTL14. Mechanistically, METTL14 facilitated the m6A methylation of TRAF6 mRNA to down-regulate TRAF6 expression, thus inactivating the cGAS-STING pathway.
    CONCLUSION: METTL14 down-regulated TRAF6 expression through TRAF6 m6A methylation to inactivate the cGAS-STING pathway, thereby relieving mitochondrial dysfunction and ferroptosis in DA neurons.
    Keywords:  Dopaminergic neurons; Ferroptosis; METTL14; Mitochondrial dysfunction; Parkinson's disease; TRAF6; cGAS-STING pathway
    DOI:  https://doi.org/10.2174/0115665240263859231018110107
  60. Genes (Basel). 2023 Oct 07. pii: 1913. [Epub ahead of print]14(10):
    Longitudinal Changes in Mitochondrial DNA Copy Number and Telomere Length in Patients with Parkinson's Disease.
    Alberto Ortega-Vázquez, Salvador Sánchez-Badajos, Miguel Ángel Ramírez-García, Diana Alvarez-Luquín, Marisol López-López, Laura Virginia Adalid-Peralta, Nancy Monroy-Jaramillo.
      Parkinson's disease (PD) pathophysiology includes mitochondrial dysfunction, neuroinflammation, and aging as its biggest risk factors. Mitochondrial DNA copy number (mtDNA-CN) and telomere length (TL) are biological aging markers with inconclusive results regarding their association with PD. A case-control study was used to measure TL and mtDNA-CN using qPCR in PBMCs. PD patients were naive at baseline (T0) and followed-up at one (T1) and two (T2) years after the dopaminergic treatment (DRT). Plasmatic cytokines were determined by ELISA in all participants, along with clinical parameters of patients at T0. While TL was shorter in patients vs. controls at all time points evaluated (p < 0.01), mtDNA-CN showed no differences. An increase in mtDNA-CN and TL was observed in treated patients vs. naive ones (p < 0.001). Our statistical model analyzed both aging markers with covariates, showing a strong correlation between them (r = 0.57, p < 0.01), and IL-17A levels positively correlating with mtDNA-CN only in untreated patients (r = 0.45, p < 0.05). TL and mtDNA-CN could be useful markers for monitoring inflammation progression or treatment response in PD. DRT might modulate TL and mtDNA-CN, reflecting a compensatory mechanism to counteract mitochondrial dysfunction in PD, but this needs further investigation.
    Keywords:  IL-17A; Parkinson’s disease; aging; dopaminergic replacement therapy; inflammatory index; mitochondrial DNA copy number; telomere length
    DOI:  https://doi.org/10.3390/genes14101913
  61. Biomolecules. 2023 Sep 25. pii: 1441. [Epub ahead of print]13(10):
    Advance in Genomics of Rare Genetic Diseases.
    Elena Sommariva, Milena Bellin, Chiara Di Resta.
      Recent technical breakthroughs in genotyping and bioinformatics techniques have greatly facilitated the translation of genomics into clinical care [...].
    DOI:  https://doi.org/10.3390/biom13101441
  62. J Appl Lab Med. 2023 Oct 26. pii: jfad060. [Epub ahead of print]
    Low Arginine Suggesting the Diagnosis of Mitochondrial Cardiomyopathy.
    Parith Wongkittichote, Edward B Cook, Francis Jeshira Reynoso Santos, Rebecca C Ahrens-Nicklas, Xinying Hong, Rebecca D Ganetzky.
      
    DOI:  https://doi.org/10.1093/jalm/jfad060
  63. J Clin Med. 2023 Oct 11. pii: 6453. [Epub ahead of print]12(20):
    Microcirculation and Mitochondria: The Critical Unit.
    Guangjian Wang, Hui Lian, Hongmin Zhang, Xiaoting Wang.
      Critical illness is often accompanied by a hemodynamic imbalance between macrocirculation and microcirculation, as well as mitochondrial dysfunction. Microcirculatory disorders lead to abnormalities in the supply of oxygen to tissue cells, while mitochondrial dysfunction leads to abnormal energy metabolism and impaired tissue oxygen utilization, making these conditions important pathogenic factors of critical illness. At the same time, there is a close relationship between the microcirculation and mitochondria. We introduce here the concept of a "critical unit", with two core components: microcirculation, which mainly comprises the microvascular network and endothelial cells, especially the endothelial glycocalyx; and mitochondria, which are mainly involved in energy metabolism but perform other non-negligible functions. This review also introduces several techniques and devices that can be utilized for the real-time synchronous monitoring of the microcirculation and mitochondria, and thus critical unit monitoring. Finally, we put forward the concepts and strategies of critical unit-guided treatment.
    Keywords:  critical illness; critical unit; microcirculation; mitochondria; monitoring technique; treatment strategy
    DOI:  https://doi.org/10.3390/jcm12206453
  64. Nat Commun. 2023 Oct 27. 14(1): 6845
    Systematic analysis of paralogous regions in 41,755 exomes uncovers clinically relevant variation.
    Wouter Steyaert, Lonneke Haer-Wigman, Rolph Pfundt, Debby Hellebrekers, Marloes Steehouwer, Juliet Hampstead, Elke de Boer, Alexander Stegmann, Helger Yntema, Erik-Jan Kamsteeg, Han Brunner, Alexander Hoischen, Christian Gilissen.
      The short lengths of short-read sequencing reads challenge the analysis of paralogous genomic regions in exome and genome sequencing data. Most genetic variants within these homologous regions therefore remain unidentified in standard analyses. Here, we present a method (Chameleolyser) that accurately identifies single nucleotide variants and small insertions/deletions (SNVs/Indels), copy number variants and ectopic gene conversion events in duplicated genomic regions using whole-exome sequencing data. Application to a cohort of 41,755 exome samples yields 20,432 rare homozygous deletions and 2,529,791 rare SNVs/Indels, of which we show that 338,084 are due to gene conversion events. None of the SNVs/Indels are detectable using regular analysis techniques. Validation by high-fidelity long-read sequencing in 20 samples confirms >88% of called variants. Focusing on variation in known disease genes leads to a direct molecular diagnosis in 25 previously undiagnosed patients. Our method can readily be applied to existing exome data.
    DOI:  https://doi.org/10.1038/s41467-023-42531-9
  65. Biochem Biophys Res Commun. 2023 Oct 15. pii: S0006-291X(23)01200-7. [Epub ahead of print]683 149116
    CCDC127 regulates lipid droplet homeostasis by enhancing mitochondria-ER contacts.
    Yuchen Xia, Yue Zhang, Yuwei Sun, Li He.
      Lipid droplets (LDs) are both energy storage and signaling organelles playing important roles in various physiological and pathological conditions. The mitochondria-ER contacts have been implicated in regulating the homeostasis of lipid droplets. However, our knowledge about the molecular mechanism behind this regulation is still limited. In this study, we identified CCDC127, a previously uncharacterized protein, as a new regulator of LDs by enhancing the mitochondria-ER contact sites (MERCS). Knockdown and overexpression of CCDC127 in HeLa cells significantly change the LDs abundance in opposite directions, suggesting that CCDC127 positively regulates the LDs. Additional analysis showed that CCDC127 localizes on the outer membrane of mitochondria through its N-terminus and promotes mitochondria fragmentation. Importantly, knockdown or overexpression of CCDC127 significantly down- or up-regulates, respectively, the formation of MERCS. Further experiments showed that CCDC127 is required to stabilize the MERCS tether protein VAPA. And overexpression or knockdown of VAPA reversed the effects of CCDC127 reduction or overexpression on LDs. Finally, we demonstrated that knocking down CCDC127 in the mesenchymal stem cells reduced their differentiation towards adipocytes. These findings provide a new molecular connection between LD homeostasis and MERCS regulation.
    Keywords:  CCDC127; Lipid droplet; Mitochondria-ER contact
    DOI:  https://doi.org/10.1016/j.bbrc.2023.10.048
  66. Am J Hum Genet. 2023 Oct 11. pii: S0002-9297(23)00352-X. [Epub ahead of print]
    Identification of a robust DNA methylation signature for Fanconi anemia.
    Daria Pagliara, Andrea Ciolfi, Lucia Pedace, Sadegheh Haghshenas, Marco Ferilli, Michael A Levy, Evelina Miele, Claudia Nardini, Camilla Cappelletti, Raissa Relator, Angela Pitisci, Rita De Vito, Simone Pizzi, Jennifer Kerkhof, Haley McConkey, Francesca Nazio, Sarina G Kant, Maddalena Di Donato, Emanuele Agolini, Marta Matraxia, Barbara Pasini, Alessandra Pelle, Tiziana Galluccio, Antonio Novelli, Tahsin Stefan Barakat, Marco Andreani, Francesca Rossi, Cristina Mecucci, Anna Savoia, Bekim Sadikovic, Franco Locatelli, Marco Tartaglia.
      Fanconi anemia (FA) is a clinically variable and genetically heterogeneous cancer-predisposing disorder representing the most common bone marrow failure syndrome. It is caused by inactivating predominantly biallelic mutations involving >20 genes encoding proteins with roles in the FA/BRCA DNA repair pathway. Molecular diagnosis of FA is challenging due to the wide spectrum of the contributing gene mutations and structural rearrangements. The assessment of chromosomal fragility after exposure to DNA cross-linking agents is generally required to definitively confirm diagnosis. We assessed peripheral blood genome-wide DNA methylation (DNAm) profiles in 25 subjects with molecularly confirmed clinical diagnosis of FA (FANCA complementation group) using Illumina's Infinium EPIC array. We identified 82 differentially methylated CpG sites that allow to distinguish subjects with FA from healthy individuals and subjects with other genetic disorders, defining an FA-specific DNAm signature. The episignature was validated using a second cohort of subjects with FA involving different complementation groups, documenting broader genetic sensitivity and demonstrating its specificity using the EpiSign Knowledge Database. The episignature properly classified DNA samples obtained from bone marrow aspirates, demonstrating robustness. Using the selected probes, we trained a machine-learning model able to classify EPIC DNAm profiles in molecularly unsolved cases. Finally, we show that the generated episignature includes CpG sites that do not undergo functional selective pressure, allowing diagnosis of FA in individuals with reverted phenotype due to gene conversion. These findings provide a tool to accelerate diagnostic testing in FA and broaden the clinical utility of DNAm profiling in the diagnostic setting.
    Keywords:  DNA methylation profiling; Fanconi anemia; classifier; diagnostic tool; episignature; gene conversion; hematological disorders; machine learning; mosaicism; variant classification
    DOI:  https://doi.org/10.1016/j.ajhg.2023.09.014
  67. bioRxiv. 2023 Oct 09. pii: 2023.10.03.560715. [Epub ahead of print]
    Benchmark dataset for training machine learning models to predict the pathway involvement of metabolites.
    Erik D Huckvale, Christian D Powell, Huan Jin, Hunter N B Moseley.
      Metabolic pathways are a human-defined grouping of life sustaining biochemical reac-tions, metabolites being both the reactants and products of these reactions. But many public datasets include identified metabolites whose pathway involvement is unknown, hindering metabolic inter-pretation. To address these shortcomings, various machine learning models, including those trained on data from the Kyoto Encyclopedia of Genes and Genomes (KEGG), have been developed to pre-dict the pathway involvement of metabolites based on their chemical descriptions; however, these prior models are based on old metabolite KEGG-based datasets, including one benchmark dataset that is invalid due to the presence of over 1500 duplicate entries. Therefore, we have developed a new benchmark dataset derived from the KEGG following optimal standards of scientific compu-tational reproducibility and including all source code needed to update the benchmark dataset as KEGG changes. We have used this new benchmark dataset with our atom coloring methodology to develop and compare the performance of Random Forest, XGBoost, and multilayer perceptron with autoencoder models generated from our new benchmark dataset. Best overall weighted average performance across 1000 unique folds was an F1-score of 0.8180 and Matthews correlation coeffi-cient of 0.7933, which was provided by XGBoost binary classification models for 11 KEGG-defined pathway categories.
    DOI:  https://doi.org/10.1101/2023.10.03.560715
  68. Geroscience. 2023 Oct 26.
    Divergence in aerobic capacity and energy expenditure influence metabolic tissue mitochondrial protein synthesis rates in aged rats.
    Edziu Franczak, Adrianna Maurer, Vivien Csikos Drummond, Benjamin A Kugler, Emily Wells, Madi Wenger, Frederick F Peelor, Abby Crosswhite, Colin S McCoin, Lauren G Koch, Steven L Britton, Benjamin F Miller, John P Thyfault.
      Age-associated declines in aerobic capacity promote the development of various metabolic diseases. In rats selectively bred for high/low intrinsic aerobic capacity, greater aerobic capacity reduces susceptibility to metabolic disease while increasing longevity. However, little remains known how intrinsic aerobic capacity protects against metabolic disease, particularly with aging. Here, we tested the effects of aging and intrinsic aerobic capacity on systemic energy expenditure, metabolic flexibility and mitochondrial protein synthesis rates using 24-month-old low-capacity (LCR) or high-capacity runner (HCR) rats. Rats were fed low-fat diet (LFD) or high-fat diet (HFD) for eight weeks, with energy expenditure (EE) and metabolic flexibility assessed utilizing indirect calorimetry during a 48 h fast/re-feeding metabolic challenge. Deuterium oxide (D2O) labeling was used to assess mitochondrial protein fraction synthesis rates (FSR) over a 7-day period. HCR rats possessed greater EE during the metabolic challenge. Interestingly, HFD induced changes in respiratory exchange ratio (RER) in male and female rats, while HCR female rat RER was largely unaffected by diet. In addition, analysis of protein FSR in skeletal muscle, brain, and liver mitochondria showed tissue-specific adaptations between HCR and LCR rats. While brain and liver protein FSR were altered by aerobic capacity and diet, these effects were less apparent in skeletal muscle. Overall, we provide evidence that greater aerobic capacity promotes elevated EE in an aged state, while also regulating metabolic flexibility in a sex-dependent manner. Modulation of mitochondrial protein FSR by aerobic capacity is tissue-specific with aging, likely due to differential energetic requirements by each tissue.
    Keywords:  Aging; Exercise capacity; Metabolic flexibility; Mitochondrial proteostasis
    DOI:  https://doi.org/10.1007/s11357-023-00985-1
  69. Nat Commun. 2023 Oct 23. 14(1): 6737
    Metabolic regulation of proteome stability via N-terminal acetylation controls male germline stem cell differentiation and reproduction.
    Charlotte M François, Thomas Pihl, Marion Dunoyer de Segonzac, Chloé Hérault, Bruno Hudry.
      The molecular mechanisms connecting cellular metabolism with differentiation remain poorly understood. Here, we find that metabolic signals contribute to stem cell differentiation and germline homeostasis during Drosophila melanogaster spermatogenesis. We discovered that external citrate, originating outside the gonad, fuels the production of Acetyl-coenzyme A by germline ATP-citrate lyase (dACLY). We show that this pathway is essential during the final spermatogenic stages, where a high Acetyl-coenzyme A level promotes NatB-dependent N-terminal protein acetylation. Using genetic and biochemical experiments, we establish that N-terminal acetylation shields key target proteins, essential for spermatid differentiation, from proteasomal degradation by the ubiquitin ligase dUBR1. Our work uncovers crosstalk between metabolism and proteome stability that is mediated via protein post-translational modification. We propose that this system coordinates the metabolic state of the organism with gamete production. More broadly, modulation of proteome turnover by circulating metabolites may be a conserved regulatory mechanism to control cell functions.
    DOI:  https://doi.org/10.1038/s41467-023-42496-9
  70. Nucleic Acids Res. 2023 Oct 23. pii: gkad880. [Epub ahead of print]
    HALL: a comprehensive database for human aging and longevity studies.
    Hao Li, Song Wu, Jiaming Li, Zhuang Xiong, Kuan Yang, Weidong Ye, Jie Ren, Qiaoran Wang, Muzhao Xiong, Zikai Zheng, Shuo Zhang, Zichu Han, Peng Yang, Beier Jiang, Jiale Ping, Yuesheng Zuo, Xiaoyong Lu, Qiaocheng Zhai, Haoteng Yan, Si Wang, Shuai Ma, Bing Zhang, Jinlin Ye, Jing Qu, Yun-Gui Yang, Feng Zhang, Guang-Hui Liu, Yiming Bao, Weiqi Zhang.
      Diverse individuals age at different rates and display variable susceptibilities to tissue aging, functional decline and aging-related diseases. Centenarians, exemplifying extreme longevity, serve as models for healthy aging. The field of human aging and longevity research is rapidly advancing, garnering significant attention and accumulating substantial data in recent years. Omics technologies, encompassing phenomics, genomics, transcriptomics, proteomics, metabolomics and microbiomics, have provided multidimensional insights and revolutionized cohort-based investigations into human aging and longevity. Accumulated data, covering diverse cells, tissues and cohorts across the lifespan necessitates the establishment of an open and integrated database. Addressing this, we established the Human Aging and Longevity Landscape (HALL), a comprehensive multi-omics repository encompassing a diverse spectrum of human cohorts, spanning from young adults to centenarians. The core objective of HALL is to foster healthy aging by offering an extensive repository of information on biomarkers that gauge the trajectory of human aging. Moreover, the database facilitates the development of diagnostic tools for aging-related conditions and empowers targeted interventions to enhance longevity. HALL is publicly available at https://ngdc.cncb.ac.cn/hall/index.
    DOI:  https://doi.org/10.1093/nar/gkad880
  71. bioRxiv. 2023 Oct 10. pii: 2023.10.06.561293. [Epub ahead of print]
    Cell autonomous role of leucine-rich repeat kinase in protection of dopaminergic neuron survival.
    Jongkyun Kang, Guodong Huang, Long Ma, Youren Tong, Phoenix Chen, Jie Shen.
      Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common genetic cause of Parkinson's disease (PD), which is the leading neurodegenerative movement disorder characterized by the progressive loss of dopaminergic (DA) neurons in the substantia nigra pars compacta (SNpc). However, whether LRRK2 mutations cause PD and degeneration of DA neurons via a toxic gain-of-function or a loss-of-function mechanism is unresolved and has pivotal implications in LRRK2 based PD therapy. In this study, we investigate whether LRRK2 and its functional homologue LRRK1 play an essential, intrinsic role in DA neuron survival through the development of DA neuron-specific LRRK conditional double knockout (cDKO) mice. We first generated and characterized floxed LRRK1 and LRRK2 mice and then confirmed that germline deletions of the floxed LRRK1 and LRRK2 alleles result in null alleles, as evidenced by the absence of LRRK1 and LRRK2 mRNA and protein in the respective homozygous deleted mutant mice. We further examined the specificity of Cre-mediated recombination driven by the dopamine transporter - Cre ( DAT-Cre ) knockin (KI) allele using a GFP reporter line and confirmed that DAT-Cre -mediated recombination is restricted to DA neurons in the SNpc. Crossing these validated floxed LRRK1 and LRRK2 mice with DAT-Cre KI mice, we then generated DA neuron-restricted LRRK cDKO mice and further showed reduced levels of LRRK1 and LRRK2 in dissected ventral midbrains of LRRK cDKO mice. While DA neuron-restricted LRRK cDKO mice of both sexes exhibit normal mortality and body weight, they develop age-dependent loss of DA neurons in the SNpc, as demonstrated by the progressive reduction of DA neurons in the SNpc of cDKO mice at 20 and 24 months of age. Moreover, DA neurodegeneration is accompanied with increases of apoptosis and elevated microgliosis in the SNpc of LRRK cDKO mice. These findings provide unequivocal evidence for the importance of LRRK in DA neurons and raise the possibility that LRRK2 mutations may impair its protection of DA neurons, leading to the loss of DA neurons in Parkinson's disease.
    DOI:  https://doi.org/10.1101/2023.10.06.561293
  72. Iran J Basic Med Sci. 2023 ;26(11): 1320-1325
    Evaluation of fisetin as a potential inducer of mitochondrial biogenesis in SH-SY5Y neuronal cells.
    Muhammet Ay.
       Objectives: Increasing evidence implicates impaired mitochondrial biogenesis as an important contributor to mitochondrial dysfunction, which plays a central role in the pathogenesis of neurodegenerative diseases including Parkinson's disease (PD). For this reason, targeting mitochondrial biogenesis may present a promising therapeutic strategy for PD. The present study attempted to investigate the effects of fisetin, a dietary flavonoid, on mitochondrial biogenesis and the expression of PD-associated genes in neuronal cells.
    Materials and Methods: The effects of fisetin on mitochondrial biogenesis were evaluated by three different approaches; PGC-1α and TFAM mRNA expressions by RT-qPCR, mitochondrial DNA (mtDNA) content by quantitative PCR and mitochondrial mass by MitoTracker staining. Next, a PCR array was performed to evaluate the effects of fisetin on the expression profile of PD-associated genes. Finally, the common targets of fisetin and PD were analyzed by in silico analyses.
    Results: The results demonstrated that fisetin treatment can increase PGC-1α and TFAM mRNA levels, mtDNA copy number, and mitochondrial mass in neuronal cells. Fisetin also altered the expressions of some PD-related genes involved in neuroprotection and neuronal differentiation. Moreover, the bioinformatics analyses suggested that the AKT1-GSK3B signaling might be responsible for the potential neuroprotective effects of fisetin.
    Conclusion: Collectively, these results imply that fisetin could modulate some neuroprotective mechanisms including mitochondrial biogenesis, and may serve as a potential drug candidate for PD.
    Keywords:  Fisetin; Mitochondria; PCR; Parkinson’s disease; SH-SY5Y; mtDNA
    DOI:  https://doi.org/10.22038/IJBMS.2023.72272.15714
  73. S Afr Med J. 2023 Aug 03. 113(8): 8
    Introducing the South African Rare Diseases Access Initiative.
    H Malherbe.
      
    DOI:  https://doi.org/10.7196/SAMJ.2023.v113i8.1142
  74. Proc Natl Acad Sci U S A. 2023 Oct 31. 120(44): e2311219120
    DNA language models are powerful predictors of genome-wide variant effects.
    Gonzalo Benegas, Sanjit Singh Batra, Yun S Song.
      The expanding catalog of genome-wide association studies (GWAS) provides biological insights across a variety of species, but identifying the causal variants behind these associations remains a significant challenge. Experimental validation is both labor-intensive and costly, highlighting the need for accurate, scalable computational methods to predict the effects of genetic variants across the entire genome. Inspired by recent progress in natural language processing, unsupervised pretraining on large protein sequence databases has proven successful in extracting complex information related to proteins. These models showcase their ability to learn variant effects in coding regions using an unsupervised approach. Expanding on this idea, we here introduce the Genomic Pre-trained Network (GPN), a model designed to learn genome-wide variant effects through unsupervised pretraining on genomic DNA sequences. Our model also successfully learns gene structure and DNA motifs without any supervision. To demonstrate its utility, we train GPN on unaligned reference genomes of Arabidopsis thaliana and seven related species within the Brassicales order and evaluate its ability to predict the functional impact of genetic variants in A. thaliana by utilizing allele frequencies from the 1001 Genomes Project and a comprehensive database of GWAS. Notably, GPN outperforms predictors based on popular conservation scores such as phyloP and phastCons. Our predictions for A. thaliana can be visualized as sequence logos in the UCSC Genome Browser (https://genome.ucsc.edu/s/gbenegas/gpn-arabidopsis). We provide code (https://github.com/songlab-cal/gpn) to train GPN for any given species using its DNA sequence alone, enabling unsupervised prediction of variant effects across the entire genome.
    Keywords:  Arabidopsis thaliana; genome-wide association study; language models; machine learning; variant effect prediction
    DOI:  https://doi.org/10.1073/pnas.2311219120
  75. Nat Commun. 2023 Oct 27. 14(1): 6598
    Lactate biosensors for spectrally and spatially multiplexed fluorescence imaging.
    Yusuke Nasu, Abhi Aggarwal, Giang N T Le, Camilla Trang Vo, Yuki Kambe, Xinxing Wang, Felix R M Beinlich, Ashley Bomin Lee, Tina R Ram, Fangying Wang, Kelsea A Gorzo, Yuki Kamijo, Marc Boisvert, Suguru Nishinami, Genki Kawamura, Takeaki Ozawa, Hirofumi Toda, Grant R Gordon, Shaoyu Ge, Hajime Hirase, Maiken Nedergaard, Marie-Eve Paquet, Mikhail Drobizhev, Kaspar Podgorski, Robert E Campbell.
      L-Lactate is increasingly appreciated as a key metabolite and signaling molecule in mammals. However, investigations of the inter- and intra-cellular dynamics of L-lactate are currently hampered by the limited selection and performance of L-lactate-specific genetically encoded biosensors. Here we now report a spectrally and functionally orthogonal pair of high-performance genetically encoded biosensors: a green fluorescent extracellular L-lactate biosensor, designated eLACCO2.1, and a red fluorescent intracellular L-lactate biosensor, designated R-iLACCO1. eLACCO2.1 exhibits excellent membrane localization and robust fluorescence response. To the best of our knowledge, R-iLACCO1 and its affinity variants exhibit larger fluorescence responses than any previously reported intracellular L-lactate biosensor. We demonstrate spectrally and spatially multiplexed imaging of L-lactate dynamics by coexpression of eLACCO2.1 and R-iLACCO1 in cultured cells, and in vivo imaging of extracellular and intracellular L-lactate dynamics in mice.
    DOI:  https://doi.org/10.1038/s41467-023-42230-5
  76. Proc Natl Acad Sci U S A. 2023 Oct 31. 120(44): e2315171120
    Localization of PPM1H phosphatase tunes Parkinson's disease-linked LRRK2 kinase-mediated Rab GTPase phosphorylation and ciliogenesis.
    Wondwossen M Yeshaw, Ayan Adhikari, Claire Y Chiang, Herschel S Dhekne, Paulina S Wawro, Suzanne R Pfeffer.
      PPM1H phosphatase reverses Parkinson's disease-associated, Leucine Rich Repeat Kinase 2-mediated Rab GTPase phosphorylation. We show here that PPM1H relies on an N-terminal amphipathic helix for Golgi localization. The amphipathic helix enables PPM1H to bind to liposomes in vitro, and small, highly curved liposomes stimulate PPM1H activity. We artificially anchored PPM1H to the Golgi, mitochondria, or mother centriole. Our data show that regulation of Rab10 GTPase phosphorylation requires PPM1H access to Rab10 at or near the mother centriole. Moreover, poor colocalization of Rab12 explains in part why it is a poor substrate for PPM1H in cells but not in vitro. These data support a model in which localization drives PPM1H substrate selection and centriolar PPM1H is critical for regulation of Rab GTPase-regulated ciliogenesis. Moreover, Golgi localized PPM1H may maintain active Rab GTPases on the Golgi to carry out their nonciliogenesis-related functions in membrane trafficking.
    Keywords:  LRRK2 kinase; Parkinson’s disease; Rab GTPase; phosphatase; primary cilia
    DOI:  https://doi.org/10.1073/pnas.2315171120
  77. medRxiv. 2023 Oct 16. pii: 2023.10.12.23296976. [Epub ahead of print]
    Large-scale characterization of gender differences in diagnosis prevalence and time to diagnosis.
    Tony Yue Sun, Jill Hardin, Harry Reyes Nieva, Karthik Natarajan, Ru-Fong Cheng, Patrick Ryan, Noémie Elhadad.
      We carry out an analysis of gender differences in patterns of disease diagnosis across four large observational health datasets and find that women are routinely older when first assigned most diagnoses. Among 112 acute and chronic diseases, women experience longer lengths of time between symptom onset and disease diagnosis than men for most diseases regardless of metric used, even when only symptoms common to both genders are considered. These findings are consistent for patients with private as well as government insurance. Our analysis highlights systematic gender differences in patterns of disease diagnosis and suggests that symptoms of disease are measured or weighed differently for women and men. Data and code leverage the open-source common data model and analytic code and results are publicly available.
    One-Sentence Summary: In large populations, across insurance coverage and many conditions, women are older than men when diagnosed and experience longer time to diagnosis.
    DOI:  https://doi.org/10.1101/2023.10.12.23296976
  78. Biochim Biophys Acta Gen Subj. 2023 Oct 21. pii: S0304-4165(23)00190-3. [Epub ahead of print]1867(12): 130492
    Screening for new inhibitors of the human Mitochondrial Pyruvate Carrier and their effects on hepatic glucose production and diabetes.
    Sébastien Herzig, Lingzi Li, Cecilia Jiménez-Sánchez, Jean-Claude Martinou, Pierre Maechler.
       BACKGROUND: The mitochondrial pyruvate carrier (MPC) is a protein complex composed of two subunits, MPC1 and MPC2. This carrier is at the interface between glycolysis and mitochondrial metabolism and plays an essential role in hepatic glucose production.
    METHODS: Here we describe an in vitro screen for small molecule inhibitors of the MPC using a strain of Lactococcus lactis that has been engineered to co-express the two subunits of the human MPC and is able to import exogenous 14C-pyruvate. We then tested the top candidates for potential antidiabetic effects through the repression of gluconeogenesis.
    RESULTS: By screening the Prestwick compound library of 1'200 drugs approved by the Food and Drug Administration for inhibitors of pyruvate uptake, twelve hit molecules were identified. In a secondary screen, the most potent inhibitors were found to inhibit pyruvate-driven oxygen consumption in mouse C2C12 muscle cells. Assessment of gluconeogenesis showed that Zaprinast, as well as the established MPC inhibitor UK5099, inhibited in vitro and in vivo hepatic glucose production. However, when tested acutely in mice without the administration of gluconeogenic substrates, MPC inhibitors raised blood glucose levels, pointing to liver-independent effects. Furthermore, chronic treatment with Zaprinast failed to correct hyperglycemia in both lean and obese diabetic mouse models.
    CONCLUSIONS: New MPC inhibitors have been identified, showing inhibitory effects on hepatic glucose production.
    GENERAL SIGNIFICANCE: For potential antidiabetic applications, MPC inhibitors should target the liver without undesired inhibition of mitochondrial pyruvate metabolism in the skeletal muscles or pancreatic beta-cells in order to avoid dual effects on glycemia.
    Keywords:  Diabetes; Drug screening; Gluconeogenesis; Inhibitor; Mitochondrial pyruvate carrier
    DOI:  https://doi.org/10.1016/j.bbagen.2023.130492
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