bims-mitdis 2021-08-22 papers

bims-mitdis

Biomed News

on Mitochondrial disorders

Issue of 2021–08–22
39 papers selected by
Catalina Vasilescu, University of Helsinki

The m.3890G>A/MT-ND1 mtDNA rare pathogenic variant: expanding clinical and MRI phenotypes.
Mechanisms of impaired mitochondrial homeostasis and NAD+ metabolism in a model of mitochondrial heart disease exhibiting redox active iron accumulation.
A Novel Mitochondrial Mutation for Lebers Hereditary Optic Neuropathy Presenting With Vitamin B12 Deficiency.
Skeletal muscle mitochondrial network dynamics in metabolic disorders and aging.
Structural characterization of the mitochondrial Ca2+ uniporter provides insights into Ca2+ uptake and regulation.
A novel homoplasmic mt-tRNAGlu m.14701C>T variant presenting with a partially reversible infantile respiratory chain deficiency.
Adaptive optimization of the OXPHOS assembly line partially compensates lrpprc-dependent mitochondrial translation defects in mice.
IRC3 regulates mitochondrial translation in response to metabolic cues in Saccharomyces cerevisiae.
Linking transport and translation of mRNAs with endosomes and mitochondria.
Ca2+ handling at the mitochondria-ER contact sites in neurodegeneration.
Spatiotemporally-resolved mapping of RNA binding proteins via functional proximity labeling reveals a mitochondrial mRNA anchor promoting stress recovery.
Genome sequencing and RNA-seq analyses of mitochondrial complex I deficiency revealed Alu insertion-mediated deletion in NDUFV2.
Boosting mitochondrial metabolism with dietary supplements in heart failure.
Neutrophil HIF-1α stabilisation is augmented by mitochondrial ROS produced via the glycerol 3-phosphate shuttle.
Protocol for rapid manipulation of mitochondrial morphology in living cells using inducible counter mitochondrial morphology (iCMM).
Post-translational Acetylation Control of Cardiac Energy Metabolism.
An engineered transcriptional reporter of protein localization identifies regulators of mitochondrial and ER membrane protein trafficking in high-throughput CRISPRi screens.
Effect of crista morphology on mitochondrial ATP output: A computational study.
Whole genome sequencing identifies pathogenic RNU4ATAC variants in a child with recurrent encephalitis, microcephaly, and normal stature.
Charcot-Marie-Tooth mutation in glycyl-tRNA synthetase stalls ribosomes in a pre-accommodation state and activates integrated stress response.
Genetic Editing of Long Noncoding RNA Using CRISPR/Cas9 Technology.
Metabolic decisions in development and disease-a Keystone Symposia report.
Automated segmentation and tracking of mitochondria in live-cell time-lapse images.
Mechanisms that ensure speed and fidelity in eukaryotic translation termination.
Contact and competition between mitochondria and microbes.
Isoform Age - Splice Isoform Profiling Using Long-Read Technologies.
Molecular mechanism of thiamine pyrophosphate import into mitochondria: a molecular simulation study.
Inborn errors of metabolism associated with 3-methylglutaconic aciduria.
Mitochondrial fatty acid utilization increases chromatin oxidative stress in cardiomyocytes.
Mitochondrial Lon protease is a gatekeeper for proteins newly imported into the matrix.
The role of mitochondria dysfunction and hepatic senescence in NAFLD development and progression.
PhenoDB, GeneMatcher and VariantMatcher, tools for analysis and sharing of sequence data.
Abnormal Mitochondria-Endoplasmic Reticulum Communication Promotes Myocardial Infarction.
PPA2-associated sudden cardiac death: extending the clinical and allelic spectrum in 20 new families.
Analysis of Hsp90 allosteric modulators interactome reveals a potential dual action mode involving mitochondrial MDH2.
Magnetic Resonance Imaging Findings in the Pregeniculate Visual Pathway in Leber Hereditary Optic Neuropathy.
RANBP2 mutation causing autosomal dominant acute necrotizing encephalopathy attenuates its interaction with COX11.
Methods for Characterization of Alternative RNA Splicing.
Epigenome-wide association study of mitochondrial genome copy number.

Mitochondrion. 2021 Aug 11. pii: S1567-7249(21)00108-2. [Epub ahead of print]

The m.3890G>A/MT-ND1 mtDNA rare pathogenic variant: expanding clinical and MRI phenotypes.

Veria Vacchiano, Leonardo Caporali, Chiara La Morgia, Michele Carbonelli, Giulia Amore, Ilaria Bartolomei, Maria Luisa Cascavilla, Piero Barboni, Costanza Lamperti, Alessia Catania, Jane W Chan, Rustum Karanja, Alfredo A Sadun, Rocco Liguori, Andrea Bianchi, Gioele Gavazzi, Mario Mascalchi, Fabrizio Salvi, Valerio Carelli.

   INTRODUCTION: Isolated complex I deficiency causes several clinical syndromes, including Leigh syndrome (LS), Leber hereditary optic neuropathy (LHON) and mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes (MELAS). Here we reported two new patients carrying the rare m.3890G>A/MT-ND1 (p.Arg195Gln) mitochondrial DNA (mtDNA) pathogenic variant, revisited another two previously reported cases, and reviewed the remaining published cases, to refine the clinical and neuroimaging features. We also quantitatively assessed the mtDNA heteroplasmy in all available tissues.
CASES PRESENTATION: The first patient was a 25-year-old male presenting with axonal polyneuropathy, optic atrophy consistent with LHON, gaze palsy and parkinsonism. MRI correlates included transient centromedullary T2 hyperintensity in the conus medullaris, transient signal intensity and increased lactate in the midbrain periaqueductal gray matter, and late atrophy of the optic nerves and chiasm, dorsal midbrain and conus medullaris. The second patient was a 65-year-old woman with a classical LHON phenotype and a normal MRI.
DISCUSSION: Including the previously published cases, the clinical spectrum ranged from LHON to Leigh-like syndrome with peculiar CNS lesions and encephalopatic clinical symptoms. The most severe and complex cases were associated with very high heteroplasmy, or nearly homoplasmic m.3890G>A/MT-ND1 pathogenic variant in skeletal muscle, displaying neurological symptoms/signs consistent with Leigh-like lesions on brain MRI. Lower heteroplasmic mutational loads were instead associated with isolated LHON-like optic neuropathy of variable severity.
CONCLUSION: The m.3890G>A/MT-ND1 mtDNA pathogenic variant increasingly impairs complex I function dependent on heteroplasmic loads, leading to a spectrum of LHON and Leigh-like encephalopathy with distinguishing MRI features.

Keywords:  LHON; Leigh syndrome; MRI; clinical phenotype; m.3890G>A/MT-ND1 mtDNA pathogenic variant

DOI:  https://doi.org/10.1016/j.mito.2021.08.007
Redox Biol. 2021 Jun 10. pii: S2213-2317(21)00197-X. [Epub ahead of print]46 102038

Mechanisms of impaired mitochondrial homeostasis and NAD+ metabolism in a model of mitochondrial heart disease exhibiting redox active iron accumulation.

Shannon Chiang, Nady Braidy, Sanaz Maleki, Sean Lal, Des R Richardson, Michael L-H Huang.

