bims-mitdis 2021-02-07 papers

bims-mitdis

Biomed News

on Mitochondrial disorders

Issue of 2021–02–07
33 papers selected by
Catalina Vasilescu, University of Helsinki

C9orf72 regulates energy homeostasis by stabilizing mitochondrial complex I assembly.
An mtDNA mutant mouse demonstrates that mitochondrial deficiency can result in autism endophenotypes.
Single-molecule level structural dynamics of DNA unwinding by human mitochondrial Twinkle helicase.
Sulthiame impairs mitochondrial function in vitro and may trigger onset of visual loss in Leber hereditary optic neuropathy.
High-resolution imaging reveals compartmentalization of mitochondrial protein synthesis in cultured human cells.
ARMC12 regulates spatiotemporal mitochondrial dynamics during spermiogenesis and is required for male fertility.
Astrocyte Mitochondria in White-Matter Injury.
From fuzziness to precision medicine: on the rapidly evolving proteomics with implications in mitochondrial connectivity to rare human disease.
DNA polymerase β outperforms DNA polymerase γ in key mitochondrial base excision repair activities.
Therapeutic Potential of Mitochondrial Uncouplers for the Treatment of Metabolic Associated Fatty Liver Disease and NASH.
TFEB-deficiency attenuates mitochondrial degradation upon brown adipose tissue whitening at thermoneutrality.
Interface mobility between monomers in dimeric bovine ATP synthase participates in the ultrastructure of inner mitochondrial membranes.
Mitochondrial Dysfunction in Astrocytes: A Role in Parkinson's Disease?
Variant calling and quality control of large-scale human genome sequencing data.
Stem cell-derived mitochondria transplantation: A promising therapy for mitochondrial encephalomyopathy.
A Ketogenic Diet Differentially Affects Neuron And Astrocyte Transcription.
A fast and efficient colocalization algorithm for identifying shared genetic risk factors across multiple traits.
At the heart of mitochondrial quality control: many roads to the top.
Exacerbated age-related hearing loss in mice lacking the p43 mitochondrial T3 receptor.
Cardiolipin content controls mitochondrial coupling and energetic efficiency in muscle.
Mitochondrial dysfunction in neurodegenerative diseases: A focus on iPSC-derived neuronal models.
Metabolic control of DNA methylation in naive pluripotent cells.
Identification of Candidate Parkinson Disease Genes by Integrating Genome-Wide Association Study, Expression, and Epigenetic Data Sets.
IRGM1, a guardian of mitochondrial DAMP-mediated autoinflammation.
Identification of unusual phospholipids from bovine heart mitochondria by HPLC-MS/MS.
GUÍA: a digital platform to facilitate result disclosure in genetic counseling.
BAG6 promotes PINK1 signaling pathway and is essential for mitophagy.
Mitochondrial DNA Content Is Linked to Cardiovascular Disease Patient Phenotypes.
GeneWalk identifies relevant gene functions for a biological context using network representation learning.
A Novel Exercise Testing Algorithm to Diagnose Mitochondrial Myopathy.
Function and regulation of the divisome for mitochondrial fission.
Mitochondrial metabolism is a key regulator of the fibro-inflammatory and adipogenic stromal subpopulations in white adipose tissue.
Mitochondrial translation deficiency impairs NAD+ -mediated lysosomal acidification.

Cell Metab. 2021 Feb 02. pii: S1550-4131(21)00005-X. [Epub ahead of print]

C9orf72 regulates energy homeostasis by stabilizing mitochondrial complex I assembly.

Tao Wang, Honghe Liu, Kie Itoh, Sungtaek Oh, Liang Zhao, Daisuke Murata, Hiromi Sesaki, Thomas Hartung, Chan Hyun Na, Jiou Wang.

  The haploinsufficiency of C9orf72 is implicated in the most common forms of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), but the full spectrum of C9orf72 functions remains to be established. Here, we report that C9orf72 is a mitochondrial inner-membrane-associated protein regulating cellular energy homeostasis via its critical role in the control of oxidative phosphorylation (OXPHOS). The translocation of C9orf72 from the cytosol to the inter-membrane space is mediated by the redox-sensitive AIFM1/CHCHD4 pathway. In mitochondria, C9orf72 specifically stabilizes translocase of inner mitochondrial membrane domain containing 1 (TIMMDC1), a crucial factor for the assembly of OXPHOS complex I. C9orf72 directly recruits the prohibitin complex to inhibit the m-AAA protease-dependent degradation of TIMMDC1. The mitochondrial complex I function is impaired in C9orf72-linked ALS/FTD patient-derived neurons. These results reveal a previously unknown function of C9orf72 in mitochondria and suggest that defective energy metabolism may underlie the pathogenesis of relevant diseases.

Keywords:  ALS; C9orf72; FTD; OXPHOS; TIMMDC1; complex I; mitochondrial import; mitochondrion; neurodegeneration; oxidative phosphorylation

DOI:  https://doi.org/10.1016/j.cmet.2021.01.005
Proc Natl Acad Sci U S A. 2021 Feb 09. pii: e2021429118. [Epub ahead of print]118(6):

An mtDNA mutant mouse demonstrates that mitochondrial deficiency can result in autism endophenotypes.

Tal Yardeni, Ana G Cristancho, Almedia J McCoy, Patrick M Schaefer, Meagan J McManus, Eric D Marsh, Douglas C Wallace.

  Autism spectrum disorders (ASDs) are characterized by a deficit in social communication, pathologic repetitive behaviors, restricted interests, and electroencephalogram (EEG) aberrations. While exhaustive analysis of nuclear DNA (nDNA) variation has revealed hundreds of copy number variants (CNVs) and loss-of-function (LOF) mutations, no unifying hypothesis as to the pathophysiology of ASD has yet emerged. Based on biochemical and physiological analyses, it has been hypothesized that ASD may be the result of a systemic mitochondrial deficiency with brain-specific manifestations. This proposal has been supported by recent mitochondrial DNA (mtDNA) analyses identifying both germline and somatic mtDNA variants in ASD. If mitochondrial defects do predispose to ASD, then mice with certain mtDNA mutations should present with autism endophenotypes. To test this prediction, we examined a mouse strain harboring an mtDNA ND6 gene missense mutation (P25L). This mouse manifests impaired social interactions, increased repetitive behaviors and anxiety, EEG alterations, and a decreased seizure threshold, in the absence of reduced hippocampal interneuron numbers. EEG aberrations were most pronounced in the cortex followed by the hippocampus. Aberrations in mitochondrial respiratory function and reactive oxygen species (ROS) levels were also most pronounced in the cortex followed by the hippocampus, but absent in the olfactory bulb. These data demonstrate that mild systemic mitochondrial defects can result in ASD without apparent neuroanatomical defects and that systemic mitochondrial mutations can cause tissue-specific brain defects accompanied by regional neurophysiological alterations.

Keywords:  ROS; autism; mitochondrial dysfunction

DOI:  https://doi.org/10.1073/pnas.2021429118
J Biol Chem. 2020 Apr 24. pii: S0021-9258(17)50288-4. [Epub ahead of print]295(17): 5564-5576

Single-molecule level structural dynamics of DNA unwinding by human mitochondrial Twinkle helicase.

Parminder Kaur, Matthew J Longley, Hai Pan, Wendy Wang, Preston Countryman, Hong Wang, William C Copeland.

  Knowledge of the molecular events in mitochondrial DNA (mtDNA) replication is crucial to understanding the origins of human disorders arising from mitochondrial dysfunction. Twinkle helicase is an essential component of mtDNA replication. Here, we employed atomic force microscopy imaging in air and liquids to visualize ring assembly, DNA binding, and unwinding activity of individual Twinkle hexamers at the single-molecule level. We observed that the Twinkle subunits self-assemble into hexamers and higher-order complexes that can switch between open and closed-ring configurations in the absence of DNA. Our analyses helped visualize Twinkle loading onto and unloading from DNA in an open-ringed configuration. They also revealed that closed-ring conformers bind and unwind several hundred base pairs of duplex DNA at an average rate of ∼240 bp/min. We found that the addition of mitochondrial single-stranded (ss) DNA-binding protein both influences the ways Twinkle loads onto defined DNA substrates and stabilizes the unwound ssDNA product, resulting in a ∼5-fold stimulation of the apparent DNA-unwinding rate. Mitochondrial ssDNA-binding protein also increased the estimated translocation processivity from 1750 to >9000 bp before helicase disassociation, suggesting that more than half of the mitochondrial genome could be unwound by Twinkle during a single DNA-binding event. The strategies used in this work provide a new platform to examine Twinkle disease variants and the core mtDNA replication machinery. They also offer an enhanced framework to investigate molecular mechanisms underlying deletion and depletion of the mitochondrial genome as observed in mitochondrial diseases.

Keywords:  DNA binding protein; DNA helicase; DNA replication; Twinkle helicase; atomic force microscopy (AFM); mitochondrial DNA (mtDNA); mitochondrial disease; single-molecule biophysics; ssDNA-binding protein (SSB); structural dynamics

DOI:  https://doi.org/10.1074/jbc.RA120.012795
Orphanet J Rare Dis. 2021 Feb 04. 16(1): 64

Sulthiame impairs mitochondrial function in vitro and may trigger onset of visual loss in Leber hereditary optic neuropathy.

Marie-Christine Reinert, David Pacheu-Grau, Claudia B Catarino, Thomas Klopstock, Andreas Ohlenbusch, Michael Schittkowski, Ekkehard Wilichowski, Peter Rehling, Knut Brockmann.

   BACKGROUND: Leber hereditary optic neuropathy (LHON) is the most common mitochondrial disorder and characterized by acute or subacute painless visual loss. Environmental factors reported to trigger visual loss in LHON mutation carriers include smoking, heavy intake of alcohol, raised intraocular pressure, and some drugs, including several carbonic anhydrase inhibitors. The antiepileptic drug sulthiame (STM) is effective especially in focal seizures, particularly in benign epilepsy of childhood with centrotemporal spikes, and widely used in pediatric epileptology. STM is a sulfonamide derivate and an inhibitor of mammalian carbonic anhydrase isoforms I-XIV.
RESULTS: We describe two unrelated patients, an 8-year-old girl and an 11-year-old boy, with cryptogenic focal epilepsy, who suffered binocular (subject #1) or monocular (subject #2) visual loss in close temporal connection with starting antiepileptic pharmacotherapy with STM. In both subjects, visual loss was due to LHON. We used real-time respirometry in fibroblasts derived from LHON patients carrying the same mitochondrial mutations as our two subjects to investigate the effect of STM on oxidative phosphorylation. Oxygen consumption rate in fibroblasts from a healthy control was not impaired by STM compared with a vehicle control. In contrast, fibroblasts carrying the m.14484T>C or the m.3460G>A LHON mutation displayed a drastic reduction of the respiration rate when treated with STM compared to vehicle control.
CONCLUSIONS: Our observations point to a causal relationship between STM treatment and onset or worsening of visual failure in two subjects with LHON rather than pure coincidence. We conclude that antiepileptic medication with STM may pose a risk for visual loss in LHON mutation carriers and should be avoided in these patients.

Keywords:  Adverse effects; Carbonic anhydrase inhibitor; LHON; Leber hereditary optic neuropathy; Oxygen consumption rate; Sulthiame

DOI:  https://doi.org/10.1186/s13023-021-01690-y
Proc Natl Acad Sci U S A. 2021 Feb 09. pii: e2008778118. [Epub ahead of print]118(6):

High-resolution imaging reveals compartmentalization of mitochondrial protein synthesis in cultured human cells.

Matthew Zorkau, Christin A Albus, Rolando Berlinguer-Palmini, Zofia M A Chrzanowska-Lightowlers, Robert N Lightowlers.

  Human mitochondria contain their own genome, mitochondrial DNA, that is expressed in the mitochondrial matrix. This genome encodes 13 vital polypeptides that are components of the multisubunit complexes that couple oxidative phosphorylation (OXPHOS). The inner mitochondrial membrane that houses these complexes comprises the inner boundary membrane that runs parallel to the outer membrane, infoldings that form the cristae membranes, and the cristae junctions that separate the two. It is in these cristae membranes that the OXPHOS complexes have been shown to reside in various species. The majority of the OXPHOS subunits are nuclear-encoded and must therefore be imported from the cytosol through the outer membrane at contact sites with the inner boundary membrane. As the mitochondrially encoded components are also integral members of these complexes, where does protein synthesis occur? As transcription, mRNA processing, maturation, and at least part of the mitoribosome assembly process occur at the nucleoid and the spatially juxtaposed mitochondrial RNA granules, is protein synthesis also performed at the RNA granules close to these entities, or does it occur distal to these sites? We have adapted a click chemistry-based method coupled with stimulated emission depletion nanoscopy to address these questions. We report that, in human cells in culture, within the limits of our methodology, the majority of mitochondrial protein synthesis is detected at the cristae membranes and is spatially separated from the sites of RNA processing and maturation.

Keywords:  click chemistry; human mitochondria; mitoribosomes; protein synthesis

DOI:  https://doi.org/10.1073/pnas.2008778118
Proc Natl Acad Sci U S A. 2021 Feb 09. pii: e2018355118. [Epub ahead of print]118(6):

ARMC12 regulates spatiotemporal mitochondrial dynamics during spermiogenesis and is required for male fertility.

Keisuke Shimada, Soojin Park, Haruhiko Miyata, Zhifeng Yu, Akane Morohoshi, Seiya Oura, Martin M Matzuk, Masahito Ikawa.

  The mammalian sperm midpiece has a unique double-helical structure called the mitochondrial sheath that wraps tightly around the axoneme. Despite the remarkable organization of the mitochondrial sheath, the molecular mechanisms involved in mitochondrial sheath formation are unclear. In the process of screening testis-enriched genes for functions in mice, we identified armadillo repeat-containing 12 (ARMC12) as an essential protein for mitochondrial sheath formation. Here, we engineered Armc12-null mice, FLAG-tagged Armc12 knock-in mice, and TBC1 domain family member 21 (Tbc1d21)-null mice to define the functions of ARMC12 in mitochondrial sheath formation in vivo. We discovered that absence of ARMC12 causes abnormal mitochondrial coiling along the flagellum, resulting in reduced sperm motility and male sterility. During spermiogenesis, sperm mitochondria in Armc12-null mice cannot elongate properly at the mitochondrial interlocking step which disrupts abnormal mitochondrial coiling. ARMC12 is a mitochondrial peripheral membrane protein and functions as an adherence factor between mitochondria in cultured cells. ARMC12 in testicular germ cells interacts with mitochondrial proteins MIC60, VDAC2, and VDAC3 as well as TBC1D21 and GK2, which are required for mitochondrial sheath formation. We also observed that TBC1D21 is essential for the interaction between ARMC12 and VDAC proteins in vivo. These results indicate that ARMC12 uses integral mitochondrial membrane proteins VDAC2 and VDAC3 as scaffolds to link mitochondria and works cooperatively with TBC1D21. Thus, our studies have revealed that ARMC12 regulates spatiotemporal mitochondrial dynamics to form the mitochondrial sheath through cooperative interactions with several proteins on the sperm mitochondrial surface.

Keywords:  infertility; mitochondrial sheath formation; sperm mitochondrial dynamics; spermatogenesis

DOI:  https://doi.org/10.1073/pnas.2018355118
Neurochem Res. 2021 Feb 01.

Astrocyte Mitochondria in White-Matter Injury.

Hung Nguyen, Sarah Zerimech, Selva Baltan.

  This review summarizes the diverse structure and function of astrocytes to describe the bioenergetic versatility required of astrocytes that are situated at different locations. The intercellular domain of astrocyte mitochondria defines their roles in supporting and regulating astrocyte-neuron coupling and survival against ischemia. The heterogeneity of astrocyte mitochondria, and how subpopulations of astrocyte mitochondria adapt to interact with other glia and regulate axon function, require further investigation. It has become clear that mitochondrial permeability transition pores play a key role in a wide variety of human diseases, whose common pathology may be based on mitochondrial dysfunction triggered by Ca2+ and potentiated by oxidative stress. Reactive oxygen species cause axonal degeneration and a reduction in axonal transport, leading to axonal dystrophies and neurodegeneration including Alzheimer's disease, amyotrophic lateral sclerosis, Parkinson's disease, and Huntington's disease. Developing new tools to allow better investigation of mitochondrial structure and function in astrocytes, and techniques to specifically target astrocyte mitochondria, can help to unravel the role of mitochondrial health and dysfunction in a more inclusive context outside of neuronal cells. Overall, this review will assess the value of astrocyte mitochondria as a therapeutic target to mitigate acute and chronic injury in the CNS.

Keywords:  Astroglial interactions; Axonal degeneration; Glial cells; Mitochondrial dynamics; Neurodegenerative diseases; Neurovascular injuries

DOI:  https://doi.org/10.1007/s11064-021-03239-8
iScience. 2021 Feb 19. 24(2): 102030

From fuzziness to precision medicine: on the rapidly evolving proteomics with implications in mitochondrial connectivity to rare human disease.

Khaled A Aly, Mohamed Taha Moutaoufik, Sadhna Phanse, Qingzhou Zhang, Mohan Babu.

  Mitochondrial (mt) dysfunction is linked to rare diseases (RDs) such as respiratory chain complex (RCC) deficiency, MELAS, and ARSACS. Yet, how altered mt protein networks contribute to these ailments remains understudied. In this perspective article, we identified 21 mt proteins from public repositories that associate with RCC deficiency, MELAS, or ARSACS, engaging in a relatively small number of protein-protein interactions (PPIs), underscoring the need for advanced proteomic and interactomic platforms to uncover the complete scope of mt connectivity to RDs. Accordingly, we discuss innovative untargeted label-free proteomics in identifying RD-specific mt or other macromolecular assemblies and mapping of protein networks in complex tissue, organoid, and stem cell-differentiated neurons. Furthermore, tag- and label-based proteomics, genealogical proteomics, and combinatorial affinity purification-mass spectrometry, along with advancements in detecting and integrating transient PPIs with single-cell proteomics and transcriptomics, collectively offer seminal follow-ups to enrich for RD-relevant networks, with implications in RD precision medicine.

Keywords:  Complex Systems; Disease; Proteomics; Systems Biology

DOI:  https://doi.org/10.1016/j.isci.2020.102030
DNA Repair (Amst). 2021 Jan 21. pii: S1568-7864(21)00004-5. [Epub ahead of print]99 103050

DNA polymerase β outperforms DNA polymerase γ in key mitochondrial base excision repair activities.

Beverly A Baptiste, Stephanie L Baringer, Tomasz Kulikowicz, Joshua A Sommers, Deborah L Croteau, Robert M Brosh, Vilhelm A Bohr.

  DNA polymerase beta (POLβ), well known for its role in nuclear DNA base excision repair (BER), has been shown to be present in the mitochondria of several different cell types. Here we present a side-by-side comparison of BER activities of POLβ and POLγ, the mitochondrial replicative polymerase, previously thought to be the only mitochondrial polymerase. We find that POLβ is significantly more proficient at single-nucleotide gap filling, both in substrates with ends that require polymerase processing, and those that do not. We also show that POLβ has a helicase-independent functional interaction with the mitochondrial helicase, TWINKLE. This interaction stimulates strand-displacement synthesis, but not single-nucleotide gap filling. Importantly, we find that purified mitochondrial extracts from cells lacking POLβ are severely deficient in processing BER intermediates, suggesting that mitochondrially localized DNA POLβ may be critical for cells with high energetic demands that produce greater levels of oxidative stress and therefore depend upon efficient BER for mitochondrial health.

Keywords:  Ber; Mitochondria; Polb; Polg

DOI:  https://doi.org/10.1016/j.dnarep.2021.103050
Mol Metab. 2021 Feb 02. pii: S2212-8778(21)00018-1. [Epub ahead of print] 101178

Therapeutic Potential of Mitochondrial Uncouplers for the Treatment of Metabolic Associated Fatty Liver Disease and NASH.

Leigh Goedeke, Gerald I Shulman.

   BACKGROUND: Mitochondrial uncouplers shuttle protons across the inner mitochondrial membrane via a pathway that is independent of ATP synthase, thereby uncoupling nutrient oxidation from ATP production and dissipating the proton gradient as heat. While initial toxicity concerns hindered their therapeutic development in the early 1930s, there has been increased interest in exploring the therapeutic potential of mitochondrial uncouplers for the treatment of metabolic diseases.
SCOPE OF REVIEW: In this review, we cover recent advances in the mechanisms by which mitochondrial uncouplers regulate biological processes and disease, with a particular focus on metabolic associated fatty liver disease (MAFLD), NASH, insulin resistance, and type 2 diabetes (T2D). In addition, we discuss the challenges that remain to be addressed before synthetic and natural mitochondrial uncouplers can successfully enter the clinic.
MAJOR CONCLUSIONS: Rodent and nonhuman primate studies suggest that a myriad of small molecule mitochondrial uncouplers can safely reverse MAFLD/NASH with a wide-therapeutic index. Despite this, further characterization of the tissue and cell-specific effects of mitochondrial uncouplers are needed. We propose to target the dosing of mitochondrial uncouplers to specific tissues, such as the liver, and/or to develop molecules with self-limiting properties to induce a subtle, sustained increase in mitochondrial inefficiency, thereby avoiding systemic toxicity concerns.

Keywords:  MAFLD; NAFLD/NASH; diabetes; insulin resistance; liver fibrosis; metabolic syndrome; mitochondrial uncouplers

DOI:  https://doi.org/10.1016/j.molmet.2021.101178
Mol Metab. 2021 Jan 28. pii: S2212-8778(21)00013-2. [Epub ahead of print] 101173

TFEB-deficiency attenuates mitochondrial degradation upon brown adipose tissue whitening at thermoneutrality.

Frederike Sass, Christian Schlein, Michelle Y Jaeckstein, Paul Pertzborn, Michaela Schweizer, Thorsten Schinke, Andrea Ballabio, Ludger Scheja, Joerg Heeren, Alexander W Fischer.

   OBJECTIVE: Brown adipose tissue (BAT) thermogenesis offers the potential to improve metabolic health in mice and men. However, humans predominantly live under thermoneutral conditions, leading to BAT whitening - a reduction in BAT mitochondrial content and metabolic activity. Recent studies have established mitophagy as a major driver of mitochondrial degradation in the whitening of thermogenic brite/beige adipocytes, yet the pathways mediating mitochondrial breakdown in whitening of classical BAT remain largely elusive. The transcription factor EB (TFEB), a master regulator of lysosomal biogenesis and autophagy belonging to the MIT family of transcription factors, is the only member of this family that is upregulated during whitening, pointing towards a role of TFEB in whitening-associated mitochondrial breakdown.
METHODS: We generated brown adipocyte-specific TFEB knockout mice, and induced BAT whitening by thermoneutral housing. We characterized gene and protein expression patterns, BAT metabolic activity, systemic metabolism as well as mitochondrial localization using in vivo and in vitro approaches.
RESULTS: Under conditions of low thermogenic activation, deletion of TFEB preserved mitochondrial mass independently of mitochondriogenesis in BAT and primary brown adipocytes. This did however not translate into elevated thermogenic capacity or protection from diet-induced obesity. Autophagosomal/lysosomal marker levels were altered in TFEB-deficient BAT and primary adipocytes, and lysosomal markers co-localized and co-purified with mitochondria in TFEB-deficient BAT, indicating trapping of mitochondria in late stages of mitophagy.
CONCLUSION: We here identify TFEB as a driver of BAT whitening, mediating mitochondrial degradation via the autophagosomal and lysosomal machinery. This study provides proof of concept that interfering with the mitochondrial degradation machinery can increase mitochondrial mass in classical BAT under human-relevant conditions. It must however be considered that interfering with autophagy may result in accumulation of non-functional mitochondria. Future studies targeting earlier steps of mitophagy or target recognition are therefore warranted.

Keywords:  TFEB; UCP1; brown adipose tissue; mitophagy; thermogenesis; whitening

DOI:  https://doi.org/10.1016/j.molmet.2021.101173
Proc Natl Acad Sci U S A. 2021 Feb 23. pii: e2021012118. [Epub ahead of print]118(8):

Interface mobility between monomers in dimeric bovine ATP synthase participates in the ultrastructure of inner mitochondrial membranes.

Tobias E Spikes, Martin G Montgomery, John E Walker.

  The ATP synthase complexes in mitochondria make the ATP required to sustain life by a rotary mechanism. Their membrane domains are embedded in the inner membranes of the organelle, and they dimerize via interactions between their membrane domains. The dimers form extensive chains along the tips of the cristae with the two rows of monomeric catalytic domains extending into the mitochondrial matrix at an angle to each other. Disruption of the interface between dimers by mutation affects the morphology of the cristae severely. By analysis of particles of purified dimeric bovine ATP synthase by cryo-electron microscopy, we have shown that the angle between the central rotatory axes of the monomeric complexes varies between ca. 76 and 95°. These particles represent active dimeric ATP synthase. Some angular variations arise directly from the catalytic mechanism of the enzyme, and others are independent of catalysis. The monomer-monomer interaction is mediated mainly by j subunits attached to the surface of wedge-shaped protein-lipid structures in the membrane domain of the complex, and the angular variation arises from rotational and translational changes in this interaction, and combinations of both. The structures also suggest how the dimeric ATP synthases might be interacting with each other to form the characteristic rows along the tips of the cristae via other interwedge contacts, molding themselves to the range of oligomeric arrangements observed by tomography of mitochondrial membranes, and at the same time allowing the ATP synthase to operate under the range of physiological conditions that influence the structure of the cristae.

Keywords:  ATP synthase; bovine mitochondria; dimer; mobility; monomer-monomer interface

DOI:  https://doi.org/10.1073/pnas.2021012118
Front Cell Dev Biol. 2020 ;8 608026

Mitochondrial Dysfunction in Astrocytes: A Role in Parkinson's Disease?

Collin M Bantle, Warren D Hirst, Andreas Weihofen, Evgeny Shlevkov.

  Mitochondrial dysfunction is a hallmark of Parkinson's disease (PD). Astrocytes are the most abundant glial cell type in the brain and are thought to play a pivotal role in the progression of PD. Emerging evidence suggests that many astrocytic functions, including glutamate metabolism, Ca2+ signaling, fatty acid metabolism, antioxidant production, and inflammation are dependent on healthy mitochondria. Here, we review how mitochondrial dysfunction impacts astrocytes, highlighting translational gaps and opening new questions for therapeutic development.

Keywords:  NLRP3; PINK1/Parkin pathway; Parkinson’s disease; astrocyte; cGAS/STING pathway; inflammation; mitochondria

DOI:  https://doi.org/10.3389/fcell.2020.608026
Emerg Top Life Sci. 2019 Aug 16. 3(4): 399-409

Variant calling and quality control of large-scale human genome sequencing data.

Brandon Jew, Jae Hoon Sul.

  Next-generation sequencing has allowed genetic studies to collect genome sequencing data from a large number of individuals. However, raw sequencing data are not usually interpretable due to fragmentation of the genome and technical biases; therefore, analysis of these data requires many computational approaches. First, for each sequenced individual, sequencing data are aligned and further processed to account for technical biases. Then, variant calling is performed to obtain information on the positions of genetic variants and their corresponding genotypes. Quality control (QC) is applied to identify individuals and genetic variants with sequencing errors. These procedures are necessary to generate accurate variant calls from sequencing data, and many computational approaches have been developed for these tasks. This review will focus on current widely used approaches for variant calling and QC.

Keywords:  next-generation sequencing; quality control; statistical genetics; variant calling

DOI:  https://doi.org/10.1042/ETLS20190007
CNS Neurosci Ther. 2021 Feb 03.

Stem cell-derived mitochondria transplantation: A promising therapy for mitochondrial encephalomyopathy.

Kaiming Liu, Zhijian Zhou, Mengxiong Pan, Lining Zhang.

  Mitochondrial encephalomyopathies are disorders caused by mitochondrial and nuclear DNA mutations which affect the nervous and muscular systems. Current therapies for mitochondrial encephalomyopathies are inadequate and mostly palliative. However, stem cell-derived mitochondria transplantation has been demonstrated to play an key part in metabolic rescue, which offers great promise for mitochondrial encephalomyopathies. Here, we summarize the present status of stem cell therapy for mitochondrial encephalomyopathy and discuss mitochondrial transfer routes and the protection mechanisms of stem cells. We also identify and summarize future perspectives and challenges for the treatment of these intractable disorders based on the concept of mitochondrial transfer from stem cells.

Keywords:  mitochondria; mitochondria quality control; mitochondrial dynamics; mitochondrial encephalomyopathy; stem cell; tunneling nanotube

DOI:  https://doi.org/10.1111/cns.13618
J Neurochem. 2021 Feb 04.

A Ketogenic Diet Differentially Affects Neuron And Astrocyte Transcription.

Scott J Koppel, Dong Pei, Heather M Wilkins, Ian W Weidling, Xiaowan Wang, Blaise W Menta, Judit Perez-Ortiz, Anuradha Kalani, Sharon Manley, Lesya Novikova, Devin C Koestler, Russell H Swerdlow.

  Ketogenic diets (KDs) alter brain metabolism. Multiple mechanisms may account for their effects, and different brain regions may variably respond. Here, we considered how a KD affects brain neuron and astrocyte transcription. We placed male C57Bl6/N mice on either a 3-month KD or chow diet, generated enriched neuron and astrocyte fractions, and used RNA-Seq to assess transcription. Neurons from KD-treated mice generally showed transcriptional pathway activation while their astrocytes showed a mix of transcriptional pathway suppression and activation. The KD especially affected pathways implicated in mitochondrial and endoplasmic reticulum function, insulin signaling, and inflammation. An unbiased analysis of KD-associated expression changes strongly implicated transcriptional pathways altered in AD, which prompted us to explore in more detail the potential molecular relevance of a KD to AD. Our results indicate a KD differently affects neurons and astrocytes, and provide unbiased evidence that KD-induced brain effects are potentially relevant to neurodegenerative diseases such as AD.

Keywords:  Alzheimer’s disease; Ketogenic diet; RNA-Seq; astrocytes; mitochondria; neurons

DOI:  https://doi.org/10.1111/jnc.15313
Nat Commun. 2021 02 03. 12(1): 764

A fast and efficient colocalization algorithm for identifying shared genetic risk factors across multiple traits.

Christopher N Foley, James R Staley, Philip G Breen, Benjamin B Sun, Paul D W Kirk, Stephen Burgess, Joanna M M Howson.

Genome-wide association studies (GWAS) have identified thousands of genomic regions affecting complex diseases. The next challenge is to elucidate the causal genes and mechanisms involved. One approach is to use statistical colocalization to assess shared genetic aetiology across multiple related traits (e.g. molecular traits, metabolic pathways and complex diseases) to identify causal pathways, prioritize causal variants and evaluate pleiotropy. We propose HyPrColoc (Hypothesis Prioritisation for multi-trait Colocalization), an efficient deterministic Bayesian algorithm using GWAS summary statistics that can detect colocalization across vast numbers of traits simultaneously (e.g. 100 traits can be jointly analysed in around 1 s). We perform a genome-wide multi-trait colocalization analysis of coronary heart disease (CHD) and fourteen related traits, identifying 43 regions in which CHD colocalized with ≥1 trait, including 5 previously unknown CHD loci. Across the 43 loci, we further integrate gene and protein expression quantitative trait loci to identify candidate causal genes.

DOI: https://doi.org/10.1038/s41467-020-20885-8
Cell Mol Life Sci. 2021 Feb 05.

At the heart of mitochondrial quality control: many roads to the top.

Roberta A Gottlieb, Honit Piplani, Jon Sin, Savannah Sawaged, Syed M Hamid, David J Taylor, Juliana de Freitas Germano.

  Mitochondrial quality control depends upon selective elimination of damaged mitochondria, replacement by mitochondrial biogenesis, redistribution of mitochondrial components across the network by fusion, and segregation of damaged mitochondria by fission prior to mitophagy. In this review, we focus on mitochondrial dynamics (fusion/fission), mitophagy, and other mechanisms supporting mitochondrial quality control including maintenance of mtDNA and the mitochondrial unfolded protein response, particularly in the context of the heart.

Keywords:  Cardiac; Fission; Fusion; Mitochondria; Mitophagy

DOI:  https://doi.org/10.1007/s00018-021-03772-3
BMC Biol. 2021 Feb 01. 19(1): 18

Exacerbated age-related hearing loss in mice lacking the p43 mitochondrial T3 receptor.

Corentin Affortit, François Casas, Sabine Ladrech, Jean-Charles Ceccato, Jérôme Bourien, Carolanne Coyat, Jean-Luc Puel, Marc Lenoir, Jing Wang.

   BACKGROUND: Age-related hearing loss (ARHL), also known as presbycusis, is the most common sensory impairment seen in elderly people. However, the cochlear aging process does not affect people uniformly, suggesting that both genetic and environmental (e.g., noise, ototoxic drugs) factors and their interaction may influence the onset and severity of ARHL. Considering the potential links between thyroid hormone, mitochondrial activity, and hearing, here, we probed the role of p43, a N-terminally truncated and ligand-binding form of the nuclear receptor TRα1, in hearing function and in the maintenance of hearing during aging in p43-/- mice through complementary approaches, including in vivo electrophysiological recording, ultrastructural assessments, biochemistry, and molecular biology.
RESULTS: We found that the p43-/- mice exhibit no obvious hearing loss in juvenile stages, but that these mice developed a premature, and more severe, ARHL resulting from the loss of cochlear sensory outer and inner hair cells and degeneration of spiral ganglion neurons. Exacerbated ARHL in p43-/- mice was associated with the early occurrence of a drastic fall of SIRT1 expression, together with an imbalance between pro-apoptotic Bax, p53 expression, and anti-apoptotic Bcl2 expression, as well as an increase in mitochondrial dysfunction, oxidative stress, and inflammatory process. Finally, p43-/- mice were also more vulnerable to noise-induced hearing loss.
CONCLUSIONS: These results demonstrate for the first time a requirement for p43 in the maintenance of hearing during aging and highlight the need to probe the potential link between human THRA gene polymorphisms and/or mutations and accelerated age-related deafness or some adult-onset syndromic deafness.

Keywords:  Age-related hearing loss; Mitochondrial dysfunction; Thyroid hormones; p43 mitochondrial T3 receptor

DOI:  https://doi.org/10.1186/s12915-021-00953-1
Sci Adv. 2021 01;pii: eabd6322. [Epub ahead of print]7(1):

Cardiolipin content controls mitochondrial coupling and energetic efficiency in muscle.

Alexandre Prola, Jordan Blondelle, Aymeline Vandestienne, Jérôme Piquereau, Raphaël G P Denis, Stéphane Guyot, Hadrien Chauvin, Arnaud Mourier, Marie Maurer, Céline Henry, Nahed Khadhraoui, Cindy Gallerne, Thibaut Molinié, Guillaume Courtin, Laurent Guillaud, Mélanie Gressette, Audrey Solgadi, Florent Dumont, Julien Castel, Julien Ternacle, Jean Demarquoy, Alexandra Malgoyre, Nathalie Koulmann, Geneviève Derumeaux, Marie-France Giraud, Frédéric Joubert, Vladimir Veksler, Serge Luquet, Frédéric Relaix, Laurent Tiret, Fanny Pilot-Storck.

Unbalanced energy partitioning participates in the rise of obesity, a major public health concern in many countries. Increasing basal energy expenditure has been proposed as a strategy to fight obesity yet raises efficiency and safety concerns. Here, we show that mice deficient for a muscle-specific enzyme of very-long-chain fatty acid synthesis display increased basal energy expenditure and protection against high-fat diet-induced obesity. Mechanistically, muscle-specific modulation of the very-long-chain fatty acid pathway was associated with a reduced content of the inner mitochondrial membrane phospholipid cardiolipin and a blunted coupling efficiency between the respiratory chain and adenosine 5'-triphosphate (ATP) synthase, which was restored by cardiolipin enrichment. Our study reveals that selective increase of lipid oxidative capacities in skeletal muscle, through the cardiolipin-dependent lowering of mitochondrial ATP production, provides an effective option against obesity at the whole-body level.

DOI: https://doi.org/10.1126/sciadv.abd6322
Cell Calcium. 2021 Jan 30. pii: S0143-4160(21)00016-6. [Epub ahead of print]94 102362

Mitochondrial dysfunction in neurodegenerative diseases: A focus on iPSC-derived neuronal models.

Marina Trombetta-Lima, Angélica María Sabogal-Guáqueta, Amalia M Dolga.

  Progressive neuronal loss is a hallmark of many neurodegenerative diseases, including Alzheimer's and Parkinson's disease. These pathologies exhibit clear signs of inflammation, mitochondrial dysfunction, calcium deregulation, and accumulation of aggregated or misfolded proteins. Over the last decades, a tremendous research effort has contributed to define some of the pathological mechanisms underlying neurodegenerative processes in these complex brain neurodegenerative disorders. To better understand molecular mechanisms responsible for neurodegenerative processes and find potential interventions and pharmacological treatments, it is important to have robust in vitro and pre-clinical animal models that can recapitulate both the early biological events undermining the maintenance of the nervous system and early pathological events. In this regard, it would be informative to determine how different inherited pathogenic mutations can compromise mitochondrial function, calcium signaling, and neuronal survival. Since post-mortem analyses cannot provide relevant information about the disease progression, it is crucial to develop model systems that enable the investigation of early molecular changes, which may be relevant as targets for novel therapeutic options. Thus, the use of human induced pluripotent stem cells (iPSCs) represents an exceptional complementary tool for the investigation of degenerative processes. In this review, we will focus on two neurodegenerative diseases, Alzheimer's and Parkinson's disease. We will provide examples of iPSC-derived neuronal models and how they have been used to study calcium and mitochondrial alterations during neurodegeneration.

Keywords:  Alzheimer’s disease; Human iPSCs; Mitochondrial dysfunction; Neurodegenerative diseases; Parkinson’s disease

DOI:  https://doi.org/10.1016/j.ceca.2021.102362
Nat Genet. 2021 Feb;53(2): 215-229

Metabolic control of DNA methylation in naive pluripotent cells.

Riccardo M Betto, Linda Diamante, Valentina Perrera, Matteo Audano, Stefania Rapelli, Andrea Lauria, Danny Incarnato, Mattia Arboit, Silvia Pedretti, Giovanni Rigoni, Vincent Guerineau, David Touboul, Giuliano Giuseppe Stirparo, Tim Lohoff, Thorsten Boroviak, Paolo Grumati, Maria E Soriano, Jennifer Nichols, Nico Mitro, Salvatore Oliviero, Graziano Martello.

Naive epiblast and embryonic stem cells (ESCs) give rise to all cells of adults. Such developmental plasticity is associated with genome hypomethylation. Here, we show that LIF-Stat3 signaling induces genomic hypomethylation via metabolic reconfiguration. Stat3-/- ESCs show decreased α-ketoglutarate production from glutamine, leading to increased Dnmt3a and Dnmt3b expression and DNA methylation. Notably, genome methylation is dynamically controlled through modulation of α-ketoglutarate availability or Stat3 activation in mitochondria. Alpha-ketoglutarate links metabolism to the epigenome by reducing the expression of Otx2 and its targets Dnmt3a and Dnmt3b. Genetic inactivation of Otx2 or Dnmt3a and Dnmt3b results in genomic hypomethylation even in the absence of active LIF-Stat3. Stat3-/- ESCs show increased methylation at imprinting control regions and altered expression of cognate transcripts. Single-cell analyses of Stat3-/- embryos confirmed the dysregulated expression of Otx2, Dnmt3a and Dnmt3b as well as imprinted genes. Several cancers display Stat3 overactivation and abnormal DNA methylation; therefore, the molecular module that we describe might be exploited under pathological conditions.

DOI: https://doi.org/10.1038/s41588-020-00770-2
JAMA Neurol. 2021 Feb 01.

Identification of Candidate Parkinson Disease Genes by Integrating Genome-Wide Association Study, Expression, and Epigenetic Data Sets.

United Kingdom Brain Expression Consortium (UKBEC) and the International Parkinson’s Disease Genomics Consortium (IPDGC)

Importance: Substantial genome-wide association study (GWAS) work in Parkinson disease (PD) has led to the discovery of an increasing number of loci shown reliably to be associated with increased risk of disease. Improved understanding of the underlying genes and mechanisms at these loci will be key to understanding the pathogenesis of PD.
Objective: To investigate what genes and genomic processes underlie the risk of sporadic PD.
Design and Setting: This genetic association study used the bioinformatic tools Coloc and transcriptome-wide association study (TWAS) to integrate PD case-control GWAS data published in 2017 with expression data (from Braineac, the Genotype-Tissue Expression [GTEx], and CommonMind) and methylation data (derived from UK Parkinson brain samples) to uncover putative gene expression and splicing mechanisms associated with PD GWAS signals. Candidate genes were further characterized using cell-type specificity, weighted gene coexpression networks, and weighted protein-protein interaction networks.
Main Outcomes and Measures: It was hypothesized a priori that some genes underlying PD loci would alter PD risk through changes to expression, splicing, or methylation. Candidate genes are presented whose change in expression, splicing, or methylation are associated with risk of PD as well as the functional pathways and cell types in which these genes have an important role.
Results: Gene-level analysis of expression revealed 5 genes (WDR6 [OMIM 606031], CD38 [OMIM 107270], GPNMB [OMIM 604368], RAB29 [OMIM 603949], and TMEM163 [OMIM 618978]) that replicated using both Coloc and TWAS analyses in both the GTEx and Braineac expression data sets. A further 6 genes (ZRANB3 [OMIM 615655], PCGF3 [OMIM 617543], NEK1 [OMIM 604588], NUPL2 [NCBI 11097], GALC [OMIM 606890], and CTSB [OMIM 116810]) showed evidence of disease-associated splicing effects. Cell-type specificity analysis revealed that gene expression was overall more prevalent in glial cell types compared with neurons. The weighted gene coexpression performed on the GTEx data set showed that NUPL2 is a key gene in 3 modules implicated in catabolic processes associated with protein ubiquitination and in the ubiquitin-dependent protein catabolic process in the nucleus accumbens, caudate, and putamen. TMEM163 and ZRANB3 were both important in modules in the frontal cortex and caudate, respectively, indicating regulation of signaling and cell communication. Protein interactor analysis and simulations using random networks demonstrated that the candidate genes interact significantly more with known mendelian PD and parkinsonism proteins than would be expected by chance.
Conclusions and Relevance: Together, these results suggest that several candidate genes and pathways are associated with the findings observed in PD GWAS studies.

DOI: https://doi.org/10.1001/jamaneurol.2020.5257
Nat Immunol. 2021 Feb 05.

IRGM1, a guardian of mitochondrial DAMP-mediated autoinflammation.

Brett A Kaufman, Ana L Mora.

DOI: https://doi.org/10.1038/s41590-021-00877-6
J Lipid Res. 2020 Dec;pii: S0022-2275(20)60030-X. [Epub ahead of print]61(12): 1707-1719

Identification of unusual phospholipids from bovine heart mitochondria by HPLC-MS/MS.

Junhwan Kim, Charles L Hoppel.

  Phospholipids, including ether phospholipids, are composed of numerous isomeric and isobaric species that have the same backbone and acyl chains. This structural resemblance results in similar fragmentation patterns by collision-induced dissociation of phospholipids regardless of class, yielding complicated MS/MS spectra when isobaric species are analyzed together. Furthermore, the presence of isobaric species can lead to misassignment of species when made solely based on their molecular weights. In this study, we used normal-phase HPLC for ESI-MS/MS analysis of phospholipids from bovine heart mitochondria. Class separation by HPLC eliminates chances for misidentification of isobaric species from different classes of phospholipids. Chromatography yields simple MS/MS spectra without interference from isobaric species, allowing clear identification of peaks corresponding to fragmented ions containing monoacylglycerol backbone derived from losing one acyl chain. Using these fragmented ions, we characterized individual and isomeric species in each class of mitochondrial phospholipids, including unusual species, such as PS, containing an ether linkage and species containing odd-numbered acyl chains in cardiolipin, PS, PI, and PG. We also characterized monolysocardiolipin and dilysocardiolipin, the least abundant but nevertheless important mitochondrial phospholipids. The results clearly show the power of HPLC-MS/MS for identification and characterization of phospholipids, including minor species.

Keywords:  acyl chain; cardiolipin; collision-induced dissociation; ether phospholipids; high-performance liquid chromatography-tandem mass spectrometry; lipidomics; odd-numbered acyl chain

DOI:  https://doi.org/10.1194/jlr.RA120001044
Genet Med. 2021 Feb 02.

GUÍA: a digital platform to facilitate result disclosure in genetic counseling.

Sabrina A Suckiel, Jaqueline A Odgis, Katie M Gallagher, Jessica E Rodriguez, Dana Watnick, Gabrielle Bertier, Monisha Sebastin, Nicole Yelton, Estefany Maria, Jessenia Lopez, Michelle Ramos, Nicole Kelly, Nehama Teitelman, Faygel Beren, Tom Kaszemacher, Kojo Davis, Irma Laguerre, Lynne D Richardson, George A Diaz, Nathaniel M Pearson, Stephen B Ellis, Christian Stolte, Mimsie Robinson, Patricia Kovatch, Carol R Horowitz, Bruce D Gelb, John M Greally, Laurie J Bauman, Randi E Zinberg, Noura S Abul-Husn, Melissa P Wasserstein, Eimear E Kenny.

PURPOSE: Use of genomic sequencing is increasing at a pace that requires technological solutions to effectively meet the needs of a growing patient population. We developed GUÍA, a web-based application, to enhance the delivery of genomic results and related clinical information to patients and families.
METHODS: GUÍA development occurred in five overlapping phases: formative research, content development, stakeholder/community member input, user interface design, and web application development. Development was informed by formative qualitative research involving parents (N = 22) whose children underwent genomic testing. Participants enrolled in the NYCKidSeq pilot study (N = 18) completed structured feedback interviews post-result disclosure using GUÍA. Genetic specialists, researchers, patients, and community stakeholders provided their perspectives on GUÍA's design to ensure technical, cultural, and literacy appropriateness.
RESULTS: NYCKidSeq participants responded positively to the use of GUÍA to deliver their children's results. All participants (N = 10) with previous experience with genetic testing felt GUÍA improved result disclosure, and 17 (94%) participants said the content was clear.
CONCLUSION: GUÍA communicates complex genomic information in an understandable and personalized manner. Initial piloting demonstrated GUÍA's utility for families enrolled in the NYCKidSeq pilot study. Findings from the NYCKidSeq clinical trial will provide insight into GUÍA's effectiveness in communicating results among diverse, multilingual populations.

DOI: https://doi.org/10.1038/s41436-020-01063-z
FASEB J. 2021 Feb;35(2): e21361

BAG6 promotes PINK1 signaling pathway and is essential for mitophagy.

Romain Ragimbeau, Leila El Kebriti, Salwa Sebti, Elise Fourgous, Abdelhay Boulahtouf, Giuseppe Arena, Lucile Espert, Andrei Turtoi, Céline Gongora, Nadine Houédé, Sophie Pattingre.

  Bcl-2-associated athanogen-6 (BAG6) is a nucleocytoplasmic shuttling protein involved in protein quality control. We previously demonstrated that BAG6 is essential for autophagy by regulating the intracellular localization of the acetyltransferase EP300, and thus, modifying accessibility to its substrates (TP53 in the nucleus and autophagy-related proteins in the cytoplasm). Here, we investigated BAG6 localization and function in the cytoplasm. First, we demonstrated that BAG6 is localized in the mitochondria. Specifically, BAG6 is expressed in the mitochondrial matrix under basal conditions, and translocates to the outer mitochondrial membrane after mitochondrial depolarization with carbonyl cyanide m-chlorophenyl hydrazine, a mitochondrial uncoupler that induces mitophagy. In SW480 cells, the deletion of BAG6 expression abrogates its ability to induce mitophagy and PINK1 accumulation. On the reverse, its ectopic expression in LoVo colon cancer cells, which do not express endogenous BAG6, reduces the size of the mitochondria, induces mitophagy, leads to the activation of the PINK1/PARKIN pathway and to the phospho-ubiquitination of mitochondrial proteins. Finally, BAG6 contains two LIR (LC3-interacting Region) domains specifically found in receptors for selective autophagy and responsible for the interaction with LC3 and for autophagosome selectivity. Site-directed mutagenesis showed that BAG6 requires wild-type LIRs domains for its ability to stimulate mitophagy. In conclusion, we propose that BAG6 is a novel mitophagy receptor or adaptor that induces PINK1/PARKIN signaling and mitophagy in a LIR-dependent manner.

Keywords:  BAG6; mitophagy; receptor; signaling

DOI:  https://doi.org/10.1096/fj.202000930R
J Am Heart Assoc. 2021 Feb 03. e018776

Mitochondrial DNA Content Is Linked to Cardiovascular Disease Patient Phenotypes.

Ruipeng Wei, Ying Ni, Peter Bazeley, Sneha Grandhi, Janet Wang, Samuel T Li, Stanley L Hazen, W H Wilson Tang, Thomas LaFramboise.

  Background We sought to determine whether mitochondrial DNA (mtDNA) content can be used as markers for 12 key phenotypes among cardiovascular disease patients, and whether these markers are valid across patients with diverse ancestries. Methods and Results DNA was collected from the peripheral blood of 996 cardiovascular disease patients at the Cleveland Clinic. The mtDNA copy number and DNA-level variation were assessed from whole-genome sequence. Patients were also ascertained retrospectively for histories of 10 clinical events, as well as for maximum stenosis and extent of disease at baseline. Self-reported race and maternal ancestry inferred from mtDNA sequence were recorded. MtDNA copy number and overall mtDNA rare variant load were significantly lower in patients with histories of various adverse clinical events, and mtDNA copy number was inversely correlated with extent of disease. Strong associations were also found between absence of rare variants in the genes MT-ATP6 and MT-COII and patient histories of hyperlipidemia and myocardial infarction, respectively. Importantly, associations were not ancestry dependent. Conclusions This study provides evidence that mtDNA copy number in circulation is associated with a variety of cardiovascular disease patient phenotypes. Results also suggest a protective role for some rare inherited mtDNA variants. Overall, the study supports the potential of mtDNA content and abundance as biomarkers in heart disease, in a manner that is valid across diverse ancestries.

Keywords:  blood‐based biomarkers; cardiovascular disease; mitochondrial DNA

DOI:  https://doi.org/10.1161/JAHA.120.018776
Genome Biol. 2021 Feb 02. 22(1): 55

GeneWalk identifies relevant gene functions for a biological context using network representation learning.

Robert Ietswaart, Benjamin M Gyori, John A Bachman, Peter K Sorger, L Stirling Churchman.

  A bottleneck in high-throughput functional genomics experiments is identifying the most important genes and their relevant functions from a list of gene hits. Gene Ontology (GO) enrichment methods provide insight at the gene set level. Here, we introduce GeneWalk ( github.com/churchmanlab/genewalk ) that identifies individual genes and their relevant functions critical for the experimental setting under examination. After the automatic assembly of an experiment-specific gene regulatory network, GeneWalk uses representation learning to quantify the similarity between vector representations of each gene and its GO annotations, yielding annotation significance scores that reflect the experimental context. By performing gene- and condition-specific functional analysis, GeneWalk converts a list of genes into data-driven hypotheses.

Keywords:  Differential expression; Functional analysis; GO enrichment; Gene set enrichment analysis; GeneWalk; INDRA (Integrated Network and Dynamical Reasoning Assembler); Machine learning; NET-seq; Network representation learning; Next-generation sequencing; Pathway Commons; RNA-seq

DOI:  https://doi.org/10.1186/s13059-021-02264-8
Muscle Nerve. 2021 Feb 03.

A Novel Exercise Testing Algorithm to Diagnose Mitochondrial Myopathy.

Rajeev Bhatia, Bruce H Cohen, Neil McNinch.

   INTRODUCTION: Oxygen uptake efficiency slope (OUES) is a non-invasive cardiopulmonary exercise testing (CPET) measurement based on oxygen uptake (V&c.dotab;O2 ) and minute ventilation (V&c.dotab;E ) and is a marker of the efficiency of oxygen utilization by the body. However, it has not been studied in mitochondrial disorders. We explored noninvasive CPET parameters including OUES as a way to reliably diagnose mitochondrial myopathy.
METHODS: We performed cycle ergometer maximal exercise testing on definite and suspected mitochondrial myopathy subjects (MM-D & MM-S) and their age and sex matched controls. OUES was corrected for body surface area (OUES/BSA) to eliminate the effect of body size.
RESULTS: 40 participants [20 mitochondrial myopathy subjects {13 MM-D (6 males; aged 14-64 years) / 7 MM-S (5 males, aged 11-30 years} and 20 controls] completed the study. MM-D subjects showed lower aerobic fitness than controls. OUES/BSA was lower in MM-D subjects suggesting inefficient oxygen utilization. Area under the curve (AUC) and 95% Confidence Interval (CI) for OUES/BSA [0.91 (0.80, 1.00)], Peak V&c.dotab;O2 % predicted [0.95 (0.86, 1.00)] and V&c.dotab;O2 /Work slope [0.94 (0.85, 1.00)] showed excellent ability to diagnose mitochondrial myopathy in MM-D subjects. We applied a diagnostic approach based on the above parameters to MM-S subjects and their controls and were able to support or disprove the diagnosis of mitochondrial myopathy.
DISCUSSION: We proposed and applied an approach based on the above three CPET parameters to reliably diagnose mitochondrial myopathy and found it to be clinically useful. This article is protected by copyright. All rights reserved.

Keywords:  Cardiopulmonary exercise testing; Mitochondrial myopathy; Oxygen Uptake Efficiency Slope (OUES); Oxygen uptake (V&c.dotab;O2); V&c.dotab;O2 /Work slope

DOI:  https://doi.org/10.1002/mus.27191
Nature. 2021 Feb;590(7844): 57-66

Function and regulation of the divisome for mitochondrial fission.

Felix Kraus, Krishnendu Roy, Thomas J Pucadyil, Michael T Ryan.

Mitochondria form dynamic networks in the cell that are balanced by the flux of iterative fusion and fission events of the organelles. It is now appreciated that mitochondrial fission also represents an end-point event in a signalling axis that allows cells to sense and respond to external cues. The fission process is orchestrated by membrane-associated adaptors, influenced by organellar and cytoskeletal interactions and ultimately executed by the dynamin-like GTPase DRP1. Here we invoke the framework of the 'mitochondrial divisome', which is conceptually and operationally similar to the bacterial cell-division machinery. We review the functional and regulatory aspects of the mitochondrial divisome and, within this framework, parse the core from the accessory machinery. In so doing, we transition from a phenomenological to a mechanistic understanding of the fission process.

DOI: https://doi.org/10.1038/s41586-021-03214-x
Cell Stem Cell. 2021 Feb 01. pii: S1934-5909(21)00002-3. [Epub ahead of print]

Mitochondrial metabolism is a key regulator of the fibro-inflammatory and adipogenic stromal subpopulations in white adipose tissue.

Nolwenn Joffin, Vivian A Paschoal, Christy M Gliniak, Clair Crewe, Abdallah Elnwasany, Luke I Szweda, Qianbin Zhang, Chelsea Hepler, Christine M Kusminski, Ruth Gordillo, Da Young Oh, Rana K Gupta, Philipp E Scherer.

  The adipose tissue stroma is a rich source of molecularly distinct stem and progenitor cell populations with diverse functions in metabolic regulation, adipogenesis, and inflammation. The ontology of these populations and the mechanisms that govern their behaviors in response to stimuli, such as overfeeding, however, are unclear. Here, we show that the developmental fates and functional properties of adipose platelet-derived growth factor receptor beta (PDGFRβ)+ progenitor subpopulations are tightly regulated by mitochondrial metabolism. Reducing the mitochondrial β-oxidative capacity of PDGFRβ+ cells via inducible expression of MitoNEET drives a pro-inflammatory phenotype in adipose progenitors and alters lineage commitment. Furthermore, disrupting mitochondrial function in PDGFRβ+ cells rapidly induces alterations in immune cell composition in lean mice and impacts expansion of adipose tissue in diet-induced obesity. The adverse effects on adipose tissue remodeling can be reversed by restoring mitochondrial activity in progenitors, suggesting therapeutic potential for targeting energy metabolism in these cells.

Keywords:  adipocyte; adipogenesis; inflammation; metabolism; mitochondria; stem cells

DOI:  https://doi.org/10.1016/j.stem.2021.01.002
EMBO J. 2021 Feb 02. e105268

Mitochondrial translation deficiency impairs NAD+ -mediated lysosomal acidification.

Mikako Yagi, Takahiro Toshima, Rie Amamoto, Yura Do, Haruka Hirai, Daiki Setoyama, Dongchon Kang, Takeshi Uchiumi.

  Mitochondrial translation dysfunction is associated with neurodegenerative and cardiovascular diseases. Cells eliminate defective mitochondria by the lysosomal machinery via autophagy. The relationship between mitochondrial translation and lysosomal function is unknown. In this study, mitochondrial translation-deficient hearts from p32-knockout mice were found to exhibit enlarged lysosomes containing lipofuscin, suggesting impaired lysosome and autolysosome function. These mice also displayed autophagic abnormalities, such as p62 accumulation and LC3 localization around broken mitochondria. The expression of genes encoding for nicotinamide adenine dinucleotide (NAD+ ) biosynthetic enzymes-Nmnat3 and Nampt-and NAD+ levels were decreased, suggesting that NAD+ is essential for maintaining lysosomal acidification. Conversely, nicotinamide mononucleotide (NMN) administration or Nmnat3 overexpression rescued lysosomal acidification. Nmnat3 gene expression is suppressed by HIF1α, a transcription factor that is stabilized by mitochondrial translation dysfunction, suggesting that HIF1α-Nmnat3-mediated NAD+ production is important for lysosomal function. The glycolytic enzymes GAPDH and PGK1 were found associated with lysosomal vesicles, and NAD+ was required for ATP production around lysosomal vesicles. Thus, we conclude that NAD+ content affected by mitochondrial dysfunction is essential for lysosomal maintenance.

Keywords:  GAPDH; NAD+; Nmnat3; lysosome; mitochondria

DOI:  https://doi.org/10.15252/embj.2020105268