bims-mitdis 2022-12-04 papers

bims-mitdis

Biomed News

on Mitochondrial disorders

Issue of 2022‒12‒04
39 papers selected by
Catalina Vasilescu
Helmholz Munich

Leigh syndrome is the main clinical characteristic of PTCD3 deficiency.
An ER phospholipid hydrolase drives ER-associated mitochondrial constriction for fission and fusion.
Mathematical modeling and analysis of mitochondrial retrograde signaling dynamics.
Nicotinamide riboside kinases regulate skeletal muscle fiber-type specification and are rate-limiting for metabolic adaptations during regeneration.
Mutation accumulation in mtDNA of cancers resembles mutagenesis in normal stem cells.
Emerging mitochondrial-mediated mechanisms involved in oligodendrocyte development.
Primary Mitochondrial Disorders in the Neonate.
Low aerobic capacity in McArdle disease: a role for mitochondrial network impairment?
Mitochondrial copper in human genetic disorders.
Mitochondrial respiration and dynamics of in vivo neural stem cells.
AFG3L2 Biallelic Mutation: Clinical Heterogeneity in Two Italian Patients.
Isolation protocols and mitochondrial content for plasma extracellular vesicles.
Stochastic survival of the densest and mitochondrial DNA clonal expansion in aging.
Mitochondria-associated niches in health and disease.
The roles of a mitochondrial protein Miga in autophagy.
Mitochondria: how eminent in ageing and neurodegenerative disorders?
Inhibition of glutaminolysis restores mitochondrial function in senescent stem cells.
Metabolon formation regulates branched-chain amino acid oxidation and homeostasis.
The Depletion of NAMPT Disturbs Mitochondrial Homeostasis and Causes Neuronal Degeneration in Mouse Hippocampus.
Mitochondrial [2Fe-2S] ferredoxins: new functions for old dogs.
Requirement of hepatic pyruvate carboxylase during fasting, high fat, and ketogenic diet.
Lysosomal damage drives mitochondrial proteome remodelling and reprograms macrophage immunometabolism.
A reference human induced pluripotent stem cell line for large-scale collaborative studies.
Mitochondria-originated redox signalling regulates KLF-1 to promote longevity in Caenorhabditis elegans.
Generation of a homozygous FIS1 knockout human embryonic stem cell line GIBHe015-B by CRISPR/Cas9 system.
Profiling of mitochondrial heteroplasmy in single human oocytes by next-generation sequencing.
Loss of function of CMPK2 causes mitochondria deficiency and brain calcification.
Editorial: NGS technologies of rare diseases diagnosis.
Homozygous COQ7 mutation: a new cause of potentially treatable distal hereditary motor neuropathy.
Lin28a induced mitochondrial dysfunction in human granulosa cells via suppressing LARS2 expression.
Benchmarking challenging small variants with linked and long reads.
Targeting Mitochondrial Calcium Handling to Treat Atrial Fibrillation.
Nuclear localization of mitochondrial TCA cycle enzymes modulates pluripotency via histone acetylation.
Cardiac PI3K p110α attenuation delays aging and extends lifespan.
Cellular functions of cGAS-STING signaling.
Mitochondrial RNA stimulates beige adipocyte development in young mice.
Genome-wide data from medieval German Jews show that the Ashkenazi founder event pre-dated the 14th century.
A minimal role for synonymous variation in human disease.
Profiling lariat intermediates reveals genetic determinants of early and late co-transcriptional splicing.

Brain Pathol. 2022 Nov 30. e13134

Leigh syndrome is the main clinical characteristic of PTCD3 deficiency.

Gerard Muñoz-Pujol, Juan D Ortigoza-Escobar, Abraham J Paredes-Fuentes, Cristina Jou, Olatz Ugarteburu, Laura Gort, Delia Yubero, Angels García-Cazorla, Mar O'Callaghan, Jaume Campistol, Jordi Muchart, Vicente A Yépez, Mirjana Gusic, Julien Gagneur, Holger Prokisch, Rafael Artuch, Antonia Ribes, Roser Urreizti, Frederic Tort.

  Mitochondrial translation defects are a continuously growing group of disorders showing a large variety of clinical symptoms including a wide range of neurological abnormalities. To date, mutations in PTCD3, encoding a component of the mitochondrial ribosome, have only been reported in a single individual with clinical evidence of Leigh syndrome. Here, we describe three additional PTCD3 individuals from two unrelated families, broadening the genetic and phenotypic spectrum of this disorder, and provide definitive evidence that PTCD3 deficiency is associated with Leigh syndrome. The patients presented in the first months of life with psychomotor delay, respiratory insufficiency and feeding difficulties. The neurologic phenotype included dystonia, optic atrophy, nystagmus and tonic-clonic seizures. Brain MRI showed optic nerve atrophy and thalamic changes, consistent with Leigh syndrome. WES and RNA-seq identified compound heterozygous variants in PTCD3 in both families: c.[1453-1G>C];[1918C>G] and c.[710del];[902C>T]. The functional consequences of the identified variants were determined by a comprehensive characterization of the mitochondrial function. PTCD3 protein levels were significantly reduced in patient fibroblasts and, consistent with a mitochondrial translation defect, a severe reduction in the steady state levels of complexes I and IV subunits was detected. Accordingly, the activity of these complexes was also low, and high-resolution respirometry showed a significant decrease in the mitochondrial respiratory capacity. Functional complementation studies demonstrated the pathogenic effect of the identified variants since the expression of wild-type PTCD3 in immortalized fibroblasts restored the steady-state levels of complexes I and IV subunits as well as the mitochondrial respiratory capacity. Additionally, minigene assays demonstrated that three of the identified variants were pathogenic by altering PTCD3 mRNA processing. The fourth variant was a frameshift leading to a truncated protein. In summary, we provide evidence of PTCD3 involvement in human disease confirming that PTCD3 deficiency is definitively associated with Leigh syndrome.

Keywords:  Leigh syndrome; PTCD3; mitochondria; mitochondrial disorder; mitochondrial translation

DOI:  https://doi.org/10.1111/bpa.13134
Elife. 2022 Nov 30. pii: e84279. [Epub ahead of print]11

An ER phospholipid hydrolase drives ER-associated mitochondrial constriction for fission and fusion.

Tricia T Nguyen, Gia K Voeltz.

  Mitochondria are dynamic organelles that undergo cycles of fission and fusion at a unified platform defined by endoplasmic reticulum (ER)-mitochondria membrane contact sites (MCSs). These MCSs or nodes co-localize fission and fusion machinery. We set out to identify how ER-associated mitochondrial nodes can regulate both fission and fusion machinery assembly. We have used a promiscuous biotin ligase linked to the fusion machinery, Mfn1, and proteomics to identify an ER membrane protein, ABHD16A, as a major regulator of node formation. In the absence of ABHD16A, fission and fusion machineries fail to recruit to ER-associated mitochondrial nodes and fission and fusion rates are significantly reduced. ABHD16A contains an acyltransferase motif and an α/β hydrolase domain and point mutations in critical residues of these regions fail to rescue the formation of ER-associated mitochondrial hot spots. These data suggest a mechanism whereby ABHD16A functions by altering phospholipid composition at ER-mitochondria MCSs. Our data present the first example of an ER membrane protein that regulates the recruitment of both fission and fusion machineries to mitochondria.

Keywords:  cell biology; human

DOI:  https://doi.org/10.7554/eLife.84279
iScience. 2022 Dec 22. 25(12): 105502

Mathematical modeling and analysis of mitochondrial retrograde signaling dynamics.

Shao-Ting Chiu, Wen-Wei Tseng, An-Chi Wei.

  Mitochondria, semi-autonomous eukaryotic organelles, participate in energy production and metabolism, making mitochondrial quality control crucial. As most mitochondrial proteins are encoded by nuclear genes, maintaining mitochondrial function and quality depends on proper mitochondria-nucleus communication and designated mitochondrial retrograde signaling. Early studies focused on retrograde signaling participants and specific gene knockouts. However, mitochondrial signal modulation remains elusive. A mathematical model based on ordinary differential equations was proposed to simulate signal propagation to nucleus following mitochondrial damage in yeast. Mitochondrial retrograde signaling decisions were described using a Boolean model. Dynamics of retrograde signaling were analyzed and extended to evaluate the model response to noisy damage signals. Simulation revealed localized protein concentration dynamics, including waveforms, frequency response, and robustness under noise. Retrograde signaling is bistable with localized steady states, and increased damage compromises robustness. We elucidated mitochondrial retrograde signaling, thus providing a basis for drug design against yeast and fungi.

Keywords:  Biological sciences; Cell biology; Systems biology

DOI:  https://doi.org/10.1016/j.isci.2022.105502
Front Cell Dev Biol. 2022 ;10 1049653

Nicotinamide riboside kinases regulate skeletal muscle fiber-type specification and are rate-limiting for metabolic adaptations during regeneration.

Tanja Sonntag, Sara Ancel, Sonia Karaz, Paulina Cichosz, Guillaume Jacot, Maria Pilar Giner, José Luis Sanchez-Garcia, Alice Pannérec, Sofia Moco, Vincenzo Sorrentino, Carles Cantó, Jérôme N Feige.

  Nicotinamide riboside kinases (NRKs) control the conversion of dietary Nicotinamide Riboside (NR) to NAD+, but little is known about their contribution to endogenous NAD+ turnover and muscle plasticity during skeletal muscle growth and remodeling. Using NRK1/2 double KO (NRKdKO) mice, we investigated the influence of NRKs on NAD+ metabolism and muscle homeostasis, and on the response to neurogenic muscle atrophy and regeneration following muscle injury. Muscles from NRKdKO animals have altered nicotinamide (NAM) salvage and a decrease in mitochondrial content. In single myonuclei RNAseq of skeletal muscle, NRK2 mRNA expression is restricted to type IIx muscle fibers, and perturbed NAD+ turnover and mitochondrial metabolism shifts the fiber type composition of NRKdKO muscle to fast glycolytic IIB fibers. NRKdKO does not influence muscle atrophy during denervation but alters muscle repair after myofiber injury. During regeneration, muscle stem cells (MuSCs) from NRKdKO animals hyper-proliferate but fail to differentiate. NRKdKO also alters the recovery of NAD+ during muscle regeneration as well as mitochondrial adaptations and extracellular matrix remodeling required for tissue repair. These metabolic perturbations result in a transient delay of muscle regeneration which normalizes during myofiber maturation at late stages of regeneration via over-compensation of anabolic IGF1-Akt signaling. Altogether, we demonstrate that NAD+ synthesis controls mitochondrial metabolism and fiber type composition via NRK1/2 and is rate-limiting for myogenic commitment and mitochondrial maturation during skeletal muscle repair.

Keywords:  NAD+; NRK; fiber type; mitochondria; muscle regeneration; muscle stem cell (satellite cell); nicotinamide riboside; skeletal muscle

DOI:  https://doi.org/10.3389/fcell.2022.1049653
iScience. 2022 Dec 22. 25(12): 105610

Mutation accumulation in mtDNA of cancers resembles mutagenesis in normal stem cells.

Freek Manders, Jip van Dinter, Ruben van Boxtel.

  Mitochondria are small organelles that play an essential role in the energy production of eukaryotic cells. Defects in their genomes are associated with diseases, such as aging and cancer. Here, we analyzed the mitochondrial genomes of 532 whole-genome sequencing samples from cancers and normal clonally expanded single cells. We show that the mitochondria of normal cells accumulate mutations with age and that most of the mitochondrial mutations found in cancer are the result of healthy mutation accumulation. We also show that the normal HSPCs of patients with leukemia have an increased mitochondrial mutation load. Finally, we show that secondary pediatric cancers and chemotherapy treatments do not impact the mitochondrial mutation load and mtDNA copy numbers of most cells, suggesting that damage to the mitochondrial genome is not a major driver for carcinogenesis. Overall, these findings may contribute to our understanding of mitochondrial genomes and their role in cancer.

Keywords:  Cancer; Genomics; Stem cells research

DOI:  https://doi.org/10.1016/j.isci.2022.105610
J Neurosci Res. 2022 Dec 03.

Emerging mitochondrial-mediated mechanisms involved in oligodendrocyte development.

Melanie Gil, Vivian Gama.

  Oligodendrocytes are the myelinating glia of the central nervous system and are generated after oligodendrocyte progenitor cells (OPCs) transition into pre-oligodendrocytes and then into myelinating oligodendrocytes. Myelin is essential for proper signal transmission within the nervous system and axonal metabolic support. Although the intrinsic and extrinsic factors that support the differentiation, survival, integration, and subsequent myelination of appropriate axons have been well investigated, little is known about how mitochondria-related pathways such as mitochondrial dynamics, bioenergetics, and apoptosis finely tune these developmental events. Previous findings suggest that changes to mitochondrial morphology act as an upstream regulatory mechanism of neural stem cell (NSC) fate decisions. Whether a similar mechanism is engaged during OPC differentiation has yet to be elucidated. Maintenance of mitochondrial dynamics is vital for regulating cellular bioenergetics, functional mitochondrial networks, and the ability of cells to distribute mitochondria to subcellular locations, such as the growing processes of oligodendrocytes. Myelination is an energy-consuming event, thus, understanding the interplay between mitochondrial dynamics, metabolism, and apoptosis will provide further insight into mechanisms that mediate oligodendrocyte development in healthy and disease states. Here we will provide a concise overview of oligodendrocyte development and discuss the potential contribution of mitochondrial mitochondrial-mediated mechanisms to oligodendrocyte bioenergetics and development.

Keywords:  astrocytes; glia; glycolysis; mitochondria; neural precursor cells; neurons; oligodendrocytes; oxidative phosphorylation

DOI:  https://doi.org/10.1002/jnr.25151
Neoreviews. 2022 Dec 01. 23(12): e796-e812

Primary Mitochondrial Disorders in the Neonate.

Rodrigo Tzovenos Starosta, Marwan Shinawi.

Primary mitochondrial disorders (PMDs) are a heterogeneous group of disorders characterized by functional or structural abnormalities in the mitochondria that lead to a disturbance of cellular energy, reactive oxygen species, and free radical production, as well as impairment of other intracellular metabolic functions, causing single- or multiorgan dysfunction. PMDs are caused by pathogenic variants in nuclear and mitochondrial genes, resulting in distinct modes of inheritance. Onset of disease is variable and can occur in the neonatal period, with a high morbidity and mortality. In this article, we review the most common methods used for the diagnosis of PMDs, as well as their prenatal and neonatal presentations. We highlight the shift in the diagnostic approach for PMDs since the introduction of nontargeted molecular tests into clinical practice, which has significantly reduced the use of invasive studies. We discuss common PMDs that can present in the neonate, including general, nonsyndromic presentations as well as specific syndromic disorders. We also review current treatment advances, including the use of mitochondrial "cocktails" based on limited scientific evidence and theoretical reasoning, as well as the impending arrival of personalized mitochondrial-specific treatments.

DOI: https://doi.org/10.1542/neo.23-12-e796
Mol Metab. 2022 Nov 28. pii: S2212-8778(22)00217-4. [Epub ahead of print] 101648

Low aerobic capacity in McArdle disease: a role for mitochondrial network impairment?

M Villarreal-Salazar, A Santalla, A Real-Martínez, G Nogales-Gadea, P L Valenzuela, C Fiuza-Luces, A L Andreu, J C Rodríguez-Aguilera, M A Martín, J Arenas, J Vissing, A Lucia, T O Krag, T Pinós.

  BACKGROUND: McArdle disease is caused by myophosphorylase deficiency and results in complete inability for muscle glycogen breakdown. A hallmark of this condition is muscle oxidation impairment (e.g., low peak oxygen uptake (VO2peak)), a phenomenon traditionally attributed to reduced glycolytic flux and Krebs cycle anaplerosis. Here we hypothesized an additional role for muscle mitochondrial network alterations associated with massive intracellular glycogen accumulation.METHODS: We analyzed in depth mitochondrial characteristics--content, biogenesis, ultrastructure--and network integrity in skeletal-muscle from McArdle/control mice and two patients. We also determined VO2peak in patients (both sexes, N=145) and healthy controls (N=133).
RESULTS: Besides corroborating very poor VO2peak values in patients and impairment in muscle glycolytic flux, we found that, in McArdle muscle: (a) damaged fibers are likely those with a higher mitochondrial and glycogen content, which show major disruption of the three main cytoskeleton components--actin microfilaments, microtubules and intermediate filaments--thereby contributing to mitochondrial network disruption in skeletal muscle fibers; (b) there was an altered subcellular localization of mitochondrial fission/fusion proteins and of the sarcoplasmic reticulum protein calsequestrin--with subsequent alteration in mitochondrial dynamics/function; impairment in mitochondrial content/biogenesis; and (c) several OXPHOS-related complex proteins/activities were also affected.
CONCLUSIONS: In McArdle disease, severe muscle oxidative capacity impairment could also be explained by a disruption of the mitochondrial network, at least in those fibers with a higher capacity for glycogen accumulation. Our findings might pave the way for future research addressing the potential involvement of mitochondrial network alterations in the pathophysiology of other glycogenoses.

Keywords:  McArdle disease; aerobic capacity; cytoskeleton and mitochondrial network; glycogen; skeletal muscle

DOI:  https://doi.org/10.1016/j.molmet.2022.101648
Trends Endocrinol Metab. 2022 Nov 23. pii: S1043-2760(22)00199-0. [Epub ahead of print]

Mitochondrial copper in human genetic disorders.

Natalie M Garza, Abhinav B Swaminathan, Krishna P Maremanda, Mohammad Zulkifli, Vishal M Gohil.

  Copper is an essential micronutrient that serves as a cofactor for enzymes involved in diverse physiological processes, including mitochondrial energy generation. Copper enters cells through a dedicated copper transporter and is distributed to intracellular cuproenzymes by copper chaperones. Mitochondria are critical copper-utilizing organelles that harbor an essential cuproenzyme cytochrome c oxidase, which powers energy production. Mutations in copper transporters and chaperones that perturb mitochondrial copper homeostasis result in fatal genetic disorders. Recent studies have uncovered the therapeutic potential of elesclomol, a copper ionophore, for the treatment of copper deficiency disorders such as Menkes disease. Here we review the role of copper in mitochondrial energy metabolism in the context of human diseases and highlight the recent developments in copper therapeutics.

Keywords:  Menkes disease; Wilson disease; copper; elesclomol; mitochondria; mitochondrial disease

DOI:  https://doi.org/10.1016/j.tem.2022.11.001
Development. 2022 Dec 01. pii: dev200870. [Epub ahead of print]149(23):

Mitochondrial respiration and dynamics of in vivo neural stem cells.

Stavroula Petridi, Dnyanesh Dubal, Richa Rikhy, Jelle van den Ameele.

  Neural stem cells (NSCs) in the developing and adult brain undergo many different transitions, tightly regulated by extrinsic and intrinsic factors. While the role of signalling pathways and transcription factors is well established, recent evidence has also highlighted mitochondria as central players in NSC behaviour and fate decisions. Many aspects of cellular metabolism and mitochondrial biology change during NSC transitions, interact with signalling pathways and affect the activity of chromatin-modifying enzymes. In this Spotlight, we explore recent in vivo findings, primarily from Drosophila and mammalian model systems, about the role that mitochondrial respiration and morphology play in NSC development and function.

Keywords:  Mitochondria; Mitochondrial morphology; Neural stem cell; Notch; Oxidative phosphorylation; Reactive oxygen species

DOI:  https://doi.org/10.1242/dev.200870
Cerebellum. 2022 Nov 30.

AFG3L2 Biallelic Mutation: Clinical Heterogeneity in Two Italian Patients.

Fabiana Colucci, Marcella Neri, Fernanda Fortunato, Alessandra Ferlini, Rosalba Carrozzo, Alessandra Torraco, Eleonora Lamantea, Andrea Legati, Ginevra Tecilla, Maura Pugliatti, Mariachiara Sensi.

  AFG3-like matrix AAA peptidase subunit 2 gene (AFG3L2, OMIM * 604,581) biallelic mutations lead to autosomal recessive spastic ataxia-5 SPAX5, OMIM # 614,487), a rare hereditary form of ataxia. The clinical spectrum includes early-onset cerebellar ataxia, spasticity, and progressive myoclonic epilepsy (PME). In Italy, the epidemiology of the disease is probably underestimated. The advent of next generation sequencing (NGS) technologies has speeded up the diagnosis of hereditary diseases and increased the percentage of diagnosis of rare disorders, such as the rare hereditary ataxia groups. Here, we describe two patients from two different villages in the province of Ferrara, who manifested a different clinical ataxia-plus history, although carrying the same biallelic mutation in AFG3L2 (p.Met625Ile) identified through NGS analysis.

Keywords:  AFG3L2 gene; Late-onset cerebellar ataxia; Recessive ataxia; SPAX5

DOI:  https://doi.org/10.1007/s12311-022-01497-y
Anal Bioanal Chem. 2022 Dec 02.

Isolation protocols and mitochondrial content for plasma extracellular vesicles.

Ai Nguyen, Illarion V Turko.

  Mitochondrial content has been reported outside of cells either within extracellular vesicles (EVs) or as free mitochondria. Mitochondrial EVs can potentially play multiple physiological and pathophysiological roles. To understand their functions, isolation protocols to separate mitochondrial EVs from other mitochondrial content need to be established. In the present work, we use a multiple reaction monitoring assay with isotope labeled internal standards to quantify 11 mitochondrial, 6 plasma membrane-specific, 4 endosomal membrane-specific, and 2 soluble proteins to evaluate the efficiency of chromatographic isolation of mitochondrial EVs. The isolation protocol includes ultracentrifugation, size exclusion chromatography, and chromatography on immobilized heparin. All protein concentrations were normalized to the concentration of ATP synthase alpha subunit to generate a ratio that allows comparison of different samples obtained during the isolation. We have shown that initial samples after ultracentrifugation are contaminated with non-EV mitochondrial content that cannot be separated from EVs using size exclusion chromatography, but can be efficiently separated from EVs on the column with immobilized heparin.

Keywords:  Extracellular vesicles; Heparin-Sepharose; Mass spectrometry; Mitochondria; Targeted proteomics

DOI:  https://doi.org/10.1007/s00216-022-04465-x
Proc Natl Acad Sci U S A. 2022 Dec 06. 119(49): e2122073119

Stochastic survival of the densest and mitochondrial DNA clonal expansion in aging.

Ferdinando Insalata, Hanne Hoitzing, Juvid Aryaman, Nick S Jones.

  The expansion of mitochondrial DNA molecules with deletions has been associated with aging, particularly in skeletal muscle fibers; its mechanism has remained unclear for three decades. Previous accounts have assigned a replicative advantage (RA) to mitochondrial DNA containing deletion mutations, but there is also evidence that cells can selectively remove defective mitochondrial DNA. Here we present a spatial model that, without an RA, but instead through a combination of enhanced density for mutants and noise, produces a wave of expanding mutations with speeds consistent with experimental data. A standard model based on RA yields waves that are too fast. We provide a formula that predicts that wave speed drops with copy number, consonant with experimental data. Crucially, our model yields traveling waves of mutants even if mutants are preferentially eliminated. Additionally, we predict that mutant loads observed in single-cell experiments can be produced by de novo mutation rates that are drastically lower than previously thought for neutral models. Given this exemplar of how spatial structure (multiple linked mtDNA populations), noise, and density affect muscle cell aging, we introduce the mechanism of stochastic survival of the densest (SSD), an alternative to RA, that may underpin other evolutionary phenomena.

Keywords:  aging; biomathematics; evolution; mitochondria; stochastic

DOI:  https://doi.org/10.1073/pnas.2122073119
J Cell Sci. 2022 Dec 01. pii: jcs259634. [Epub ahead of print]135(23):

Mitochondria-associated niches in health and disease.

Mateus Milani, Philippe Pihán, Claudio Hetz.

  The appreciation of the importance of interorganelle contacts has steadily increased over the past decades. Advances in imaging, molecular biology and bioinformatic techniques allowed the discovery of new mechanisms involved in the interaction and communication between organelles, providing novel insights into the inner works of a cell. In this Review, with the mitochondria under the spotlight, we discuss the most recent findings on the mechanisms mediating the communication between organelles, focusing on Ca2+ signaling, lipid exchange, cell death and stress responses. Notably, we introduce a new integrative perspective to signaling networks that is regulated by interorganelle interactions - the mitochondria-associated niches - focusing on the link between the molecular determinants of contact sites and their functional outputs, rather than simply physical and structural communication. In addition, we highlight the neuropathological and metabolic implications of alterations in mitochondria-associated niches and outline how this concept might improve our understanding of multi-organelle interactions.

Keywords:  Apoptosis; Bioenergetics; MAMs; Mitochondria; Mitochondria-associated membranes; Stress responses

DOI:  https://doi.org/10.1242/jcs.259634
Autophagy. 2022 Nov 30.

The roles of a mitochondrial protein Miga in autophagy.

Lingna Xu, Liquan Wang, Chao Tong.

  Miga is an evolutionarily conserved protein that localizes to the outer membrane of mitochondria and mediates endoplasmic reticulum (ER)-mitochondrial contacts through interaction with VAP proteins in the ER. We recently reported that Miga is required for autophagosome-lysosome fusion during macroautophagy/autophagy. Miga binds to Atg14 and Uvrag, two alternative subunits of the class III phosphatidylinositol 3-kinase (PtdIns3K) complex. Miga regulates phosphatidylinositol-3-phosphate (PtdIns3P) levels through its interaction with Uvrag and its ER-mitochondrial contact site (ERMCS) tethering activity. Miga stabilizes Atg14, which maintains steady levels of the SNARE protein, Syx17. We propose that Miga establishes a direct link between mitochondria and autophagy to maintain cellular homeostasis.

Keywords:  Drosophila; autophagy; endoplasmic reticulum-mitochondrial contacts; mitochondrion; phosphatidylinositol-3 kinase

DOI:  https://doi.org/10.1080/15548627.2022.2153569
Hum Cell. 2022 Nov 29.

Mitochondria: how eminent in ageing and neurodegenerative disorders?

Chia Bamshad, Nima Najafi-Ghalehlou, Zahra Pourmohammadi-Bejarpasi, Kazuo Tomita, Yoshikazu Kuwahara, Tomoaki Sato, Alireza Feizkhah, Amaneh Mohammadi Roushnadeh, Mehryar Habibi Roudkenar.

  Numerous factors are implicated in the onset and progression of ageing and neurodegenerative disorders, with defects in cell energy supply and free radicals regulation designated as being the main functions of mitochondria and highly accentuated in plentiful studies. Hence, analysing the role of mitochondria as one of the main factors implicated in these disorders could undoubtedly come in handy with respect to disease prevention and treatment. In this review, first, we will explore how mitochondria account for neurodegenerative disorders and ageing and later will draw the various pathways contributing to mitochondrial dysfunction in their distinct way. Also, we will discuss the deviation-countering mechanisms, particularly mitophagy, a subset of autophagy known as a much larger cellular defence mechanism and regulatory system, along with its potential therapeutic effects. Last but not least, we will be highlighting the mitochondrial transfer experiments with animal models of neurodegenerative disorders.

Keywords:  Ageing; Free radicals; Mitochondria; Mitochondrial transfer; Mitophagy; Neurodegenerative disorders

DOI:  https://doi.org/10.1007/s13577-022-00833-y
Cell Rep. 2022 Nov 29. pii: S2211-1247(22)01622-9. [Epub ahead of print]41(9): 111744

Inhibition of glutaminolysis restores mitochondrial function in senescent stem cells.

Debanik Choudhury, Na Rong, Izuagie Ikhapoh, Nika Rajabian, Georgios Tseropoulos, Yulun Wu, Pihu Mehrotra, Ramkumar Thiyagarajan, Aref Shahini, Kenneth L Seldeen, Bruce R Troen, Pedro Lei, Stelios T Andreadis.

  Mitochondrial dysfunction, a hallmark of aging, has been associated with the onset of aging phenotypes and age-related diseases. Here, we report that impaired mitochondrial function is associated with increased glutamine catabolism in senescent human mesenchymal stem cells (MSCs) and myofibroblasts derived from patients suffering from Hutchinson-Gilford progeria syndrome. Increased glutaminase (GLS1) activity accompanied by loss of urea transporter SLC14A1 induces urea accumulation, mitochondrial dysfunction, and DNA damage. Conversely, blocking GLS1 activity restores mitochondrial function and leads to amelioration of aging hallmarks. Interestingly, GLS1 expression is regulated through the JNK pathway, as demonstrated by chemical and genetic inhibition. In agreement with our in vitro findings, tissues isolated from aged or progeria mice display increased urea accumulation and GLS1 activity, concomitant with declined mitochondrial function. Inhibition of glutaminolysis in progeria mice improves mitochondrial respiratory chain activity, suggesting that targeting glutaminolysis may be a promising strategy for restoring age-associated loss of mitochondrial function.

Keywords:  CP: Cell biology; GLS1; Hutchinson-Gilford progeria syndrome; JNK; SLC14A1; aging; glutamine; mitochondria; senescence; urea

DOI:  https://doi.org/10.1016/j.celrep.2022.111744
Nat Metab. 2022 Nov 28.

Metabolon formation regulates branched-chain amino acid oxidation and homeostasis.

McKenzie Patrick, Zhimin Gu, Gen Zhang, R Max Wynn, Pranita Kaphle, Hui Cao, Hieu Vu, Feng Cai, Xiaofei Gao, Yuannyu Zhang, Mingyi Chen, Min Ni, David T Chuang, Ralph J DeBerardinis, Jian Xu.

The branched-chain aminotransferase isozymes BCAT1 and BCAT2, segregated into distinct subcellular compartments and tissues, initiate the catabolism of branched-chain amino acids (BCAAs). However, whether and how BCAT isozymes cooperate with downstream enzymes to control BCAA homeostasis in an intact organism remains largely unknown. Here, we analyse system-wide metabolomic changes in BCAT1- and BCAT2-deficient mouse models. Loss of BCAT2 but not BCAT1 leads to accumulation of BCAAs and branched-chain α-keto acids (BCKAs), causing morbidity and mortality that can be ameliorated by dietary BCAA restriction. Through proximity labelling, isotope tracing and enzymatic assays, we provide evidence for the formation of a mitochondrial BCAA metabolon involving BCAT2 and branched-chain α-keto acid dehydrogenase. Disabling the metabolon contributes to BCAT2 deficiency-induced phenotypes, which can be reversed by BCAT1-mediated BCKA reamination. These findings establish a role for metabolon formation in BCAA metabolism in vivo and suggest a new strategy to modulate this pathway in diseases involving dysfunctional BCAA metabolism.

DOI: https://doi.org/10.1038/s42255-022-00689-4
Mol Neurobiol. 2022 Nov 28.

The Depletion of NAMPT Disturbs Mitochondrial Homeostasis and Causes Neuronal Degeneration in Mouse Hippocampus.

Chen Shen, Cong Chen, Tong Wang, Tong-Yao Gao, Min Zeng, Yun-Bi Lu, Wei-Ping Zhang.

  Nicotinamide phosphoribosyltransferase (NAMPT) is the key enzyme in the salvaging synthesis pathway of the nicotinamide adenine dinucleotide (NAD). Both NAMPT and NAD progressively decline upon aging and neurodegenerative diseases. The depletion of NAMPT induces mitochondrial dysfunction in motor neurons and causes bioenergetic stress in neurons. However, the roles of NAMPT in hippocampus neurons need to be further studied. Using floxed Nampt (Namptflox/flox) mice, we knocked out Nampt specifically in the hippocampus CA1 neurons by injecting rAAV-hSyn-Cre-APRE-pA. The depletion of NAMPT in hippocampus neurons induced cognitive deficiency in mice. Nevertheless, no morphological change of hippocampus neurons was observed with immunofluorescent imaging. Under the transmission electron microscope, we observed mitochondrial swollen and mitochondrial number decreasing in the cell body and the neurites of hippocampus neurons. In addition, we found the intracellular Aβ (6E10) increased in the hippocampus CA1 region. The intensity of Aβ42 remained unchanged, but it tended to aggregate. The GFAP level, an astrocyte marker, and the Iba1 level, a microglia marker, significantly increased in the mouse hippocampus. In the primary cultured rat neurons, NAMPT inhibition by FK866 decreased the NAD level of neurons at > 10-9 M. FK866 dropped the mitochondrial membrane potential in the cell body of neurons at > 10-9 M and in the dendrite of neurons at > 10-8 M. FK866 decreased the number and shortened the length of branches of neurons at > 10-7 M. Together, likely due to the injury of mitochondria, the decline of NAMPT level can be a critical risk factor for neurodegeneration.

Keywords:  Mitochondria homeostasis; NAD (nicotinamide adenine dinucleotide); NAMPT (nicotinamide phosphoribosyltransferase); Neurodegeneration

DOI:  https://doi.org/10.1007/s12035-022-03142-5
FEBS Lett. 2022 Nov 28.

Mitochondrial [2Fe-2S] ferredoxins: new functions for old dogs.

Vinzent Schulz, Sven-A Freibert, Linda Boss, Ulrich Mühlenhoff, Oliver Stehling, Roland Lill.

  Ferredoxins (FDXs) comprise a large family of iron-sulfur proteins that shuttle electrons from NADPH and FDX reductases into diverse biological processes. This review focuses on the structure, function and specificity of mitochondrial [2Fe-2S] FDXs that are related to bacterial FDXs due to their endosymbiotic inheritance. Their classical function in cytochrome P450-dependent steroid transformations was identified around 1960, and is exemplified by mammalian FDX1 (aka adrenodoxin). 30 years later the essential function in cellular Fe/S protein biogenesis was discovered for the yeast mitochondrial FDX Yah1 that is additionally crucial for the formation of heme a and ubiquinone CoQ6 . In mammals the former process is exclusively performed by the FDX1 paralog FDX2, despite the high structural similarity of both proteins. Recently, additional and specific roles of human FDX1 in heme a and lipoyl cofactor biosyntheses were described. For lipoyl synthesis, FDX1 transfers electrons to the radical S-adenosyl methionine-dependent lipoyl synthase to kickstart its radical chain reaction. The high target specificity of the two mammalian FDXs is contained within small conserved sequence motifs, that upon swapping change target selection of these electron donors.

Keywords:  Iron-sulfur proteins; S-adenosyl methionine; adrenodoxin; cellular respiration; cytochrome P450; glycine cleavage system; heme; iron-sulfur cluster; lipoyl synthase; mitochondria; steroid conversion; ubiquinone

DOI:  https://doi.org/10.1002/1873-3468.14546
J Biol Chem. 2022 Oct 28. pii: S0021-9258(22)01091-2. [Epub ahead of print]298(12): 102648

Requirement of hepatic pyruvate carboxylase during fasting, high fat, and ketogenic diet.

Ebru S Selen, Susana Rodriguez, Kyle S Cavagnini, Han-Byeol Kim, Chan Hyun Na, Michael J Wolfgang.

  Pyruvate has two major fates upon entry into mitochondria, the oxidative decarboxylation to acetyl-CoA via the pyruvate decarboxylase complex or the biotin-dependent carboxylation to oxaloacetate via pyruvate carboxylase (Pcx). Here, we have generated mice with a liver-specific KO of pyruvate carboxylase (PcxL-/-) to understand the role of Pcx in hepatic mitochondrial metabolism under disparate physiological states. PcxL-/- mice exhibited a deficit in hepatic gluconeogenesis and enhanced ketogenesis as expected but were able to maintain systemic euglycemia following a 24 h fast. Feeding a high-fat diet to PcxL-/- mice resulted in animals that were resistant to glucose intolerance without affecting body weight. However, we found that PcxL-/- mice fed a ketogenic diet for 1 week became severely hypoglycemic, demonstrating a requirement for hepatic Pcx for long-term glycemia under carbohydrate-limited diets. Additionally, we determined that loss of Pcx was associated with an induction in the abundance of lysine-acetylated proteins in PcxL-/- mice regardless of physiologic state. Furthermore, liver acetyl-proteomics revealed a biased induction in mitochondrial lysine-acetylated proteins. These data show that Pcx is important for maintaining the proper balance of pyruvate metabolism between oxidative and anaplerotic pathways.

Keywords:  Pyruvate Carboxylase; acetylation; fasting; gluconeogenesis; mitochondria

DOI:  https://doi.org/10.1016/j.jbc.2022.102648
Nat Commun. 2022 Nov 28. 13(1): 7338

Lysosomal damage drives mitochondrial proteome remodelling and reprograms macrophage immunometabolism.

Claudio Bussi, Tiaan Heunis, Enrica Pellegrino, Elliott M Bernard, Nourdine Bah, Mariana Silva Dos Santos, Pierre Santucci, Beren Aylan, Angela Rodgers, Antony Fearns, Julia Mitschke, Christopher Moore, James I MacRae, Maria Greco, Thomas Reinheckel, Matthias Trost, Maximiliano G Gutierrez.

Transient lysosomal damage after infection with cytosolic pathogens or silica crystals uptake results in protease leakage. Whether limited leakage of lysosomal contents into the cytosol affects the function of cytoplasmic organelles is unknown. Here, we show that sterile and non-sterile lysosomal damage triggers a cell death independent proteolytic remodelling of the mitochondrial proteome in macrophages. Mitochondrial metabolic reprogramming required leakage of lysosomal cathepsins and was independent of mitophagy, mitoproteases and proteasome degradation. In an in vivo mouse model of endomembrane damage, live lung macrophages that internalised crystals displayed impaired mitochondrial function. Single-cell RNA-sequencing revealed that lysosomal damage skewed metabolic and immune responses in alveolar macrophages subsets with increased lysosomal content. Functionally, drug modulation of macrophage metabolism impacted host responses to Mycobacterium tuberculosis infection in an endomembrane damage dependent way. This work uncovers an inter-organelle communication pathway, providing a general mechanism by which macrophages undergo mitochondrial metabolic reprograming after endomembrane damage.

DOI: https://doi.org/10.1038/s41467-022-34632-8
Cell Stem Cell. 2022 Dec 01. pii: S1934-5909(22)00451-9. [Epub ahead of print]29(12): 1685-1702.e22

A reference human induced pluripotent stem cell line for large-scale collaborative studies.

Caroline B Pantazis, Andrian Yang, Erika Lara, Justin A McDonough, Cornelis Blauwendraat, Lirong Peng, Hideyuki Oguro, Jitendra Kanaujiya, Jizhong Zou, David Sebesta, Gretchen Pratt, Erin Cross, Jeffrey Blockwick, Philip Buxton, Lauren Kinner-Bibeau, Constance Medura, Christopher Tompkins, Stephen Hughes, Marianita Santiana, Faraz Faghri, