bims-mitdis 2022-11-06 papers

bims-mitdis

Biomed News

on Mitochondrial disorders

Issue of 2022–11–06
35 papers selected by
Catalina Vasilescu, Helmholz Munich

Mitochondrial Fission Process 1 controls inner membrane integrity and protects against heart failure.
A Heterozygous Mutation in MFF Associated with a Mild Mitochondrial Phenotype.
Mitochondrial disorders: Understanding mitochondrial DNA point mutations and deletion syndromes.
Whole-exome sequencing in 415,422 individuals identifies rare variants associated with mitochondrial DNA copy number.
Identification of evolutionarily conserved regulators of muscle mitochondrial network organization.
Mitochondrial DNA quality control in the female germline requires a unique programmed mitophagy.
Opa1-mediated mitochondrial dynamics is important for osteoclast differentiation.
Parkin regulates adiposity by coordinating mitophagy with mitochondrial biogenesis in white adipocytes.
The top 10 most frequently involved genes in hereditary optic neuropathies in 2186 probands.
Expansion Microscopy-based imaging for visualization of mitochondria in Drosophila ovarian germline stem cells.
Miro1 depletion disrupts spatial distribution of mitochondria and leads to oocyte maturation defects.
TMBIM5 is the Ca2+ /H+ antiporter of mammalian mitochondria.
Aminoacyl-tRNA synthetases in human health and disease.
Mitochondrial signal transduction.
V-ATPase/TORC1-mediated ATFS-1 translation directs mitochondrial UPR activation in C. elegans.
High-dose oral glutamine supplementation reduces elevated glutamate levels in CSF in patients with MELAS syndrome.
Combination of common mtDNA variants results in mitochondrial dysfunction and a connective tissue dysregulation.
Two sensory neurons coordinate the systemic mitochondrial stress response via GPCR signaling in C. elegans.
ATF5 is a regulator of exercise-induced mitochondrial quality control in skeletal muscle.
Improvement of large copy number variant detection by whole genome nanopore sequencing.
Reversal of mitochondrial malate dehydrogenase 2 enables anaplerosis via redox rescue in respiration-deficient cells.
NAD+ Therapeutics and Skeletal Muscle Adaptation to Exercise in Humans.
Cystathionine γ lyase S-sulfhydrates Drp1 to ameliorate heart dysfunction.
Single-cell spatial proteomic imaging for human neuropathology.
Established and emerging roles for mitochondria in neutrophils.
Site-specific CRISPR-based mitochondrial DNA manipulation is limited by gRNA import.
Astrocytic dysfunction induced by ABCA1 deficiency causes optic neuropathy.
Adipose tissue macrophages exert systemic metabolic control by manipulating local iron concentrations.
Nano-positioning and tubulin conformation contribute to axonal transport regulation of mitochondria along microtubules.
Mitochondrial Redox Signaling in Aging-Related Diseases--In Honor of Dr. Bruce N. Ames: A Pioneer in Mitochondrial Redox Signaling on Aging Research.
Care4Rare Canada: Outcomes from a decade of network science for rare disease gene discovery.
mitoSomatic: a tool for accurate identification of mitochondrial DNA somatic mutations without paired controls.
Ultrasensitive sensors reveal the spatiotemporal landscape of lactate metabolism in physiology and disease.
ENT characteristics and therapeutic results in multisystemic disorders of mitochondrial encephalomyopathy.
Strengthening the link between mitophagy and Parkinson's disease.

Nat Commun. 2022 Nov 04. 13(1): 6634

Mitochondrial Fission Process 1 controls inner membrane integrity and protects against heart failure.

Erminia Donnarumma, Michael Kohlhaas, Elodie Vimont, Etienne Kornobis, Thibault Chaze, Quentin Giai Gianetto, Mariette Matondo, Maryse Moya-Nilges, Christoph Maack, Timothy Wai.

Mitochondria are paramount to the metabolism and survival of cardiomyocytes. Here we show that Mitochondrial Fission Process 1 (MTFP1) is an inner mitochondrial membrane (IMM) protein that is dispensable for mitochondrial division yet essential for cardiac structure and function. Constitutive knockout of cardiomyocyte MTFP1 in mice resulted in a fatal, adult-onset dilated cardiomyopathy accompanied by extensive mitochondrial and cardiac remodeling during the transition to heart failure. Prior to the onset of disease, knockout cardiac mitochondria displayed specific IMM defects: futile proton leak dependent upon the adenine nucleotide translocase and an increased sensitivity to the opening of the mitochondrial permeability transition pore, with which MTFP1 physically and genetically interacts. Collectively, our data reveal new functions of MTFP1 in the control of bioenergetic efficiency and cell death sensitivity and define its importance in preventing pathogenic cardiac remodeling.

DOI: https://doi.org/10.1038/s41467-022-34316-3
J Neuromuscul Dis. 2022 Oct 28.

A Heterozygous Mutation in MFF Associated with a Mild Mitochondrial Phenotype.

Daisuke Murata, Christopher Grunseich, Miho Iijima, David Chan, Andrea Corse, Ahmet Hoke, Alice Schindler, Hiromi Sesaki, Ricardo H Roda.

   BACKGROUND: The number of mutations in nuclear encoded genes causing mitochondrial disease is ever increasing. Identification of these mutations is particularly important in the diagnosis of neuromuscular disorders as their presentation may mimic other acquired disorders.We present a novel heterozygous variant in mitochondrial fission factor (MFF) which mimics myasthenia gravis.
OBJECTIVE: To determine if the MFF c.937G>A, p.E313K variant causes a mild mitochondrial phenotype.
METHODS: We used whole exome sequencing (WES) to identify a novel heterozygous variant in MFF in a patient with ptosis, fatigue and muscle weakness. Using patient derived fibroblasts, we performed assays to evaluate mitochondrial and peroxisome dynamics.
RESULTS: We show that fibroblasts derived from this patient are defective in mitochondrial fission, despite normal recruitment of Drp1 to the mitochondria.
CONCLUSIONS: The MFF c.937G>A, p.E313K variant leads to a mild mitochondrial phenotype and is associated with defective mitochondrial fission in patient-derived fibroblasts.

Keywords:  MFF; Mitochondrial myopathies; mitochondrial dynamics; mitochondrial fission factor

DOI:  https://doi.org/10.3233/JND-221532
J Am Assoc Nurse Pract. 2022 Aug 01. 34(8): 954-956

Mitochondrial disorders: Understanding mitochondrial DNA point mutations and deletion syndromes.

Beth Heuer, Diane C Seibert.

ABSTRACT: Mitochondrial disorders arise from DNA mutations in either the mitochondrial DNA (mtDNA) or nuclear DNA genomes. This article focuses on a mtDNA base-pair mutation associated with neuropathy, ataxia, and retinitis pigmentosa and Leigh syndrome and the large-scale mtDNA deletion associated with Kearns-Sayre syndrome. Disease sequelae and management strategies are reviewed, along with implications for the nurse practitioner in primary or specialty care.

DOI: https://doi.org/10.1097/JXX.0000000000000755
HGG Adv. 2023 Jan 12. 4(1): 100147

Whole-exome sequencing in 415,422 individuals identifies rare variants associated with mitochondrial DNA copy number.

Vamsee Pillalamarri, Wen Shi, Conrad Say, Stephanie Yang, John Lane, Eliseo Guallar, Nathan Pankratz, Dan E Arking.

  Inter-individual variation in the number of copies of the mitochondrial genome, called mitochondrial DNA copy number (mtDNA-CN), reflects mitochondrial function and has been associated with various aging-related diseases. We examined 415,422 exomes of self-reported White ancestry individuals from the UK Biobank and tested the impact of rare variants, at the level of single variants and through aggregate variant-set tests, on mtDNA-CN. A survey across nine variant sets tested enrichment of putatively causal variants and identified 14 genes at experiment-wide significance and three genes at marginal significance. These included associations at known mtDNA depletion syndrome genes (mtDNA helicase TWNK, p = 1.1 × 10-30; mitochondrial transcription factor TFAM, p = 4.3 × 10-15; mtDNA maintenance exonuclease MGME1, p = 2.0 × 10-6) and the V617F dominant gain-of-function mutation in the tyrosine kinase JAK2 (p = 2.7 × 10-17), associated with myeloproliferative disease. Novel genes included the ATP-dependent protease CLPX (p = 8.4 × 10-9), involved in mitochondrial proteome quality, and the mitochondrial adenylate kinase AK2 (p = 4.7 × 10-8), involved in hematopoiesis. The most significant association was a missense variant in SAMHD1 (p = 4.2 × 10-28), found on a rare, 1.2-Mb shared ancestral haplotype on chromosome 20. SAMHD1 encodes a cytoplasmic host restriction factor involved in viral defense response and the mitochondrial nucleotide salvage pathway, and is associated with Aicardi-Goutières syndrome 5, a childhood encephalopathy and chronic inflammatory response disorder. Rare variants were enriched in Mendelian mtDNA depletion syndrome loci, and these variants implicated core processes in mtDNA replication, nucleoid structure formation, and maintenance. These data indicate that strong-effect mutations from the nuclear genome contribute to the genetic architecture of mtDNA-CN.

Keywords:  Mendelian mtDNA depletion syndrome; Mitochondria; exome sequencing; mtDNA copy number; rare haplotype sharing; rare variants

DOI:  https://doi.org/10.1016/j.xhgg.2022.100147
Nat Commun. 2022 Nov 04. 13(1): 6622

Identification of evolutionarily conserved regulators of muscle mitochondrial network organization.

Prasanna Katti, Peter T Ajayi, Angel Aponte, Christopher K E Bleck, Brian Glancy.

Mitochondrial networks provide coordinated energy distribution throughout muscle cells. However, pathways specifying mitochondrial networks are incompletely understood and it is unclear how they might affect contractile fiber-type. Here, we show that natural energetic demands placed on Drosophila melanogaster muscles yield native cell-types among which contractile and mitochondrial network-types are regulated differentially. Proteomic analyses of indirect flight, jump, and leg muscles, together with muscles misexpressing known fiber-type specification factor salm, identified transcription factors H15 and cut as potential mitochondrial network regulators. We demonstrate H15 operates downstream of salm regulating flight muscle contractile and mitochondrial network-type. Conversely, H15 regulates mitochondrial network configuration but not contractile type in jump and leg muscles. Further, we find that cut regulates salm expression in flight muscles and mitochondrial network configuration in leg muscles. These data indicate cell type-specific regulation of muscle mitochondrial network organization through evolutionarily conserved transcription factors cut, salm, and H15.

DOI: https://doi.org/10.1038/s41467-022-34445-9
Cell Metab. 2022 Nov 01. pii: S1550-4131(22)00456-9. [Epub ahead of print]34(11): 1809-1823.e6

Mitochondrial DNA quality control in the female germline requires a unique programmed mitophagy.

Jonathan M Palozzi, Swathi P Jeedigunta, Anastasia V Minenkova, Vernon L Monteiro, Zoe S Thompson, Toby Lieber, Thomas R Hurd.

  Mitochondria have their own DNA (mtDNA), which is susceptible to the accumulation of disease-causing mutations. To prevent deleterious mutations from being inherited, the female germline has evolved a conserved quality control mechanism that remains poorly understood. Here, through a large-scale screen, we uncover a unique programmed germline mitophagy (PGM) that is essential for mtDNA quality control. We find that PGM is developmentally triggered as germ cells enter meiosis by inhibition of the target of rapamycin complex 1 (TORC1). We identify a role for the RNA-binding protein Ataxin-2 (Atx2) in coordinating the timing of PGM with meiosis. We show that PGM requires the mitophagy receptor BNIP3, mitochondrial fission and translation factors, and members of the Atg1 complex, but not the mitophagy factors PINK1 and Parkin. Additionally, we report several factors that are critical for germline mtDNA quality control and show that pharmacological manipulation of one of these factors promotes mtDNA quality control.

Keywords:  autophagy; germ line; germline; mitochondria; mitochondrial DNA; mitophagy; mtDNA; purifying selection; quality control

DOI:  https://doi.org/10.1016/j.cmet.2022.10.005
MicroPubl Biol. 2022 ;2022

Opa1-mediated mitochondrial dynamics is important for osteoclast differentiation.

Keizo Nishikawa, Hina Takegami, Hiromi Sesaki.

Opatic atrophy 1 (Opa1) is a mitochondrial GTPase that regulates mitochondrial fusion and maintenance of cristae architecture. Osteoclasts are mitochondrial rich-cells. However, the role of Opa1 in osteoclasts remains unclear. Here, we demonstrate that Opa1- deficient osteoclast precursor cells do not undergo efficient osteoclast differentiation and exhibit abnormal cristae morphology. Thus, Opa1 is a key factor in osteoclast differentiation through regulation of mitochondrial dynamics.

DOI: https://doi.org/10.17912/micropub.biology.000650
Nat Commun. 2022 Nov 04. 13(1): 6661

Parkin regulates adiposity by coordinating mitophagy with mitochondrial biogenesis in white adipocytes.

Timothy M Moore, Lijing Cheng, Dane M Wolf, Jennifer Ngo, Mayuko Segawa, Xiaopeng Zhu, Alexander R Strumwasser, Yang Cao, Bethan L Clifford, Alice Ma, Philip Scumpia, Orian S Shirihai, Thomas Q de Aguiar Vallim, Markku Laakso, Aldons J Lusis, Andrea L Hevener, Zhenqi Zhou.

Parkin, an E3 ubiquitin ligase, plays an essential role in mitochondrial quality control. However, the mechanisms by which Parkin connects mitochondrial homeostasis with cellular metabolism in adipose tissue remain unclear. Here, we demonstrate that Park2 gene (encodes Parkin) deletion specifically from adipose tissue protects mice against high-fat diet and aging-induced obesity. Despite a mild reduction in mitophagy, mitochondrial DNA content and mitochondrial function are increased in Park2 deficient white adipocytes. Moreover, Park2 gene deletion elevates mitochondrial biogenesis by increasing Pgc1α protein stability through mitochondrial superoxide-activated NAD(P)H quinone dehydrogenase 1 (Nqo1). Both in vitro and in vivo studies show that Nqo1 overexpression elevates Pgc1α protein level and mitochondrial DNA content and enhances mitochondrial activity in mouse and human adipocytes. Taken together, our findings indicate that Parkin regulates mitochondrial homeostasis by balancing mitophagy and Pgc1α-mediated mitochondrial biogenesis in white adipocytes, suggesting a potential therapeutic target in adipocytes to combat obesity and obesity-associated disorders.

DOI: https://doi.org/10.1038/s41467-022-34468-2
Brain. 2022 Nov 01. pii: awac395. [Epub ahead of print]

The top 10 most frequently involved genes in hereditary optic neuropathies in 2186 probands.

HON Collaborators Group

  Hereditary optic neuropathies are caused by the degeneration of retinal ganglion cells whose axons form the optic nerves, with a consistent genetic heterogeneity. As part of our diagnostic activity, we retrospectively evaluated the combination of Leber hereditary optic neuropathy mutations testing with the exon sequencing of 87 nuclear genes on 2,186 patients referred for suspected hereditary optic neuropathies. The positive diagnosis rate in individuals referred for Leber hereditary optic neuropathy testing was 18% (199/1,126 index cases), with 92% (184/199) carrying one of the three main pathogenic variants of mitochondrial DNA (m.11778G > A, 66.5%; m.3460G > A, 15% and m.14484T > C, 11%). The positive diagnosis rate in individuals referred for autosomal dominant or recessive optic neuropathies was 27% (451/1,680 index cases), with 10 genes accounting together for 96% of this cohort. This represents an overall positive diagnostic rate of 30%. The identified top 10 nuclear genes included OPA1, WFS1, ACO2, SPG7, MFN2, AFG3L2, RTN4IP1, TMEM126A, NR2F1 and FDXR. Eleven additional genes, each accounting for less than 1% of cases, were identified in 17 individuals. Our results show that 10 major genes account for more than 96% of the cases diagnosed with our nuclear gene panel.

Keywords:  Leber hereditary optic neuropathy; dominant optic atrophy; hereditary optic neuropathy; mitochondrial DNA; recessive optic atrophy

DOI:  https://doi.org/10.1093/brain/awac395
FEBS Open Bio. 2022 Nov 04.

Expansion Microscopy-based imaging for visualization of mitochondria in Drosophila ovarian germline stem cells.

Lin Chi-Hung, Tzu-Yang Lin, Shao-Chun Hsu, Hwei-Jan-Hsu.

  Recent studies have shown that mitochondrial morphology can modulate organelle function and greatly affect stem cell behavior, thus affecting tissue homeostasis. As such, we previously showed that the accumulation of fragmented mitochondria in aged Drosophila ovarian germline stem cells (GSCs) contributes to age-dependent GSC loss. However, standard immunofluorescence methods to examine mitochondrial morphology yield images with insufficient resolution for rigorous analysis, while 3-dimensional electron microscopy examination of mitochondrial morphology is labor intensive and allows only limited sampling of mitochondria. To overcome these issues, we utilized the Expansion Microscopy (ExM) technique to expand GSC samples by 4-fold in combination with mitochondrial immunofluorescence labeling. Here, we present a simple, inexpensive method for nanoscale optical imaging of mitochondria in the germline. This protocol may be beneficial for studies that require visualization of mitochondria or other fine subcellular structures in the Drosophila ovary.

Keywords:  Drosophila; ExM; Expansion Microscopy; GSC; mitochondria; ovary

DOI:  https://doi.org/10.1002/2211-5463.13506
Front Cell Dev Biol. 2022 ;10 986454

Miro1 depletion disrupts spatial distribution of mitochondria and leads to oocyte maturation defects.

In-Won Lee, Deepak Adhikari, John Carroll.

  Mitochondria are dynamic organelles that undergo regulated microtubule- and actin-mediated trafficking to meet local energy and metabolic needs. Mitochondrial trafficking may be particularly critical in large cells such as eggs and early embryos where spindle formation and polar body extrusion occur in specific regions of the cytoplasm. To investigate the role of mitochondrial distribution in oocytes we have targeted the mitochondrial membrane protein, MIRO1, which couples mitochondria to the motor protein-TRAK complex. Oocyte-specific deletion of MIRO1 leads to the formation of large aggregates of mitochondria in perinuclear and cortical compartments. Mitochondria remain capable of long-range trafficking during maturation, indicating redundancy in the mechanisms coupling mitochondria to motor proteins. Polar body extrusion in the absence of MIRO1 was reduced by approximately 20%. In MIRO1-deleted zygotes, mitochondria showed increased accumulation around the pronuclei but this did not affect mitochondrial distribution to daughter blastomeres. In vitro development of parthenogenetic embryos was also reduced, although no differences were found in the fertility of oocyte-specific Miro1 KO mice. These findings demonstrate MIRO1 acts as a mitochondrial adaptor, setting mitochondrial distribution in oocytes and early embryos, and disrupting this process compromises in vitro oocyte maturation and embryo development.

Keywords:  Miro1; embryo development; mitochondrial adaptor protein; mitochondrial transport; oocyte

DOI:  https://doi.org/10.3389/fcell.2022.986454
EMBO Rep. 2022 Nov 02. e54978

TMBIM5 is the Ca2+ /H+ antiporter of mammalian mitochondria.

Shane Austin, Ronald Mekis, Sami E M Mohammed, Mariafrancesca Scalise, Wen-An Wang, Michele Galluccio, Christina Pfeiffer, Tamara Borovec, Katja Parapatics, Dijana Vitko, Nora Dinhopl, Nicolas Demaurex, Keiryn L Bennett, Cesare Indiveri, Karin Nowikovsky.

  Mitochondrial Ca2+ ions are crucial regulators of bioenergetics and cell death pathways. Mitochondrial Ca2+ content and cytosolic Ca2+ homeostasis strictly depend on Ca2+ transporters. In recent decades, the major players responsible for mitochondrial Ca2+ uptake and release have been identified, except the mitochondrial Ca2+ /H+ exchanger (CHE). Originally identified as the mitochondrial K+ /H+ exchanger, LETM1 was also considered as a candidate for the mitochondrial CHE. Defining the mitochondrial interactome of LETM1, we identify TMBIM5/MICS1, the only mitochondrial member of the TMBIM family, and validate the physical interaction of TMBIM5 and LETM1. Cell-based and cell-free biochemical assays demonstrate the absence or greatly reduced Na+ -independent mitochondrial Ca2+ release in TMBIM5 knockout or pH-sensing site mutants, respectively, and pH-dependent Ca2+ transport by recombinant TMBIM5. Taken together, we demonstrate that TMBIM5, but not LETM1, is the long-sought mitochondrial CHE, involved in setting and regulating the mitochondrial proton gradient. This finding provides the final piece of the puzzle of mitochondrial Ca2+ transporters and opens the door to exploring its importance in health and disease, and to developing drugs modulating Ca2+ exchange.

Keywords:  LETM1; TMBIM5 (MICS1); mitochondrial Ca2+-H+ exchanger; mitochondrial metabolism; permeability transition pore

DOI:  https://doi.org/10.15252/embr.202254978
Front Physiol. 2022 ;13 1029218

Aminoacyl-tRNA synthetases in human health and disease.

Alexandra K Turvey, Gabriella A Horvath, André R O Cavalcanti.

  The Aminoacyl-tRNA Synthetases (aaRSs) are an evolutionarily ancient family of enzymes that catalyze the esterification reaction linking a transfer RNA (tRNA) with its cognate amino acid matching the anticodon triplet of the tRNA. Proper functioning of the aaRSs to create aminoacylated (or "charged") tRNAs is required for efficient and accurate protein synthesis. Beyond their basic canonical function in protein biosynthesis, aaRSs have a surprisingly diverse array of non-canonical functions that are actively being defined. The human genome contains 37 genes that encode unique aaRS proteins. To date, 56 human genetic diseases caused by damaging variants in aaRS genes have been described: 46 are autosomal recessive biallelic disorders and 10 are autosomal dominant monoallelic disorders. Our appreciation of human diseases caused by damaging genetic variants in the aaRSs has been greatly accelerated by the advent of next-generation sequencing, with 89% of these gene discoveries made since 2010. In addition to these genetic disorders of the aaRSs, anti-synthetase syndrome (ASSD) is a rare autoimmune inflammatory myopathy that involves the production of autoantibodies that disrupt aaRS proteins. This review provides an overview of the basic biology of aaRS proteins and describes the rapidly growing list of human diseases known to be caused by genetic variants or autoimmune targeting that affect both the canonical and non-canonical functions of these essential proteins.

Keywords:  aminoacyl-tRNA synthetases (aaRSs); charcot-marie-tooth (CMT) disease; genetic diseases; human health; rare disease

DOI:  https://doi.org/10.3389/fphys.2022.1029218
Cell Metab. 2022 Nov 01. pii: S1550-4131(22)00459-4. [Epub ahead of print]34(11): 1620-1653

Mitochondrial signal transduction.

Martin Picard, Orian S Shirihai.

  The analogy of mitochondria as powerhouses has expired. Mitochondria are living, dynamic, maternally inherited, energy-transforming, biosynthetic, and signaling organelles that actively transduce biological information. We argue that mitochondria are the processor of the cell, and together with the nucleus and other organelles they constitute the mitochondrial information processing system (MIPS). In a three-step process, mitochondria (1) sense and respond to both endogenous and environmental inputs through morphological and functional remodeling; (2) integrate information through dynamic, network-based physical interactions and diffusion mechanisms; and (3) produce output signals that tune the functions of other organelles and systemically regulate physiology. This input-to-output transformation allows mitochondria to transduce metabolic, biochemical, neuroendocrine, and other local or systemic signals that enhance organismal adaptation. An explicit focus on mitochondrial signal transduction emphasizes the role of communication in mitochondrial biology. This framework also opens new avenues to understand how mitochondria mediate inter-organ processes underlying human health.

Keywords:  amplification; communication; energy; evolution; health; membrane potential; metabokines; mito-nuclear signaling; mitochondrial networks; mitokines; mitotypes; receptors; signal transduction; steroid hormones; stress responses; tissue-specific

DOI:  https://doi.org/10.1016/j.cmet.2022.10.008
J Cell Biol. 2023 Jan 02. pii: e202205045. [Epub ahead of print]222(1):

V-ATPase/TORC1-mediated ATFS-1 translation directs mitochondrial UPR activation in C. elegans.

Terytty Yang Li, Arwen W Gao, Xiaoxu Li, Hao Li, Yasmine J Liu, Amelia Lalou, Nagammal Neelagandan, Felix Naef, Kristina Schoonjans, Johan Auwerx.

To adapt mitochondrial function to the ever-changing intra- and extracellular environment, multiple mitochondrial stress response (MSR) pathways, including the mitochondrial unfolded protein response (UPRmt), have evolved. However, how the mitochondrial stress signal is sensed and relayed to UPRmt transcription factors, such as ATFS-1 in Caenorhabditis elegans, remains largely unknown. Here, we show that a panel of vacuolar H+-ATPase (v-ATPase) subunits and the target of rapamycin complex 1 (TORC1) activity are essential for the cytosolic relay of mitochondrial stress to ATFS-1 and for the induction of the UPRmt. Mechanistically, mitochondrial stress stimulates v-ATPase/Rheb-dependent TORC1 activation, subsequently promoting ATFS-1 translation. Increased translation of ATFS-1 upon mitochondrial stress furthermore relies on a set of ribosomal components but is independent of GCN-2/PEK-1 signaling. Finally, the v-ATPase and ribosomal subunits are required for mitochondrial surveillance and mitochondrial stress-induced longevity. These results reveal a v-ATPase-TORC1-ATFS-1 signaling pathway that links mitochondrial stress to the UPRmt through intimate crosstalks between multiple organelles.

DOI: https://doi.org/10.1083/jcb.202205045
Eur J Neurol. 2022 Nov 05.

High-dose oral glutamine supplementation reduces elevated glutamate levels in CSF in patients with MELAS syndrome.

María Paz Guerrero-Molina, Montserrat Morales-Conejo, Aitor Delmiro, María Morán, Cristina Domínguez-González, Elena Arranz-Canales, Ana Ramos-González, Joaquín Arenas, Miguel A Martín, Jesús González de la Aleja.

   BACKGROUND AND OBJECTIVES: Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) syndrome is a genetically heterogeneous disorder caused by mitochondrial DNA mutations. There are no disease-modifying therapies, and treatment remains mainly supportive. We previously showed that patients with MELAS syndrome had significantly increased CSF glutamate and significantly decreased CSF glutamine levels compared to controls. Glutamine has many metabolic fates in neurons and astrocytes, and the glutamate-glutamine cycle couples with many metabolic pathways depending on cellular requirements. We aimed to compare CSF glutamate and glutamine levels before and after dietary glutamine supplementation. We postulated that high-dose oral glutamine supplementation could reduce the increase in glutamate levels.
METHODS: This open-label, single-cohort study determined the safety and changes in glutamate and glutamine levels in CSF after twelve weeks of oral glutamine supplementation.
RESULTS: Nine adult patients with MELAS syndrome (66.7% females, mean age 35.8 ± 3.2 years) were included. After glutamine supplementation, CSF glutamate levels were significantly reduced (9.77 ± 1.21 vs. 18.48 ± 1.34 μmol/L, p <0.001), and CSF glutamine levels were significantly increased (433.66 ± 15.31 vs. 336.31 ± 12.92 μmol/L, p=0.002). A side effect observed in four of nine patients was a mild sensation of satiety. One patient developed mild and transient elevation of transaminases, and another patient was admitted for an epileptic status without stroke-like episode.
DISCUSSION: This study demonstrates that high-dose oral glutamine supplementation significantly reduces CSF glutamate and increases CSF glutamine levels in patients with MELAS syndrome. These findings may have potential therapeutic implications in these patients.

Keywords:  Glutamate; Glutamine supplementation; MELAS syndrome; Mitochondrial disease

DOI:  https://doi.org/10.1111/ene.15626
Proc Natl Acad Sci U S A. 2022 Nov 08. 119(45): e2212417119

Combination of common mtDNA variants results in mitochondrial dysfunction and a connective tissue dysregulation.

Patrick M Schaefer, Leonardo Scherer Alves, Maria Lvova, Jessica Huang, Komal Rathi, Kevin Janssen, Arrienne Butic, Tal Yardeni, Ryan Morrow, Marie Lott, Deborah Murdock, Angela Song, Kierstin Keller, Benjamin A Garcia, Clair A Francomano, Douglas C Wallace.

  Mitochondrial dysfunction can be associated with a range of clinical manifestations. Here, we report a family with a complex phenotype including combinations of connective tissue, neurological, and metabolic symptoms that were passed on to all surviving children. Analysis of the maternally inherited mtDNA revealed a novel genotype encompassing the haplogroup J - defining mitochondrial DNA (mtDNA) ND5 m.13708G>A (A458T) variant arising on the mtDNA haplogroup H7A background, an extremely rare combination. Analysis of transmitochondrial cybrids with the 13708A-H7 mtDNA revealed a lower mitochondrial respiration, increased reactive oxygen species production (mROS), and dysregulation of connective tissue gene expression. The mitochondrial dysfunction was exacerbated by histamine, explaining why all eight surviving children inherited the dysfunctional histidine decarboxylase allele (W327X) from the father. Thus, certain combinations of common mtDNA variants can cause mitochondrial dysfunction, mitochondrial dysfunction can affect extracellular matrix gene expression, and histamine-activated mROS production can augment the severity of mitochondrial dysfunction. Most important, we have identified a previously unreported genetic cause of mitochondrial disorder arising from the incompatibility of common, nonpathogenic mtDNA variants.

Keywords:  connective tissue disorder; histamine signaling; mitochondrial disorder; mtDNA haplogroups

DOI:  https://doi.org/10.1073/pnas.2212417119
Dev Cell. 2022 Oct 25. pii: S1534-5807(22)00720-1. [Epub ahead of print]

Two sensory neurons coordinate the systemic mitochondrial stress response via GPCR signaling in C. elegans.

Yangli Liu, Jun Zhou, Ning Zhang, Xueying Wu, Qian Zhang, Wenfeng Zhang, Xinyu Li, Ye Tian.

  Mitochondrial perturbations within neurons communicate stress signals to peripheral tissues, coordinating organismal-wide mitochondrial homeostasis for optimal fitness. However, the neuronal control of the systemic stress regulation remains poorly understood. Here, we identified a G-protein-coupled receptor (GPCR), SRZ-75, that couples with Gαq signaling in a pair of chemosensory ADL neurons to drive the mitochondrial unfolded protein response (UPRmt) activation in the intestine via the release of neuropeptides in Caenorhabditis elegans. Constitutive activation of Gαq signaling in the ADL neurons is sufficient to induce the intestinal UPRmt, leading to increased stress resistance and metabolic adaptations. Ablation of ADL neurons attenuates the intestinal UPRmt activation in response to various forms of neuronal mitochondrial dysfunction. Thus, GPCR and its Gαq downstream signaling in two sensory neurons coordinate the systemic UPRmt activation, representing a previously uncharacterized, but potentially conserved, neuronal signaling for organismal-wide mitochondrial stress regulation.

Keywords:  ADL chemosensory neurons; G-protein-coupled receptor; GPCR; Gαq signaling; SRZ-75; UPR(mt); cell-non-autonomous regulation; the mitochondrial unfolded protein response

DOI:  https://doi.org/10.1016/j.devcel.2022.10.001
Mol Metab. 2022 Nov 01. pii: S2212-8778(22)00192-2. [Epub ahead of print] 101623

ATF5 is a regulator of exercise-induced mitochondrial quality control in skeletal muscle.

Mikhaela B Slavin, Rita Kumari, David A Hood.

   OBJECTIVES: The Mitochondrial Unfolded Protein Response (UPRmt) is a compartment-specific mitochondrial quality control (MQC) mechanism that uses the transcription factor ATF5 to induce the expression of protective enzymes to restore mitochondrial function. Acute exercise is a stressor that has the potential to temporarily disrupt organellar protein homeostasis, however, the roles of ATF5 and the UPRmt in maintaining basal mitochondrial content, function and exercise-induced MQC mechanisms in skeletal muscle are not known.
METHODS: ATF5 KO and WT mice were examined at rest or after a bout of acute endurance exercise. We measured protein content in whole muscle, nuclear, cytosolic and mitochondrial fractions, in addition to mRNA transcript levels in whole muscle. Using isolated mitochondria, we quantified rates of oxygen consumption and ROS emission to observe the effects of the absence of ATF5 on organelle function.
RESULTS: ATF5 KO mice exhibited a larger and less functional muscle mitochondrial pool, most likely a culmination of enhanced biogenesis via increased PGC-1 α expression, and attenuated mitophagy. The absence of ATF5 resulted in a reduction in antioxidant proteins and increases in mitochondrial ROS emission, cytosolic cytochrome c, and the expression of mitochondrial chaperones. KO muscle also displayed enhanced exercise-induced stress kinase signaling, but a blunted mitophagic and UPRmt gene expression response, complemented by significant increases in the basal mRNA abundance and nuclear localization of ATF4. Instead of promoting its nuclear translocation, acute exercise caused the enrichment of ATF5 in mitochondrial fractions. We also identified PGC-1 α as an additional regulator of the basal expression of UPRmt genes.
CONCLUSION: The transcription factor ATF5 retains a critical role in the maintenance of mitochondrial homeostasis and the appropriate response of muscle to acute exercise for the optimization of mitochondrial quality control.

Keywords:  Exercise; Mitochondria; Mitochondrial Quality Control; Mitochondrial Unfolded Protein Response (UPR(mt)); Protein Homeostasis; Skeletal Muscle

DOI:  https://doi.org/10.1016/j.molmet.2022.101623
J Adv Res. 2022 Oct 30. pii: S2090-1232(22)00241-7. [Epub ahead of print]

Improvement of large copy number variant detection by whole genome nanopore sequencing.

Javier Cuenca-Guardiola, Belén de la Morena-Barrio, Juan L García, Alba Sanchis-Juan, Javier Corral, Jesualdo T Fernández-Breis.

   INTRODUCTION: Whole-genome sequencing using nanopore technologies can uncover structural variants, which are DNA rearrangements larger than 50 base pairs. Nanopore technologies can also characterize their boundaries with single-base accuracy, owing to the kilobase-long reads that encompass either full variants or their junctions. Other methods, such as next-generation short read sequencing or PCR assays, are limited in their capabilities to detect or characterize structural variants. However, the existing software for nanopore sequencing data analysis still reports incomplete variant sets, which also contain erroneous calls, a considerable obstacle for the molecular diagnosis or accurate genotyping of populations.
METHODS: We compared multiple factors affecting variant calling, such as reference genome version, aligner (minimap2, NGMLR, and lra) choice, and variant caller combinations (Sniffles, CuteSV, SVIM, and NanoVar), to find the optimal group of tools for calling large (>50 kb) deletions and duplications, using data from seven patients exhibiting gross gene defects on SERPINC1 and from a reference variant set as the control. The goal was to obtain the most complete, yet reasonably specific group of large variants using a single cell of PromethION sequencing, which yielded lower depth coverage than short-read sequencing. We also used a custom method for the statistical analysis of the coverage value to refine the resulting datasets.
RESULTS: We found that for large deletions and duplications (>50 kb), the existing software performed worse than for smaller ones, in terms of both sensitivity and specificity, and newer tools had not improved this. Our novel software, disCoverage, could polish variant callers' results, improving specificity by up to 62% and sensitivity by 15%, the latter requiring other data or samples.
CONCLUSION: We analyzed the current situation of >50-kb copy number variants with nanopore sequencing, which could be improved. The methods presented in this work could help to identify the known deletions and duplications in a set of patients, while also helping to filter out erroneous calls for these variants, which might aid the efforts to characterize a not-yet well-known fraction of genetic variability in the human genome.

Keywords:  SERPINC1; nanopore; structural variant; third-generation sequencing

DOI:  https://doi.org/10.1016/j.jare.2022.10.012
Mol Cell. 2022 Oct 31. pii: S1097-2765(22)00962-5. [Epub ahead of print]

Reversal of mitochondrial malate dehydrogenase 2 enables anaplerosis via redox rescue in respiration-deficient cells.

Patricia Altea-Manzano, Anke Vandekeere, Joy Edwards-Hicks, Mar Roldan, Emily Abraham, Xhordi Lleshi, Ania Naila Guerrieri, Domenica Berardi, Jimi Wills, Jair Marques Junior, Asimina Pantazi, Juan Carlos Acosta, Rosario M Sanchez-Martin, Sarah-Maria Fendt, Miguel Martin-Hernandez, Andrew J Finch.

  Inhibition of the electron transport chain (ETC) prevents the regeneration of mitochondrial NAD+, resulting in cessation of the oxidative tricarboxylic acid (TCA) cycle and a consequent dependence upon reductive carboxylation for aspartate synthesis. NAD+ regeneration alone in the cytosol can rescue the viability of ETC-deficient cells. Yet, how this occurs and whether transfer of oxidative equivalents to the mitochondrion is required remain unknown. Here, we show that inhibition of the ETC drives reversal of the mitochondrial aspartate transaminase (GOT2) as well as malate and succinate dehydrogenases (MDH2 and SDH) to transfer oxidative NAD+ equivalents into the mitochondrion. This supports the NAD+-dependent activity of the mitochondrial glutamate dehydrogenase (GDH) and thereby enables anaplerosis-the entry of glutamine-derived carbon into the TCA cycle and connected biosynthetic pathways. Thus, under impaired ETC function, the cytosolic redox state is communicated into the mitochondrion and acts as a rheostat to support GDH activity and cell viability.

Keywords:  anaplerosis; cancer; cancer metabolism; metabolism; mitochondrion; redox; redox transfer; respiration

DOI:  https://doi.org/10.1016/j.molcel.2022.10.005
Sports Med. 2022 Nov 04.

NAD+ Therapeutics and Skeletal Muscle Adaptation to Exercise in Humans.

Dean Campelj, Andrew Philp.

Nicotinamide adenine dinucleotide (NAD+) is a vital energy intermediate in skeletal muscle. The discovery of dietary-derived NAD+ precursors has led to the rapid development of NAD+ therapeutics designed to manipulate NAD+ content in target tissues. Of those developed, nicotinamide riboside and nicotinamide mononucleotide have been reported to display health benefit in humans under clinical scenarios of NAD+ deficiency. In contrast, relatively little is known regarding the potential benefit of nicotinamide riboside and nicotinamide mononucleotide supplementation in healthy individuals, with questions remaining as to whether NAD+ therapeutics can be used to support training adaptation or improve performance in athletic populations. Examining animal and human nicotinamide riboside supplementation studies, this review discusses current evidence suggesting that NAD+ therapeutics do not alter skeletal muscle metabolism or improve athletic performance in healthy humans. Further, we will highlight potential reasons why nicotinamide riboside supplementation studies do not translate to healthy populations and discuss the futility of testing NAD+ therapeutics outside of the clinical populations where NAD+ deficiency is present.

DOI: https://doi.org/10.1007/s40279-022-01772-2
Redox Biol. 2022 Oct 28. pii: S2213-2317(22)00291-9. [Epub ahead of print]58 102519

Cystathionine γ lyase S-sulfhydrates Drp1 to ameliorate heart dysfunction.

Dan Wu, Bo Tan, Yuanyuan Sun, Qingxun Hu.

  Hydrogen sulfide (H2S), produced by cystathionine γ lyase (CSE), is an important endogenous gasotransmitter to maintain heart function. However, the molecular mechanism for how H2S influences the mitochondrial morphology during heart failure remains poorly understood. Here, we found that CSE/H2S pathway mediated cardiac function and mitochondrial morphology through regulating dynamin related protein 1 (Drp1) activity and translocation. Mechanistically, elevation of H2S levels by CSE overexpression declined protein level, phosphorylation (Ser 616), oligomerization and GTPase activity of Drp1 by S-sulfhydration in mouse hearts. Interestingly, Drp1 S-sulfhydration directly competed with S-nitrosylation by nitric oxide at the specific cysteine 607. The non-S-sulfhydration of Drp1 mutation (C607A) attenuated the regulatory effect of H2S on Drp1 activation, mitochondrial fission and heart function. Moreover, the non-canonical role of Drp1 mediated isoprenaline-induced mitochondrial dysfunction and cardiomyocyte death through interaction with voltage-dependent anion channel 1. These results uncover that a novel mechanism that H2S S-sulfhydrated Drp1 at cysteine 607 to prevent heart failure through modulating its activity and mitochondrial translocation. Our findings also provide initial evidence demonstrating that Drp1 may be a critical regulator as well as an effective strategy for heart dysfunction.

Keywords:  Dynamin related protein 1; Heart failure; Hydrogen sulfide; Mitochondrial fission; S-Sulfhydration

DOI:  https://doi.org/10.1016/j.redox.2022.102519
Acta Neuropathol Commun. 2022 Nov 04. 10(1): 158

Single-cell spatial proteomic imaging for human neuropathology.

Kausalia Vijayaragavan, Bryan J Cannon, Dmitry Tebaykin, Marc Bossé, Alex Baranski, J P Oliveria, Syed A Bukhari, Dunja Mrdjen, M Ryan Corces, Erin F McCaffrey, Noah F Greenwald, Yari Sigal, Diana Marquez, Zumana Khair, Trevor Bruce, Mako Goldston, Anusha Bharadwaj, Kathleen S Montine, R Michael Angelo, Thomas J Montine, Sean C Bendall.

Neurodegenerative disorders are characterized by phenotypic changes and hallmark proteopathies. Quantifying these in archival human brain tissues remains indispensable for validating animal models and understanding disease mechanisms. We present a framework for nanometer-scale, spatial proteomics with multiplex ion beam imaging (MIBI) for capturing neuropathological features. MIBI facilitated simultaneous, quantitative imaging of 36 proteins on archival human hippocampus from individuals spanning cognitively normal to dementia. Customized analysis strategies identified cell types and proteopathies in the hippocampus across stages of Alzheimer's disease (AD) neuropathologic change. We show microglia-pathologic tau interactions in hippocampal CA1 subfield in AD dementia. Data driven, sample independent creation of spatial proteomic regions identified persistent neurons in pathologic tau neighborhoods expressing mitochondrial protein MFN2, regardless of cognitive status, suggesting a survival advantage. Our study revealed unique insights from multiplexed imaging and data-driven approaches for neuropathologic analysis and serves broadly as a methodology for spatial proteomic analysis of archival human neuropathology. TEASER: Multiplex Ion beam Imaging enables deep spatial phenotyping of human neuropathology-associated cellular and disease features.

DOI: https://doi.org/10.1186/s40478-022-01465-x
Immunol Rev. 2022 Nov 04.

Established and emerging roles for mitochondria in neutrophils.

Shuang Peng, Jian Gao, Darko Stojkov, Shida Yousefi, Hans-Uwe Simon.

  Neutrophils are the most abundant innate immune cells in human blood, emerging as important players in a variety of diseases. Mitochondria are bioenergetic, biosynthetic, and signaling organelles critical for cell fate and function. Mitochondria have been overlooked in neutrophil research owing to the conventional view that neutrophils contain few, if any, competent mitochondria and do not rely on these organelles for adenosine triphosphate production. A growing body of evidence suggests that mitochondria participate in neutrophil biology at many levels, ranging from neutrophil development to chemotaxis, effector function, and cell death. Moreover, mitochondria and mitochondrial components, such as mitochondrial deoxyribonucleic acid, can be released by neutrophils to eliminate infection and/or shape immune response, depending on the specific context. In this review, we provide an update on the functional role of mitochondria in neutrophils, highlight mitochondria as key players in modulating the neutrophil phenotype and function during infection and inflammation, and discuss the possibilities and challenges to exploit the unique aspects of mitochondria in neutrophils for disease treatment.

Keywords:  immune response; infection; inflammation; mitochondria; neutrophils

DOI:  https://doi.org/10.1111/imr.13158
Sci Rep. 2022 Nov 04. 12(1): 18687

Site-specific CRISPR-based mitochondrial DNA manipulation is limited by gRNA import.

Ludwig Schmiderer, David Yudovich, Leal Oburoglu, Martin Hjort, Jonas Larsson.

Achieving CRISPR Cas9-based manipulation of mitochondrial DNA (mtDNA) has been a long-standing goal and would be of great relevance for disease modeling and for clinical applications. In this project, we aimed to deliver Cas9 into the mitochondria of human cells and analyzed Cas9-induced mtDNA cleavage and measured the resulting mtDNA depletion with multiplexed qPCR. In initial experiments, we found that measuring subtle effects on mtDNA copy numbers is challenging because of high biological variability, and detected no significant Cas9-caused mtDNA degradation. To overcome the challenge of being able to detect Cas9 activity on mtDNA, we delivered cytosine base editor Cas9-BE3 to mitochondria and measured its effect (C → T mutations) on mtDNA. Unlike regular Cas9-cutting, this leaves a permanent mark on mtDNA that can be detected with amplicon sequencing, even if the efficiency is low. We detected low levels of C → T mutations in cells that were exposed to mitochondrially targeted Cas9-BE3, but, surprisingly, these occurred regardless of whether a guide RNA (gRNA) specific to the targeted site, or non-targeting gRNA was used. This unspecific off-target activity shows that Cas9-BE3 can technically edit mtDNA, but also strongly indicates that gRNA import to mitochondria was not successful. Going forward mitochondria-targeted Cas9 base editors will be a useful tool for validating successful gRNA delivery to mitochondria without the ambiguity of approaches that rely on quantifying mtDNA copy numbers.

DOI: https://doi.org/10.1038/s41598-022-21794-0
Sci Adv. 2022 Nov 04. 8(44): eabq1081

Astrocytic dysfunction induced by ABCA1 deficiency causes optic neuropathy.

Youichi Shinozaki, Alex Leung, Kazuhiko Namekata, Sei Saitoh, Huy Bang Nguyen, Akiko Takeda, Yosuke Danjo, Yosuke M Morizawa, Eiji Shigetomi, Fumikazu Sano, Nozomu Yoshioka, Hirohide Takebayashi, Nobuhiko Ohno, Takahiro Segawa, Kunio Miyake, Kenji Kashiwagi, Takayuki Harada, Shin-Ichi Ohnuma, Schuichi Koizumi.

Astrocyte abnormalities have received great attention for their association with various diseases in the brain but not so much in the eye. Recent independent genome-wide association studies of glaucoma, optic neuropathy characterized by retinal ganglion cell (RGC) degeneration, and vision loss found that single-nucleotide polymorphisms near the ABCA1 locus were common risk factors. Here, we show that Abca1 loss in retinal astrocytes causes glaucoma-like optic neuropathy in aged mice. ABCA1 was highly expressed in retinal astrocytes in mice. Thus, we generated macroglia-specific Abca1-deficient mice (Glia-KO) and found that aged Glia-KO mice had RGC degeneration and ocular dysfunction without affected intraocular pressure, a conventional risk factor for glaucoma. Single-cell RNA sequencing revealed that Abca1 deficiency in aged Glia-KO mice caused astrocyte-triggered inflammation and increased the susceptibility of certain RGC clusters to excitotoxicity. Together, astrocytes play a pivotal role in eye diseases, and loss of ABCA1 in astrocytes causes glaucoma-like neuropathy.

DOI: https://doi.org/10.1126/sciadv.abq1081
Nat Metab. 2022 Nov 03.

Adipose tissue macrophages exert systemic metabolic control by manipulating local iron concentrations.

Nolwenn Joffin, Christy M Gliniak, Jan-Bernd Funcke, Vivian A Paschoal, Clair Crewe, Shiuhwei Chen, Ruth Gordillo, Christine M Kusminski, Da Young Oh, Werner J Geldenhuys, Philipp E Scherer.

Iron is essential to many fundamental biological processes, but its cellular compartmentalization and concentration must be tightly controlled. Although iron overload can contribute to obesity-associated metabolic deterioration, the subcellular localization and accumulation of iron in adipose tissue macrophages is largely unknown. Here, we show that macrophage mitochondrial iron levels control systemic metabolism in male mice by altering adipocyte iron concentrations. Using various transgenic mouse models to manipulate the macrophage mitochondrial matrix iron content in an inducible fashion, we demonstrate that lowering macrophage mitochondrial matrix iron increases numbers of M2-like macrophages in adipose tissue, lowers iron levels in adipocytes, attenuates inflammation and protects from high-fat-diet-induced metabolic deterioration. Conversely, elevating macrophage mitochondrial matrix iron increases M1-like macrophages and iron levels in adipocytes, exacerbates inflammation and worsens high-fat-diet-induced metabolic dysfunction. These phenotypes are robustly reproduced by transplantation of a small amount of fat from transgenic to wild-type mice. Taken together, we identify macrophage mitochondrial iron levels as a crucial determinant of systemic metabolic homeostasis in mice.

DOI: https://doi.org/10.1038/s42255-022-00664-z
Proc Natl Acad Sci U S A. 2022 Nov 08. 119(45): e2203499119

Nano-positioning and tubulin conformation contribute to axonal transport regulation of mitochondria along microtubules.

Valérie Van Steenbergen, Flavie Lavoie-Cardinal, Youcef Kazwiny, Marianna Decet, Tobie Martens, Patrik Verstreken, Werend Boesmans, Paul De Koninck, Pieter Vanden Berghe.

  Correct spatiotemporal distribution of organelles and vesicles is crucial for healthy cell functioning and is regulated by intracellular transport mechanisms. Controlled transport of bulky mitochondria is especially important in polarized cells such as neurons that rely on these organelles to locally produce energy and buffer calcium. Mitochondrial transport requires and depends on microtubules that fill much of the available axonal space. How mitochondrial transport is affected by their position within the microtubule bundles is not known. Here, we found that anterograde transport, driven by kinesin motors, is susceptible to the molecular conformation of tubulin in neurons both in vitro and in vivo. Anterograde velocities negatively correlate with the density of elongated tubulin dimers like guanosine triphosphate (GTP)-tubulin. The impact of the tubulin conformation depends primarily on where a mitochondrion is positioned, either within or at the rim of microtubule bundle. Increasing elongated tubulin levels lowers the number of motile anterograde mitochondria within the microtubule bundle and increases anterograde transport speed at the microtubule bundle rim. We demonstrate that the increased kinesin velocity and density on microtubules consisting of elongated dimers add to the increased mitochondrial dynamics. Our work indicates that the molecular conformation of tubulin contributes to the regulation of mitochondrial motility and as such to the local distribution of mitochondria along axons.

Keywords:  STED; microtubules; mitochondria; neuronal axon; transport

DOI:  https://doi.org/10.1073/pnas.2203499119
Free Radic Biol Med. 2022 Oct 07. pii: S0891-5849(22)00635-9. [Epub ahead of print]

Mitochondrial Redox Signaling in Aging-Related Diseases--In Honor of Dr. Bruce N. Ames: A Pioneer in Mitochondrial Redox Signaling on Aging Research.

Jiankang Liu, Douglas C Wallace.

DOI: https://doi.org/10.1016/j.freeradbiomed.2022.10.005
Am J Hum Genet. 2022 Nov 03. pii: S0002-9297(22)00450-5. [Epub ahead of print]109(11): 1947-1959

Care4Rare Canada: Outcomes from a decade of network science for rare disease gene discovery.

Care4Rare Canada Consortium

  The past decade has witnessed a rapid evolution in rare disease (RD) research, fueled by the availability of genome-wide (exome and genome) sequencing. In 2011, as this transformative technology was introduced to the research community, the Care4Rare Canada Consortium was launched: initially as FORGE, followed by Care4Rare, and Care4Rare SOLVE. Over what amounted to three eras of diagnosis and discovery, the Care4Rare Consortium used exome sequencing and, more recently, genome and other 'omic technologies to identify the molecular cause of unsolved RDs. We achieved a diagnostic yield of 34% (623/1,806 of participating families), including the discovery of deleterious variants in 121 genes not previously associated with disease, and we continue to study candidate variants in novel genes for 145 families. The Consortium has made significant contributions to RD research, including development of platforms for data collection and sharing and instigating a Canadian network to catalyze functional characterization research of novel genes. The Consortium was instrumental to implementing genome-wide sequencing as a publicly funded test for RD diagnosis in Canada. Despite the successes of the past decade, the challenge of solving all RDs remains enormous, and the work is far from over. We must leverage clinical and 'omic data for secondary use, develop tools and policies to support safe data sharing, continue to explore the utility of new and emerging technologies, and optimize research protocols to delineate complex disease mechanisms. Successful approaches in each of these realms is required to offer diagnostic clarity to all families with RDs.

Keywords:  Care4Rare Canada; FORGE Canada; exome sequencing; gene discovery; genome sequencing; rare diseases

DOI:  https://doi.org/10.1016/j.ajhg.2022.10.002
Mol Oncol. 2022 Nov 04.

mitoSomatic: a tool for accurate identification of mitochondrial DNA somatic mutations without paired controls.

Wenjie Guo, Yang Liu, Liping Su, Shanshan Guo, Fanfan Xie, Xiaoying Ji, Kaixiang Zhou, Xu Guo, Xiwen Gu, Jinliang Xing.

  Mitochondrial DNA (mtDNA) somatic mutations play important roles in the initiation and progression of cancer. Although next-generation sequencing (NGS) of paired tumor and control samples has become a common practice to identify tumor-specific mtDNA mutations, the unique nature of mtDNA and NGS-associated sequencing bias could cause false positive/negative somatic mutation calling. Additionally, there are clinical scenarios where matched control tissues are unavailable for comparison. Therefore, a novel approach for accurately identifying somatic mtDNA variants is greatly needed, particularly in the absence of matched controls. In this study, the ground truth mtDNA variants orthogonally validated by triple-paired tumor, adjacent non-tumor, and blood samples were used to develop mitoSomatic, a random-forest-based machine learning tool. We demonstrated that mitoSomatic achieved area under the curve (AUC) values over 0.99 for identifying somatic mtDNA variants without paired control in three tumor types. In addition, mitoSomatic was also applicable in non-tumor tissues such as adjacent non-tumor and blood samples, suggesting the flexibility of mitoSomatic's classification capability. Furthermore, analysis of triple-paired samples identified a small group of variants with uncertain somatic/germline origin, whereas application of mitoSomatic significantly facilitated the prediction of their possible source. Finally, a control-free evaluation of the public pan-cancer NGS dataset with mitoSomatic revealed a substantial number of variants that were probably misclassified by conventional tumor-control comparison, further emphasizing the usefulness of mitoSomatic in application. Taken together, our study demonstrates that mitoSomatic is valuable for accurately identifying somatic mtDNA variants in mtDNA NGS data without paired controls, applicable for both tumor and non-tumor tissues.

Keywords:  machine learning; mitochondrial DNA; next-generation sequencing; somatic mutations

DOI:  https://doi.org/10.1002/1878-0261.13335
Cell Metab. 2022 Oct 22. pii: S1550-4131(22)00453-3. [Epub ahead of print]

Ultrasensitive sensors reveal the spatiotemporal landscape of lactate metabolism in physiology and disease.

Xie Li, Yinan Zhang, Lingyan Xu, Aoxue Wang, Yejun Zou, Ting Li, Li Huang, Weicai Chen, Shuning Liu, Kun Jiang, Xiuze Zhang, Dongmei Wang, Lijuan Zhang, Zhuo Zhang, Zeyi Zhang, Xianjun Chen, Wei Jia, Aihua Zhao, Xinfeng Yan, Haimeng Zhou, Linyong Zhu, Xinran Ma, Zhenyu Ju, Weiping Jia, Congrong Wang, Joseph Loscalzo, Yi Yang, Yuzheng Zhao.

  Despite its central importance in cellular metabolism, many details remain to be determined regarding subcellular lactate metabolism and its regulation in physiology and disease, as there is sensitive spatiotemporal resolution of lactate distribution, and dynamics remains a technical challenge. Here, we develop and characterize an ultrasensitive, highly responsive, ratiometric lactate sensor, named FiLa, enabling the monitoring of subtle lactate fluctuations in living cells and animals. Utilizing FiLa, we demonstrate that lactate is highly enriched in mammalian mitochondria and compile an atlas of subcellular lactate metabolism that reveals lactate as a key hub sensing various metabolic activities. In addition, FiLa sensors also enable direct imaging of elevated lactate levels in diabetic mice and facilitate the establishment of a simple, rapid, and sensitive lactate assay for point-of-care clinical screening. Thus, FiLa sensors provide powerful, broadly applicable tools for defining the spatiotemporal landscape of lactate metabolism in health and disease.

Keywords:  highly responsive lactate sensors; lactate metabolism; point-of-care clinical screening; real-time monitoring; subcellular lactate landscape

DOI:  https://doi.org/10.1016/j.cmet.2022.10.002
Eur J Med Res. 2022 Oct 29. 27(1): 221

ENT characteristics and therapeutic results in multisystemic disorders of mitochondrial encephalomyopathy.

Haishan Long, Cheng Wen, Juan Zhao, Jiawei Wang, Yang Li, Xinxing Fu, Lihui Huang.

  Here we report the evaluation of the frequency of subjective and objective otolaryngologic findings and therapeutic results in 32 patients with mitochondrial encephalomyopathy (MEM) from September 2001 to June 2021. Our analysis included studying the patients' family histories, the clinical manifestations of MEM, and the therapeutic effects of treatments. The patients' ages ranged from 2 to 77 years, with a median age of 12.3 years. We found that MEM ENT symptoms were characterized by hearing loss, dysphagia, and facial weakness. Most cases of sensorineural hearing loss were bilateral symmetrical progressive or sudden deafness since adolescence, which were often underestimated. Associated neuromuscular symptoms required mtDNA testing. Dysphagia and facial weakness occurred preferentially in middle-aged patients, and muscle biopsies were advised. Distortion product otoacoustic emissions and auditory brainstem responsetesting were more sensitive and reliable than pure tone averages for objective monitoring of pathogenesis. Administration of the mitochondrial synthase complex benefited patients with acute episodes. If patients did not fully recover and exhibitedresidual language deficits, hearing aids or cochlear implants were recommended. Counsel was given regarding synthetical treatments for facial weakness, endoscopic circopharyngealmyotomy for dysphagia, and surgical correction of ptosis. This study demonstrates that increased awareness of these symptoms is important to address appropriate interventions and avoid complications such as ablepsia, aphasia, social isolation, malnutrition, aspiration pneumonia, and heart failure in the setting of MEM.

Keywords:  Dysphagia; Exercise intolerance; Facial weakness; Hearing loss; Mitochondrial; Ptosis

DOI:  https://doi.org/10.1186/s40001-022-00832-7
Brain. 2022 Nov 02. pii: awac405. [Epub ahead of print]

Strengthening the link between mitophagy and Parkinson's disease.

Ian G Ganley.

DOI: https://doi.org/10.1093/brain/awac405