  Due to the high redox activity of the mitochondrion, this organelle can suffer oxidative stress. To manage energy demands while minimizing redox stress, mitochondrial homeostasis is maintained by the dynamic processes of mitochondrial biogenesis, mitochondrial network dynamics (fusion/fission), and mitochondrial clearance by mitophagy. Friedreich's ataxia (FA) is a mitochondrial disease resulting in a fatal hypertrophic cardiomyopathy due to the deficiency of the mitochondrial protein, frataxin. Our previous studies identified defective mitochondrial iron metabolism and oxidative stress potentiating cardiac pathology in FA. However, how these factors alter mitochondrial homeostasis remains uncharacterized in FA cardiomyopathy. This investigation examined the muscle creatine kinase conditional frataxin knockout mouse, which closely mimics FA cardiomyopathy, to dissect the mechanisms of dysfunctional mitochondrial homeostasis. Dysfunction of key mitochondrial homeostatic mechanisms were elucidated in the knockout hearts relative to wild-type littermates, namely: (1) mitochondrial proliferation with condensed cristae; (2) impaired NAD+ metabolism due to perturbations in Sirt1 activity and NAD+ salvage; (3) increased mitochondrial biogenesis, fusion and fission; and (4) mitochondrial accumulation of Pink1/Parkin with increased autophagic/mitophagic flux. Immunohistochemistry of FA patients' heart confirmed significantly enhanced expression of markers of mitochondrial biogenesis, fusion/fission and autophagy. These novel findings demonstrate cardiac frataxin-deficiency results in significant changes to metabolic mechanisms critical for mitochondrial homeostasis. This mechanistic dissection provides critical insight, offering the potential for maintaining mitochondrial homeostasis in FA and potentially other cardio-degenerative diseases by implementing innovative treatments targeting mitochondrial homeostasis and NAD+ metabolism.

Keywords:  Cardiomyopathy; Iron; Iron loading; Mitochondria; Mitochondrial homeostasis

DOI:  https://doi.org/10.1016/j.redox.2021.102038
J Neuroophthalmol. 2021 Aug 17.

A Novel Mitochondrial Mutation for Lebers Hereditary Optic Neuropathy Presenting With Vitamin B12 Deficiency.

Vladislav P Bekerman, Eric Berman, Bei You, Roger Turbin, Larry Frohman.

DOI: https://doi.org/10.1097/WNO.0000000000001391
Trends Mol Med. 2021 Aug 17. pii: S1471-4914(21)00198-2. [Epub ahead of print]

Skeletal muscle mitochondrial network dynamics in metabolic disorders and aging.

Ciarán E Fealy, Lotte Grevendonk, Joris Hoeks, Matthijs K C Hesselink.

  With global demographics trending towards an aging population, the numbers of individuals with an age-associated loss of independence is increasing. A key contributing factor is loss of skeletal muscle mitochondrial, metabolic, and contractile function. Recent advances in imaging technologies have demonstrated the importance of mitochondrial morphology and dynamics in the pathogenesis of disease. In this review, we examine the evidence for altered mitochondrial dynamics as a mechanism in age and obesity-associated loss of skeletal muscle function, with a particular focus on the available human data. We highlight some of the areas where more data are needed to identify the specific mechanisms connecting mitochondrial morphology and skeletal muscle dysfunction.

Keywords:  aging; metabolic disease; mitochondria; mitochondrial dynamics; sarcopenia

DOI:  https://doi.org/10.1016/j.molmed.2021.07.013
iScience. 2021 Aug 20. 24(8): 102895

Structural characterization of the mitochondrial Ca2+ uniporter provides insights into Ca2+ uptake and regulation.

Wenping Wu, Jimin Zheng, Zongchao Jia.

  The mitochondrial uniporter is a Ca2+-selective ion-conducting channel in the inner mitochondrial membrane that is involved in various cellular processes. The components of this uniporter, including the pore-forming membrane subunit MCU and the modulatory subunits MCUb, EMRE, MICU1, and MICU2, have been identified in recent years. Previously, extensive studies revealed various aspects of uniporter activities and proposed multiple regulatory models of mitochondrial Ca2+ uptake. Recently, the individual auxiliary components of the uniporter and its holocomplex have been structurally characterized, providing the first insight into the component structures and their spatial relationship within the context of the uniporter. Here, we review recent uniporter structural studies in an attempt to establish an architectural framework, elucidating the mechanism that governs mitochondrial Ca2+ uptake and regulation, and to address some apparent controversies. This information could facilitate further characterization of mitochondrial Ca2+ permeation and a better understanding of uniporter-related disease conditions.

Keywords:  Ion; Membranes; Molecular biology

DOI:  https://doi.org/10.1016/j.isci.2021.102895
Eur J Med Genet. 2021 Aug 13. pii: S1769-7212(21)00172-5. [Epub ahead of print] 104306

A novel homoplasmic mt-tRNAGlu m.14701C>T variant presenting with a partially reversible infantile respiratory chain deficiency.

Alberte A Lundquist, Stense Farholt, Malene L Børresen, Morten Dunø, Flemming Wibrand, Nanna Witting, Elsebet Østergaard.

   BACKGROUND: Reversible infantile respiratory chain deficiency (RIRCD) is a rare mitochondrial disorder associated with variable penetrance and partial to full remission of symptoms.
OBJECTIVE: To describe features of maternally related individuals with a novel variant associated with RIRCD.
MATERIALS AND METHODS: Nine maternally related individuals aged 23 months to 64 years are described through physical examinations, muscle biopsies, histochemical and biochemical analyses, genome sequencing, and cerebral imaging.
RESULTS: A homoplasmic mitochondrial transfer ribonucleic acid for glutamic acid (mt-tRNAGlu) m.14701C > T variant was identified in eight tested individuals out of nine maternally related individuals. Two individuals presented with hypotonia, muscle weakness, feeding difficulties and lactic acidosis at age 3-4 months, and improvement around age 15-23 months with mild residual symptoms at last examination. One individual with less severe symptoms had unknown age at onset and improved around age 4-5 years. Five individuals developed lipoma on the upper back, and one adult individual developed ataxia, while one was unaffected.
CONCLUSIONS: We have identified a novel homoplasmic mt-tRNAGlu m.14701C > T variant presenting with phenotypic and paraclinical features associated with RIRCD as well as ataxia and lipomas, which to our knowledge are new features associated to RIRCD.

Keywords:  Homoplasmy; MT-TE; Mitochondrial disorders; Mt-tRNA(Glu); RIRCD

DOI:  https://doi.org/10.1016/j.ejmg.2021.104306
Commun Biol. 2021 Aug 19. 4(1): 989

Adaptive optimization of the OXPHOS assembly line partially compensates lrpprc-dependent mitochondrial translation defects in mice.

LSFC Consortium

Mouse models of genetic mitochondrial disorders are generally used to understand specific molecular defects and their biochemical consequences, but rarely to map compensatory changes allowing survival. Here we took advantage of the extraordinary mitochondrial resilience of hepatic Lrpprc knockout mice to explore this question using native proteomics profiling and lipidomics. In these mice, low levels of the mtRNA binding protein LRPPRC induce a global mitochondrial translation defect and a severe reduction (>80%) in the assembly and activity of the electron transport chain (ETC) complex IV (CIV). Yet, animals show no signs of overt liver failure and capacity of the ETC is preserved. Beyond stimulation of mitochondrial biogenesis, results show that the abundance of mitoribosomes per unit of mitochondria is increased and proteostatic mechanisms are induced in presence of low LRPPRC levels to preserve a balance in the availability of mitochondrial- vs nuclear-encoded ETC subunits. At the level of individual organelles, a stabilization of residual CIV in supercomplexes (SCs) is observed, pointing to a role of these supramolecular arrangements in preserving ETC function. While the SC assembly factor COX7A2L could not contribute to the stabilization of CIV, important changes in membrane glycerophospholipid (GPL), most notably an increase in SC-stabilizing cardiolipins species (CLs), were observed along with an increased abundance of other supramolecular assemblies known to be stabilized by, and/or participate in CL metabolism. Together these data reveal a complex in vivo network of molecular adjustments involved in preserving mitochondrial integrity in energy consuming organs facing OXPHOS defects, which could be therapeutically exploited.

DOI: https://doi.org/10.1038/s42003-021-02492-5
Mol Cell Biol. 2021 Aug 16. MCB0023321

IRC3 regulates mitochondrial translation in response to metabolic cues in Saccharomyces cerevisiae.

Jaswinder Kaur, Kaustuv Datta.

Mitochondrial oxidative phosphorylation (OXPHOS) enzymes are made up of dual genetic origin. Mechanisms regulating the expression of nuclear-encoded OXPHOS subunits in response to metabolic cues (glucose vs. glycerol), is significantly understood while regulation of mitochondrially encoded OXPHOS subunits is poorly defined. Here, we show that IRC3 a DEAD/H box helicase, previously implicated in mitochondrial DNA maintenance, is central to integrating metabolic cues with mitochondrial translation. Irc3 associates with mitochondrial small ribosomal subunit in cells consistent with its role in regulating translation elongation based on Arg8m reporter system. IRC3 deleted cells retained mitochondrial DNA despite growth defect on glycerol plates. Glucose grown Δirc3ρ+ and irc3 temperature-sensitive cells at 370C have reduced translation rates from majority of mRNAs. In contrast, when galactose was the carbon source, reduction in mitochondrial translation was observed predominantly from Cox1 mRNA in Δirc3ρ+ but no defect was observed in irc3 temperature-sensitive cells, at 370C. In support, of a model whereby IRC3 responds to metabolic cues to regulate mitochondrial translation, suppressors of Δirc3 isolated for restoration of growth on glycerol media restore mitochondrial protein synthesis differentially in presence of glucose vs. glycerol.

DOI: https://doi.org/10.1128/MCB.00233-21
EMBO Rep. 2021 Aug 17. e52445

Linking transport and translation of mRNAs with endosomes and mitochondria.

Kira Müntjes, Senthil Kumar Devan, Andreas S Reichert, Michael Feldbrügge.

  In eukaryotic cells, proteins are targeted to their final subcellular locations with precise timing. A key underlying mechanism is the active transport of cognate mRNAs, which in many systems can be linked intimately to membrane trafficking. A prominent example is the long-distance endosomal transport of mRNAs and their local translation. Here, we describe current highlights of fundamental mechanisms of the underlying transport process as well as of biological functions ranging from endosperm development in plants to fungal pathogenicity and neuronal processes. Translation of endosome-associated mRNAs often occurs at the cytoplasmic surface of endosomes, a process that is needed for membrane-assisted formation of heteromeric protein complexes and for accurate subcellular targeting of proteins. Importantly, endosome-coupled translation of mRNAs encoding mitochondrial proteins, for example, seems to be particularly important for efficient organelle import and for regulating subcellular mitochondrial activity. In essence, these findings reveal a new mechanism of loading newly synthesised proteins onto endocytic membranes enabling intimate crosstalk between organelles. The novel link between endosomes and mitochondria adds an inspiring new level of complexity to trafficking and organelle biology.

Keywords:  RNA transport; endosomes; local translation; microtubules; mitochondria; organelle

DOI:  https://doi.org/10.15252/embr.202152445
Cell Calcium. 2021 Aug 05. pii: S0143-4160(21)00107-X. [Epub ahead of print]98 102453

Ca2+ handling at the mitochondria-ER contact sites in neurodegeneration.

Dmitry Lim, Giulia Dematteis, Laura Tapella, Armando A Genazzani, Tito Calì, Marisa Brini, Alexei Verkhratsky.

  Mitochondria-endoplasmic reticulum (ER) contact sites (MERCS) are morpho-functional units, formed at the loci of close apposition of the ER-forming endomembrane and outer mitochondrial membrane (OMM). These sites contribute to fundamental cellular processes including lipid biosynthesis, autophagy, apoptosis, ER-stress and calcium (Ca2+) signalling. At MERCS, Ca2+ ions are transferred from the ER directly to mitochondria through a core protein complex composed of inositol-1,4,5 trisphosphate receptor (InsP3R), voltage-gated anion channel 1 (VDAC1), mitochondrial calcium uniporter (MCU) and adaptor protein glucose-regulated protein 75 (Grp75); this complex is regulated by several associated proteins. Deregulation of ER-mitochondria Ca2+ transfer contributes to pathogenesis of neurodegenerative and other diseases. The efficacy of Ca2+ transfer between ER and mitochondria depends on the protein composition of MERCS, which controls ER-mitochondria interaction regulating, for example, the transversal distance between ER membrane and OMM and the extension of the longitudinal interface between ER and mitochondria. These parameters are altered in neurodegeneration. Here we overview the ER and mitochondrial Ca2+ homeostasis, the composition of ER-mitochondrial Ca2+ transfer machinery and alterations of the ER-mitochondria Ca2+ transfer in three major neurodegenerative diseases: motor neurone diseases, Parkinson disease and Alzheimer's disease.

Keywords:  Alzheimer's disease; Amyotrophic lateral sclerosis; Endoplasmic reticulum; Mitochondria; Mitochondria-ER contact sites; Motor neurone disease; Parkinson's disease

DOI:  https://doi.org/10.1016/j.ceca.2021.102453
Nat Commun. 2021 08 17. 12(1): 4980

Spatiotemporally-resolved mapping of RNA binding proteins via functional proximity labeling reveals a mitochondrial mRNA anchor promoting stress recovery.

Wei Qin, Samuel A Myers, Dominique K Carey, Steven A Carr, Alice Y Ting.

Proximity labeling (PL) with genetically-targeted promiscuous enzymes has emerged as a powerful tool for unbiased proteome discovery. By combining the spatiotemporal specificity of PL with methods for functional protein enrichment, we show that it is possible to map specific protein subclasses within distinct compartments of living cells. In particular, we develop a method to enrich subcompartment-specific RNA binding proteins (RBPs) by combining peroxidase-catalyzed PL with organic-aqueous phase separation of crosslinked protein-RNA complexes ("APEX-PS"). We use APEX-PS to generate datasets of nuclear, nucleolar, and outer mitochondrial membrane (OMM) RBPs, which can be mined for novel functions. For example, we find that the OMM RBP SYNJ2BP retains specific nuclear-encoded mitochondrial mRNAs at the OMM during translation stress, facilitating their local translation and import of protein products into the mitochondrion during stress recovery. Functional PL in general, and APEX-PS in particular, represent versatile approaches for the discovery of proteins with novel function in specific subcellular compartments.

DOI: https://doi.org/10.1038/s41467-021-25259-2
Hum Mutat. 2021 Aug 18.

Genome sequencing and RNA-seq analyses of mitochondrial complex I deficiency revealed Alu insertion-mediated deletion in NDUFV2.

Yoshihito Kishita, Masaru Shimura, Masakazu Kohda, Takuya Fushimi, Kazuhiro R Nitta, Yukiko Yatsuka, Akira Ohtake, Kei Murayama, Yasushi Okazaki.

  Isolated complex I deficiency is the most common cause of pediatric mitochondrial disease. Exome sequencing (ES) has revealed many complex I causative genes. However, there are limitations associated with identifying causative genes by ES analysis. In this study, we performed multi-omics analysis to reveal the causal variants. We here report two cases with mitochondrial complex I deficiency. In both cases, ES identified a novelc.580G>A (p.Glu194Lys) variant in NDUFV2. One case additionally harbored c.427C>T (p.Arg143*), but no other variants were observed in the other case. RNA sequencing showed aberrant exon splicing of NDUFV2 in the unsolved case. GS revealed a novel heterozygous deletion in NDUFV2, which included one exon and resulted in exon skipping. Detailed examination of the breakpoint revealed that an Alu insertion-mediated rearrangement caused the deletion. Our report reveals that combined use of transcriptome sequencing and GS was effective for diagnosing cases that were unresolved by ES. This article is protected by copyright. All rights reserved.

Keywords:   Alu element; Mitochondrial disorder; RNA-seq; genome sequencing; mitochondrial complex I

DOI:  https://doi.org/10.1002/humu.24274
Nat Rev Cardiol. 2021 Aug 17.

Boosting mitochondrial metabolism with dietary supplements in heart failure.

Kevin D O'Brien, Rong Tian.

DOI: https://doi.org/10.1038/s41569-021-00610-8
Blood. 2021 Aug 19. pii: blood.2021011010. [Epub ahead of print]

Neutrophil HIF-1α stabilisation is augmented by mitochondrial ROS produced via the glycerol 3-phosphate shuttle.

Joseph Alexander Willson, Simone Arienti, Pranvera Sadiku, Leila Reyes, Patricia Coelho, Tyler Morrison, Giulia Rinaldi, David H Dockrell, Moira K B Whyte, Sarah R Walmsley.

Neutrophils are predominantly glycolytic cells that derive little ATP from oxidative phosphorylation; however, they possess an extensive mitochondrial network and maintain a mitochondrial membrane potential. Although studies have shown neutrophils need their mitochondria to undergo apoptosis and regulate NETosis, the metabolic role of the respiratory chain in these highly glycolytic cells is still unclear. Recent studies have expanded on the role of reactive oxygen species (ROS) released from the mitochondria as intracellular signalling molecules. Our study shows that neutrophils can use their mitochondria to generate ROS and that mitochondrial ROS release is increased in hypoxic conditions. This is needed for the stabilisation of a high level of the critical hypoxic response factor and pro-survival protein HIF-1α in hypoxia. Further, we demonstrate that neutrophils use the glycerol 3-phosphate pathway as a way of directly regulating mitochondrial function through glycolysis, specifically to maintain polarised mitochondria and produce ROS. This illustrates an additional pathway by which neutrophils can regulate HIF-1α stability and will therefore be of important consideration when looking for treatments of chronic inflammatory conditions where HIF-1α activation and neutrophil persistence at the site of inflammation are linked to disease severity.

DOI: https://doi.org/10.1182/blood.2021011010
STAR Protoc. 2021 Sep 17. 2(3): 100721

Protocol for rapid manipulation of mitochondrial morphology in living cells using inducible counter mitochondrial morphology (iCMM).

Takafumi Miyamoto, Song-Iee Han, Hitoshi Shimano.

  Disruption of mitochondrial morphology occurs during various diseases, but the biological significance is not entirely clear. Here, we describe a detailed step-by-step protocol for a chemically inducible dimerization system-based synthetic protein device, termed inducible counter mitochondrial morphology. This system allows artificial manipulation of mitochondrial morphology on a timescale of minutes in living mammalian cells. We also describe an AI-assisted imaging processing approach. For complete details on the use and execution of this protocol, please refer to Miyamoto et al., 2021.

Keywords:  Biotechnology and bioengineering; Cell Biology; Molecular/Chemical Probes; Protein Biochemistry

DOI:  https://doi.org/10.1016/j.xpro.2021.100721
Front Cardiovasc Med. 2021 ;8 723996

Post-translational Acetylation Control of Cardiac Energy Metabolism.

Ezra B Ketema, Gary D Lopaschuk.

  Perturbations in myocardial energy substrate metabolism are key contributors to the pathogenesis of heart diseases. However, the underlying causes of these metabolic alterations remain poorly understood. Recently, post-translational acetylation-mediated modification of metabolic enzymes has emerged as one of the important regulatory mechanisms for these metabolic changes. Nevertheless, despite the growing reports of a large number of acetylated cardiac mitochondrial proteins involved in energy metabolism, the functional consequences of these acetylation changes and how they correlate to metabolic alterations and myocardial dysfunction are not clearly defined. This review summarizes the evidence for a role of cardiac mitochondrial protein acetylation in altering the function of major metabolic enzymes and myocardial energy metabolism in various cardiovascular disease conditions.

Keywords:  fatty acid oxidation; glucose oxidation; lysine acetylation; mitochondria; sirtuins; succinylation

DOI:  https://doi.org/10.3389/fcvm.2021.723996
Elife. 2021 Aug 20. pii: e69142. [Epub ahead of print]10

An engineered transcriptional reporter of protein localization identifies regulators of mitochondrial and ER membrane protein trafficking in high-throughput CRISPRi screens.

Robert W Coukos, David Yao, Mateo Lopez Sanchez, Eric T Strand, Meagan E Olive, Namrata D Udeshi, Jonathan S Weissman, Steven A Carr, Michael C Bassik, Alice Y Ting.

  The trafficking of specific protein cohorts to correct subcellular locations at correct times is essential for every signaling and regulatory process in biology. Gene perturbation screens could provide a powerful approach to probe the molecular mechanisms of protein trafficking, but only if protein localization or mislocalization can be tied to a simple and robust phenotype for cell selection, such as cell proliferation or fluorescence-activated cell sorting (FACS). To empower the study of protein trafficking processes with gene perturbation, we developed a genetically-encoded molecular tool named HiLITR. HiLITR converts protein colocalization into proteolytic release of a membrane-anchored transcription factor, which drives the expression of a chosen reporter gene. Using HiLITR in combination with FACS-based CRISPRi screening in human cell lines, we identified genes that influence the trafficking of mitochondrial and ER tail-anchored proteins. We show that loss of the SUMO E1 component SAE1 results in mislocalization and destabilization of many mitochondrial tail-anchored proteins. We also demonstrate a distinct regulatory role for EMC10 in the ER membrane complex, opposing the transmembrane-domain insertion activity of the complex. Through transcriptional integration of complex cellular functions, HiLITR expands the scope of biological processes that can be studied by genetic perturbation screening technologies.

Keywords:  biochemistry; cell biology; chemical biology; human

DOI:  https://doi.org/10.7554/eLife.69142
Curr Res Physiol. 2021 ;4 163-176

Effect of crista morphology on mitochondrial ATP output: A computational study.

Nasrin Afzal, W Jonathan Lederer, M Saleet Jafri, Carmen A Mannella.

  Folding of the mitochondrial inner membrane (IM) into cristae greatly increases the ATP-generating surface area, S IM, per unit volume but also creates diffusional bottlenecks that could limit reaction rates inside mitochondria. This study explores possible effects of inner membrane folding on mitochondrial ATP output, using a mathematical model for energy metabolism developed by the Jafri group and two- and three-dimensional spatial models for mitochondria, implemented on the Virtual Cell platform. Simulations demonstrate that cristae are micro-compartments functionally distinct from the cytosol. At physiological steady states, standing gradients of ADP form inside cristae that depend on the size and shape of the compartments, and reduce local flux (rate per unit area) of the adenine nucleotide translocase. This causes matrix ADP levels to drop, which in turn reduces the flux of ATP synthase. The adverse effects of membrane folding on reaction fluxes increase with crista length and are greater for lamellar than tubular crista. However, total ATP output per mitochondrion is the product of flux of ATP synthase and S IM which can be two-fold greater for mitochondria with lamellar than tubular cristae, resulting in greater ATP output for the former. The simulations also demonstrate the crucial role played by intracristal kinases (adenylate kinase, creatine kinase) in maintaining the energy advantage of IM folding.

Keywords:  ATP synthesis; Computational modeling; Cristae; Energy metabolism; Kinases; Mitochondria

DOI:  https://doi.org/10.1016/j.crphys.2021.03.005
Am J Med Genet A. 2021 Aug 18.

Whole genome sequencing identifies pathogenic RNU4ATAC variants in a child with recurrent encephalitis, microcephaly, and normal stature.

Care4Rare Canada Consortium

  Biallelic pathogenic variants in RNU4ATAC have been linked to microcephalic osteodysplastic primordial dwarfism type 1 (MOPD1). Although children with MOPD1 have been reported to show profound, life-limiting clinical decompensation at the time of a febrile illness, these episodes including magnetic resonance imaging (MRI) findings have not been well characterized. We present acute MRI brain findings for a 10-year-old girl with homozygous variants in RNU4ATAC (NR_023343.1) n.55G>A, who presented with two episodes of clinical decompensation associated with a febrile illness in early childhood. The pathogenic variants were identified by whole genome sequencing as RNU4ATAC is not captured in most exome products. Her MRI of the brain revealed symmetric, diffusion restriction of the deep gray nuclei that initially pointed to a mitochondrial disease or acute necrotizing encephalopathy. Her phenotype included microcephaly and profound cognitive impairment that can be seen with MOPD1. However, she did not demonstrate clinical or radiographic evidence of a spondyloepimetaphyseal dysplasia or "primordial dwarfism" that is characteristic of this disease. As such, the predominant neurological presentation of this child represents an atypical variant of RNU4ATAC-associated disease and should be a diagnostic consideration for geneticists and neurologists caring for children, particularly in the event of an acute clinical decline.

Keywords:  RNU4ATAC RNA; encephalitis; human; magnetic resonance imaging; microcephalic osteodysplastic primordial dwarfism; mitochondrial diseases; type 1

DOI:  https://doi.org/10.1002/ajmg.a.62457
Nucleic Acids Res. 2021 Aug 17. pii: gkab730. [Epub ahead of print]

Charcot-Marie-Tooth mutation in glycyl-tRNA synthetase stalls ribosomes in a pre-accommodation state and activates integrated stress response.

Samantha Mendonsa, Nicolai von Kuegelgen, Lucija Bujanic, Marina Chekulaeva.

Toxic gain-of-function mutations in aminoacyl-tRNA synthetases cause a degeneration of peripheral motor and sensory axons, known as Charcot-Marie-Tooth (CMT) disease. While these mutations do not disrupt overall aminoacylation activity, they interfere with translation via an unknown mechanism. Here, we dissect the mechanism of function of CMT mutant glycyl-tRNA synthetase (CMT-GARS), using high-resolution ribosome profiling and reporter assays. We find that CMT-GARS mutants deplete the pool of glycyl-tRNAGly available for translation and inhibit the first stage of elongation, the accommodation of glycyl-tRNA into the ribosomal A-site, which causes ribosomes to pause at glycine codons. Moreover, ribosome pausing activates a secondary repression mechanism at the level of translation initiation, by inducing the phosphorylation of the alpha subunit of eIF2 and the integrated stress response. Thus, CMT-GARS mutant triggers translational repression via two interconnected mechanisms, affecting both elongation and initiation of translation.

DOI: https://doi.org/10.1093/nar/gkab730
Methods Mol Biol. 2021 ;2372 169-177

Genetic Editing of Long Noncoding RNA Using CRISPR/Cas9 Technology.

Kristina Larter, Bin Yi, Yaguang Xi.

  Long noncoding RNAs (lncRNAs) are a class of RNA transcripts greater than 200 nucleotides in length and makeup a considerable part of the human genome. LncRNAs are well established as crucial players in a myriad of physiological and pathological processes; however, despite their abundance and versatility, the functional characteristics of lncRNAs remain largely unknown predominantly due to the lack of suitable genetic editing strategies. The complexity of their genetic structure and regulation combined with their unique functionality poses several limitations in the application of classic genetic manipulation methods in lncRNA functional studies. Several reports have demonstrated the successful implementation of CRISPR/Cas9 technology in screening and identifying the function of specific lncRNAs. Here, we describe a detailed protocol utilizing CRISPR/Cas9 genetic editing technology for knocking down lncRNAs in vitro.

Keywords:  CRISPR/cas9; Genetic editing; Knockdown; Long noncoding RNA

DOI:  https://doi.org/10.1007/978-1-0716-1697-0_15
Ann N Y Acad Sci. 2021 Aug 19.

Metabolic decisions in development and disease-a Keystone Symposia report.

Jennifer Cable, Olivier Pourquié, Kathryn E Wellen, Lydia W S Finley, Alexander Aulehla, Alex P Gould, Aurelio Teleman, William B Tu, Wendy Sarah Garrett, Irene Miguel-Aliaga, Norbert Perrimon, Lora V Hooper, A J Marian Walhout, Wei Wei, Theodore Alexandrov, Ayelet Erez, Markus Ralser, Joshua D Rabinowitz, Anupama Hemalatha, Paula Gutiérrez-Pérez, Navdeep S Chandel, Jared Rutter, Jason W Locasale, Juan C Landoni, Heather Christofk.

  There is an increasing appreciation for the role of metabolism in cell signaling and cell decision making. Precise metabolic control is essential in development, as evident by the disorders caused by mutations in metabolic enzymes. The metabolic profile of cells is often cell-type specific, changing as cells differentiate or during tumorigenesis. Recent evidence has shown that changes in metabolism are not merely a consequence of changes in cell state but that metabolites can serve to promote and/or inhibit these changes. Metabolites can link metabolic pathways with cell signaling pathways via several mechanisms, for example, by serving as substrates for protein post-translational modifications, by affecting enzyme activity via allosteric mechanisms, or by altering epigenetic markers. Unraveling the complex interactions governing metabolism, gene expression, and protein activity that ultimately govern a cell's fate will require new tools and interactions across disciplines. On March 24 and 25, 2021, experts in cell metabolism, developmental biology, and human disease met virtually for the Keystone eSymposium, "Metabolic Decisions in Development and Disease." The discussions explored how metabolites impact cellular and developmental decisions in a diverse range of model systems used to investigate normal development, developmental disorders, dietary effects, and cancer-mediated changes in metabolism.

Keywords:  cell signaling; development; inborn errors of metabolism; metabolism; metabolome; stem cell differentiation

DOI:  https://doi.org/10.1111/nyas.14678
Nat Methods. 2021 Aug 19.

Automated segmentation and tracking of mitochondria in live-cell time-lapse images.

Austin E Y T Lefebvre, Dennis Ma, Kai Kessenbrock, Devon A Lawson, Michelle A Digman.

Mitochondria display complex morphology and movements, which complicates their segmentation and tracking in time-lapse images. Here, we introduce Mitometer, an algorithm for fast, unbiased, and automated segmentation and tracking of mitochondria in live-cell two-dimensional and three-dimensional time-lapse images. Mitometer requires only the pixel size and the time between frames to identify mitochondrial motion and morphology, including fusion and fission events. The segmentation algorithm isolates individual mitochondria via a shape- and size-preserving background removal process. The tracking algorithm links mitochondria via differences in morphological features and displacement, followed by a gap-closing scheme. Using Mitometer, we show that mitochondria of triple-negative breast cancer cells are faster, more directional, and more elongated than those in their receptor-positive counterparts. Furthermore, we show that mitochondrial motility and morphology in breast cancer, but not in normal breast epithelia, correlate with metabolic activity. Mitometer is an unbiased and user-friendly tool that will help resolve fundamental questions regarding mitochondrial form and function.

DOI: https://doi.org/10.1038/s41592-021-01234-z
Science. 2021 08 20. 373(6557): 876-882

Mechanisms that ensure speed and fidelity in eukaryotic translation termination.

Michael R Lawson, Laura N Lessen, Jinfan Wang, Arjun Prabhakar, Nicholas C Corsepius, Rachel Green, Joseph D Puglisi.

Translation termination, which liberates a nascent polypeptide from the ribosome specifically at stop codons, must occur accurately and rapidly. We established single-molecule fluorescence assays to track the dynamics of ribosomes and two requisite release factors (eRF1 and eRF3) throughout termination using an in vitro-reconstituted yeast translation system. We found that the two eukaryotic release factors bound together to recognize stop codons rapidly and elicit termination through a tightly regulated, multistep process that resembles transfer RNA selection during translation elongation. Because the release factors are conserved from yeast to humans, the molecular events that underlie yeast translation termination are likely broadly fundamental to eukaryotic protein synthesis.

DOI: https://doi.org/10.1126/science.abi7801
Curr Opin Microbiol. 2021 Aug 16. pii: S1369-5274(21)00101-6. [Epub ahead of print]63 189-194

Contact and competition between mitochondria and microbes.

Tânia C Medeiros, Chahat Mehra, Lena Pernas.

Invading microbes occupy the host cytosol and take up nutrients on which host organelles are also dependent. Thus, host organelles are poised to interact with intracellular microbes. Despite the essential role of host mitochondria in cellular metabolic homeostasis and in mediating cellular responses to microbial infection, we know little of how these organelles interact with intracellular pathogens, and how such interactions affect disease pathogenesis. Here, we give an overview of the different classes of physical and metabolic interactions reported to occur between mitochondria and eukaryotic pathogens. Investigating the underlying molecular mechanisms and functions of such interactions will reveal novel aspects of infection biology.

DOI: https://doi.org/10.1016/j.mib.2021.07.014
Front Mol Biosci. 2021 ;8 711733

Isoform Age - Splice Isoform Profiling Using Long-Read Technologies.

Ricardo De Paoli-Iseppi, Josie Gleeson, Michael B Clark.

  Alternative splicing (AS) of RNA is a key mechanism that results in the expression of multiple transcript isoforms from single genes and leads to an increase in the complexity of both the transcriptome and proteome. Regulation of AS is critical for the correct functioning of many biological pathways, while disruption of AS can be directly pathogenic in diseases such as cancer or cause risk for complex disorders. Current short-read sequencing technologies achieve high read depth but are limited in their ability to resolve complex isoforms. In this review we examine how long-read sequencing (LRS) technologies can address this challenge by covering the entire RNA sequence in a single read and thereby distinguish isoform changes that could impact RNA regulation or protein function. Coupling LRS with technologies such as single cell sequencing, targeted sequencing and spatial transcriptomics is producing a rapidly expanding suite of technological approaches to profile alternative splicing at the isoform level with unprecedented detail. In addition, integrating LRS with genotype now allows the impact of genetic variation on isoform expression to be determined. Recent results demonstrate the potential of these techniques to elucidate the landscape of splicing, including in tissues such as the brain where AS is particularly prevalent. Finally, we also discuss how AS can impact protein function, potentially leading to novel therapeutic targets for a range of diseases.

Keywords:  Oxford Nanopore Technologies nanopore sequencing; PacBio; alternative splicing; isoform; long-read sequencing; single cell sequencing; spatial transcriptomics; targeted RNA sequencing

DOI:  https://doi.org/10.3389/fmolb.2021.711733
J Comput Aided Mol Des. 2021 Aug 18.

Molecular mechanism of thiamine pyrophosphate import into mitochondria: a molecular simulation study.

F Van Liefferinge, E-M Krammer, J Waeytens, M Prévost.

  The import of thiamine pyrophosphate (TPP) through both mitochondrial membranes was studied using a total of 3-µs molecular dynamics simulations. Regarding the translocation through the mitochondrial outer membrane, our simulations support the conjecture that TPP uses the voltage-dependent anion channel, the major pore of this membrane, for its passage to the intermembrane space, as its transport presents significant analogies with that used by other metabolites previously studied, in particular with ATP. As far as passing through the mitochondrial inner membrane is concerned, our simulations show that the specific carrier of TPP has a single binding site that becomes accessible, through an alternating access mechanism. The preference of this transporter for TPP can be rationalized mainly by three residues located in the binding site that differ from those identified in the ATP/ADP carrier, the most studied member of the mitochondrial carrier family. The simulated transport mechanism of TPP highlights the essential role, at the energetic level, of the contributions coming from the formation and breakage of two networks of salt bridges, one on the side of the matrix and the other on the side of the intermembrane space, as well as the interactions, mainly of an ionic nature, formed by TPP upon its binding. The energy contribution provided by the cytosolic network establishes a lower barrier than that of the matrix network, which can be explained by the lower interaction energy of TPP on the matrix side or possibly a uniport activity.

Keywords:  Membrane Transporters; Membrane channels; Metabolite transport; Molecular dynamics; Thiamine pyrophophate

DOI:  https://doi.org/10.1007/s10822-021-00414-5
Clin Chim Acta. 2021 Aug 16. pii: S0009-8981(21)00294-1. [Epub ahead of print]

Inborn errors of metabolism associated with 3-methylglutaconic aciduria.

Dylan E Jones, Emma Klacking, Robert O Ryan.

  A growing number of inborn errors of metabolism (IEM) associated with compromised mitochondrial energy metabolism manifest an unusual phenotypic feature: 3-methylglutaconic (3MGC) aciduria. Two major categories of 3MGC aciduria, primary and secondary, have been described. In primary 3MGC aciduria, IEMs in 3MGC CoA hydratase (AUH) or HMG CoA lyase block leucine catabolism, resulting in a buildup of pathway intermediates, including 3MGC CoA. Subsequent thioester hydrolysis yields 3MGC acid, which is excreted in urine. In secondary 3MGC aciduria, no deficiencies in leucine catabolism enzymes exist and 3MGC CoA is formed de novo from acetyl CoA. In the "acetyl CoA diversion pathway", when IEMs directly, or indirectly, interfere with TCA cycle activity, acetyl CoA accumulates in the matrix space. This leads to condensation of two acetyl CoA to form acetoacetyl CoA, followed by another condensation between acetyl CoA and acetoacetyl CoA to form 3-hydroxy, 3-methylglutaryl (HMG) CoA. Once formed, HMG CoA serves as a substrate for AUH, producing trans-3MGC CoA. Non enzymatic isomerization of trans-3MGC CoA to cis-3MGC CoA precedes intramolecular cyclization to cis-3MGC anhydride plus CoA. Subsequent hydrolysis of cis-3MGC anhydride gives rise to cis-3MGC acid, which is excreted in urine. In reviewing 20 discrete IEMs that manifest secondary 3MGC aciduria, evidence supporting the acetyl CoA diversion pathway was obtained. This biochemical pathway serves as an "overflow valve" in muscle / brain tissue to redirect acetyl CoA to 3MGC CoA when entry to the TCA cycle is impeded.

Keywords:  3-methylglutaconic aciduria; energy metabolism; inborn error of metabolism; mitochondria

DOI:  https://doi.org/10.1016/j.cca.2021.08.016
Proc Natl Acad Sci U S A. 2021 Aug 24. pii: e2101674118. [Epub ahead of print]118(34):

Mitochondrial fatty acid utilization increases chromatin oxidative stress in cardiomyocytes.

Ivan Menendez-Montes, Salim Abdisalaam, Feng Xiao, Nicholas T Lam, Shibani Mukherjee, Luke I Szweda, Aroumougame Asaithamby, Hesham A Sadek.

  The inability of adult mammalian cardiomyocytes to proliferate underpins the development of heart failure following myocardial injury. Although the newborn mammalian heart can spontaneously regenerate for a short period of time after birth, this ability is lost within the first week after birth in mice, partly due to increased mitochondrial reactive oxygen species (ROS) production which results in oxidative DNA damage and activation of DNA damage response. This increase in ROS levels coincides with a postnatal switch from anaerobic glycolysis to fatty acid (FA) oxidation by cardiac mitochondria. However, to date, a direct link between mitochondrial substrate utilization and oxidative DNA damage is lacking. Here, we generated ROS-sensitive fluorescent sensors targeted to different subnuclear compartments (chromatin, heterochromatin, telomeres, and nuclear lamin) in neonatal rat ventricular cardiomyocytes, which allowed us to determine the spatial localization of ROS in cardiomyocyte nuclei upon manipulation of mitochondrial respiration. Our results demonstrate that FA utilization by the mitochondria induces a significant increase in ROS detection at the chromatin level compared to other nuclear compartments. These results indicate that mitochondrial metabolic perturbations directly alter the nuclear redox status and that the chromatin appears to be particularly sensitive to the prooxidant effect of FA utilization by the mitochondria.

Keywords:  metabolism; mitochondria; reactive oxygen species

DOI:  https://doi.org/10.1073/pnas.2101674118
Commun Biol. 2021 Aug 16. 4(1): 974

Mitochondrial Lon protease is a gatekeeper for proteins newly imported into the matrix.

Yuichi Matsushima, Kazuya Takahashi, Song Yue, Yuki Fujiyoshi, Hideaki Yoshioka, Masamune Aihara, Daiki Setoyama, Takeshi Uchiumi, Satoshi Fukuchi, Dongchon Kang.

Human ATP-dependent Lon protease (LONP1) forms homohexameric, ring-shaped complexes. Depletion of LONP1 causes aggregation of a broad range of proteins in the mitochondrial matrix and decreases the levels of their soluble forms. The ATP hydrolysis activity, but not protease activity, of LONP1 is critical for its chaperone-like anti-aggregation activity. LONP1 forms a complex with the import machinery and an incoming protein, and protein aggregation is linked with matrix protein import. LONP1 also contributes to the degradation of imported, aberrant, unprocessed proteins using its protease activity. Taken together, our results show that LONP1 functions as a gatekeeper for specific proteins imported into the mitochondrial matrix.

DOI: https://doi.org/10.1038/s42003-021-02498-z
Biomed Pharmacother. 2021 Aug 16. pii: S0753-3322(21)00824-6. [Epub ahead of print]142 112041

The role of mitochondria dysfunction and hepatic senescence in NAFLD development and progression.

Siarhei A Dabravolski, Evgeny E Bezsonov, Alexander N Orekhov.

  Senescence is a crucial player in several metabolic disorders and chronic inflammatory diseases. Recent data prove the involvement of hepatocyte senescence in the development of NAFLD (non-alcoholic fatty liver disease). As the main energy and ROS (reactive oxygen species) producing organelle, mitochondria play the central role in accelerated senescence and diseases development. In this review, we focus on the role of regulation of mitochondrial Ca2+ homeostasis, NAD+/NADH ratio, UPRmt (mitochondrial unfolded protein response), phospholipids and fatty acid oxidation in hepatic senescence, lifespan and NAFLD disease susceptibility. Additionally, the involvement of mitochondrial and nuclear mutations in lifespan-modulation and NAFLD development is discussed. While nuclear and mitochondria DNA mutations and SNPs (single nucleotide polymorphisms) can be used as effective diagnostic markers and targets for treatments, advanced age should be considered as an independent risk factor for NAFLD development.

Keywords:  DNA damage response; Hepatic senescence; Mitochondrial dysfunction; NAFLD; ROS; UPR(mt)

DOI:  https://doi.org/10.1016/j.biopha.2021.112041
Orphanet J Rare Dis. 2021 Aug 18. 16(1): 365

PhenoDB, GeneMatcher and VariantMatcher, tools for analysis and sharing of sequence data.

Elizabeth Wohler, Renan Martin, Sean Griffith, Eliete da S Rodrigues, Corina Antonescu, Jennifer E Posey, Zeynep Coban-Akdemir, Shalini N Jhangiani, Kimberly F Doheny, James R Lupski, David Valle, Ada Hamosh, Nara Sobreira.

   BACKGROUND: With the advent of whole exome (ES) and genome sequencing (GS) as tools for disease gene discovery, rare variant filtering, prioritization and data sharing have become essential components of the search for disease genes and variants potentially contributing to disease phenotypes. The computational storage, data manipulation, and bioinformatic interpretation of thousands to millions of variants identified in ES and GS, respectively, is a challenging task. To aid in that endeavor, we constructed PhenoDB, GeneMatcher and VariantMatcher.
RESULTS: PhenoDB is an accessible, freely available, web-based platform that allows users to store, share, analyze and interpret their patients' phenotypes and variants from ES/GS data. GeneMatcher is accessible to all stakeholders as a web-based tool developed to connect individuals (researchers, clinicians, health care providers and patients) around the globe with interest in the same gene(s), variant(s) or phenotype(s). Finally, VariantMatcher was developed to enable public sharing of variant-level data and phenotypic information from individuals sequenced as part of multiple disease gene discovery projects. Here we provide updates on PhenoDB and GeneMatcher applications and implementation and introduce VariantMatcher.
CONCLUSION: Each of these tools has facilitated worldwide data sharing and data analysis and improved our ability to connect genes to phenotypic traits. Further development of these platforms will expand variant analysis, interpretation, novel disease-gene discovery and facilitate functional annotation of the human genome for clinical genomics implementation and the precision medicine initiative.

Keywords:  Data sharing; GeneMatcher; Genomic data; PhenoDB; VariantMatcher

DOI:  https://doi.org/10.1186/s13023-021-01916-z
Front Physiol. 2021 ;12 717187

Abnormal Mitochondria-Endoplasmic Reticulum Communication Promotes Myocardial Infarction.

Degang Cheng, Jia Zheng, Fang Hu, Wei Lv, Chengzhi Lu.

  Myocardial infarction is characterized by cardiomyocyte death, and can be exacerbated by mitochondrial damage and endoplasmic reticulum injury. In the present study, we investigated whether communication between mitochondria and the endoplasmic reticulum contributes to cardiomyocyte death after myocardial infarction. Our data demonstrated that hypoxia treatment (mimicking myocardial infarction) promoted cardiomyocyte death by inducing the c-Jun N-terminal kinase (JNK) pathway. The activation of JNK under hypoxic conditions was dependent on overproduction of mitochondrial reactive oxygen species (mtROS) in cardiomyocytes, and mitochondrial division was identified as the upstream inducer of mtROS overproduction. Silencing mitochondrial division activators, such as B cell receptor associated protein 31 (BAP31) and mitochondrial fission 1 (Fis1), repressed mitochondrial division, thereby inhibiting mtROS overproduction and preventing JNK-induced cardiomyocyte death under hypoxic conditions. These data revealed that a novel death-inducing mechanism involving the BAP31/Fis1/mtROS/JNK axis promotes hypoxia-induced cardiomyocyte damage. Considering that BAP31 is localized within the endoplasmic reticulum and Fis1 is localized in mitochondria, abnormal mitochondria-endoplasmic reticulum communication may be a useful therapeutic target after myocardial infarction.

Keywords:  BAP31; FIS1; cell death; mitochondria-endoplasmic reticulum communication; myocardial infarction

DOI:  https://doi.org/10.3389/fphys.2021.717187
Genet Med. 2021 Aug 16.

PPA2-associated sudden cardiac death: extending the clinical and allelic spectrum in 20 new families.

Anne Guimier, Melanie T Achleitner, Anne Moreau de Bellaing, Matthew Edwards, Loïc de Pontual, Kirti Mittal, Kyla E Dunn, Megan E Grove, Carolyn J Tysoe, Clémantine Dimartino, Jessie Cameron, Anil Kanthi, Anju Shukla, Florence van den Broek, Diptendu Chatterjee, Charlotte L Alston, Charlotte V Knowles, Laura Brett, Jan A Till, Tessa Homfray, Paul French, Georgia Spentzou, Noha A Elserafy, Kate S Lichkus, Bindu P Sankaran, Hannah L Kennedy, Peter M George, Alexa Kidd, Saskia B Wortmann, Dianna G Fisk, Tamara T Koopmann, Muhammad A Rafiq, Jason D Merker, Sumith Parikh, Priyanka Ahimaz, Robert G Weintraub, Alan S Ma, Christian Turner, Carolyn J Ellaway, Liza K Phillips, David R Thorburn, Wendy K Chung, Sajel L Kana, Ona M Faye-Petersen, Michelle L Thompson, Alexandre Janin, Karen McLeod, Ruth McGowan, Robert McFarland, Katta M Girisha, Deborah J Morris-Rosendahl, Anna C E Hurst, Claire L S Turner, Robert M Hamilton, Robert W Taylor, Fanny Bajolle, Christopher T Gordon, Jeanne Amiel, Johannes A Mayr, Kit Doudney.

PURPOSE: Biallelic hypomorphic variants in PPA2, encoding the mitochondrial inorganic pyrophosphatase 2 protein, have been recently identified in individuals presenting with sudden cardiac death, occasionally triggered by alcohol intake or a viral infection. Here we report 20 new families harboring PPA2 variants.
METHODS: Synthesis of clinical and molecular data concerning 34 individuals harboring five previously reported PPA2 variants and 12 novel variants, 11 of which were functionally characterized.
RESULTS: Among the 34 individuals, only 6 remain alive. Twenty-three died before the age of 2 years while five died between 14 and 16 years. Within these 28 cases, 15 died of sudden cardiac arrest and 13 of acute heart failure. One case was diagnosed prenatally with cardiomyopathy. Four teenagers drank alcohol before sudden cardiac arrest. Progressive neurological signs were observed in 2/6 surviving individuals. For 11 variants, recombinant PPA2 enzyme activities were significantly decreased and sensitive to temperature, compared to wild-type PPA2 enzyme activity.
CONCLUSION: We expand the clinical and mutational spectrum associated with PPA2 dysfunction. Heart failure and sudden cardiac arrest occur at various ages with inter- and intrafamilial phenotypic variability, and presentation can include progressive neurological disease. Alcohol intake can trigger cardiac arrest and should be strictly avoided.

DOI: https://doi.org/10.1038/s41436-021-01296-6
Bioorg Chem. 2021 Aug 09. pii: S0045-2068(21)00635-0. [Epub ahead of print]115 105258

Analysis of Hsp90 allosteric modulators interactome reveals a potential dual action mode involving mitochondrial MDH2.

Chiara Cassiano, Elva Morretta, Matteo Costantini, Enrico M A Fassi, Giorgio Colombo, Sara Sattin, Agostino Casapullo.

  Hsp90 (i.e., Heat shock protein 90) is a well-established therapeutic target for several diseases, ranging from misfolding-related disfunctions to cancer. In this framework, we have developed in recent years a family of benzofuran compounds that act as Hsp90 allosteric modulators. Such molecules can interfere with the stability of some relevant Hsp90 client oncoproteins, showing a low μM cytotoxic activity in vitro in cancer cell lines. Here we identify the target profile of these chemical probes by means of chemical proteomics, which established MDH2 (mitochondrial malate dehydrogenase) as an additional relevant cellular target that might help elucidate the molecular mechanism of their citotoxicity. Western blotting, DARTS (i.e., Drug Affinity Responsive Target Stability) and enzymatic assays data confirmed a dose-dependent interaction of MDH2 with several members of the benzofuran Hsp90 modulators family and a computational model allowed to interpret the observed interactions.

Keywords:  Benzofurans; Chemical proteomics; Docking; Hsp90; Mitochondrial malate dehydrogenase

DOI:  https://doi.org/10.1016/j.bioorg.2021.105258
J Neuroophthalmol. 2021 Aug 17.

Magnetic Resonance Imaging Findings in the Pregeniculate Visual Pathway in Leber Hereditary Optic Neuropathy.

Juan Zhao, Qing Zhang, Jiawei Wang.

BACKGROUND: Current research has not provided a consistent and qualitative description of MRI features in Leber hereditary optic neuropathy (LHON). Our study aims to investigate the MRI findings in the pregeniculate visual pathway and discuss their clinical significance in LHON.
METHODS: Orbital MRI was retrospectively analyzed for 53 patients with LHON (101 afflicted eyes) admitted to the Department of Neurology, Beijing Tongren Hospital, Capital Medical University, from 2014 to 2019. We described the imaging abnormalities and discussed their associations with the time interval from the onset of vision loss to the performance of MRI (TIOVP), prevalence of m.11778G>A, and best-corrected visual acuity (BCVA).
RESULTS: T2 hyperintense signal (HS) was determined in 82 afflicted eyes, with 34 located in the intraorbital segment (IO) of the optic nerve (ON), 26 in the IO concurrent with intracanalicular segment (ICn), 14 in the IO and ICn concurrent with intracranial segment (ICr) of the ON, 4 in the IO, ICn, and ICr concurrent with optic chiasm (OCh), and 4 in the IO, ICn, ICr, and OCh concurrent with optic tract (OTr). MRI was normal in the remaining 19 afflicted eyes. Among the 6 groups, no statistical differences were found in the TIOVP (P = 0.071), prevalence of m.11778G>A (P = 0.234), and BCVA (P = 0.076). As T2 HS extended, the BCVA gradually decreased. Nineteen of the 54 afflicted eyes revealed contrast enhancement, with the TIOVP ranging from 0.25 to 6 months.
CONCLUSIONS: T2 HS was common in the pregeniculate visual pathway in LHON. It was not correlated with the prevalence of m.11778G>A and did not benefit in disease staging. As it extended, the BCVA gradually decreased. Contrast enhancement was relatively rare, always occurring in the subacute stage.

DOI: https://doi.org/10.1097/WNO.0000000000001383
Neurosci Lett. 2021 Aug 13. pii: S0304-3940(21)00551-6. [Epub ahead of print] 136173

RANBP2 mutation causing autosomal dominant acute necrotizing encephalopathy attenuates its interaction with COX11.

Akiko Shibata, Mariko Kasai, Ai Hoshino, Teruyuki Tanaka, Masashi Mizuguchi.

   PURPOSE: Autosomal dominant acute necrotizing encephalopathy (ADANE) is caused by missense mutations in the gene encoding Ran-binding protein 2 (RANBP2), a nuclear pore protein regulating mitochondrial localization and function. Previous studies have found that RANBP2 binds to COX11 and suppresses its inhibitory activity over hexokinase1. To further elucidate mitochondrial dysfunction in ADANE, we analyzed the interaction between mutated RANBP2 and COX11.
METHODS: We extracted cDNA from a patient and constructed pGEX wild-type or mutant-type vectors including RANBP2 c.1754 C>T, the commonest variant in ADANE. We transformed E. coli competent cells with the vectors and had them express GST-RANBP2 recombinant protein, and conducted a pull-down assay of RANBP2 and COX11.
RESULTS: The amount of COX11 bound to mutated RANBP2 was significantly smaller than that bound to the wild-type RANBP2.
CONCLUSION: Mutated RANBP2 had an attenuated binding ability to COX11. Whether this change indeed decreases ATP production remains to be further explored.

Keywords:  Autosomal dominant acute necrotizing encephalopathy; Ran-binding protein 2; cytochrome c oxidase copper chaperone COX11; energy failure; mitochondrial dysfunction

DOI:  https://doi.org/10.1016/j.neulet.2021.136173
Methods Mol Biol. 2021 ;2372 209-222

Methods for Characterization of Alternative RNA Splicing.

Samuel E Harvey, Jingyi Lyu, Chonghui Cheng.

  Quantification of alternative splicing to detect the abundance of differentially spliced isoforms of a gene in total RNA can be accomplished via RT-PCR using both quantitative real-time and semiquantitative PCR methods. These methods require careful PCR primer design to ensure specific detection of particular splice isoforms. We will also describe analysis of alternative splicing using a splicing "minigene" in mammalian cell tissue culture to facilitate investigation of the regulation of alternative splicing of a particular exon of interest.

Keywords:  Alternative splicing; Minigene; RNA; RT-PCR; Splicing factors; Splicing regulation; Variable exon

DOI:  https://doi.org/10.1007/978-1-0716-1697-0_19
Hum Mol Genet. 2021 Aug 20. pii: ddab240. [Epub ahead of print]

Epigenome-wide association study of mitochondrial genome copy number.

NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium

We conducted cohort- and race-specific epigenome-wide association analyses of mtDNA copy number (mtDNA CN) measured in whole blood from participants of African and European origins in five cohorts (n = 6182, mean age 57-67 years, 65% women). In the meta-analysis of all the participants, we discovered 21 mtDNA CN-associated CpG sites (p < 1 x 10-7), with a 0.7 to 3.0 standard deviation increase (3 CpGs) or decrease (18 CpGs) in mtDNA CN corresponding to a 1% increase in DNA methylation. Several significant CpGs have been reported to be associated with at least two risk factors (e.g. chronological age or smoking) for cardiovascular disease (CVD). Five genes (PRDM16, NR1H3, XRCC3, POLK, and PDSS2), which harbor nine significant CpGs, are known to be involved in mitochondrial biosynthesis and functions. For example, NR1H3 encodes a transcription factor that is differentially expressed during an adipose tissue transition. The methylation level of cg09548275 in NR1H3 was negatively associated with mtDNA CN (effect size = -1.71, p = 4 x 10-8) and positively associated with the NR1H3 expression level (effect size = 0.43, p = 0.0003), which indicates that the methylation level in NR1H3 may underlie the relationship between mtDNA CN, the NR1H3 transcription factor, and energy expenditure. In summary, the study results suggest that mtDNA CN variation in whole blood is associated with DNA methylation levels in genes that are involved in a wide range of mitochondrial activities. These findings will help reveal molecular mechanisms between mtDNA CN and CVD.

DOI: https://doi.org/10.1093/hmg/ddab240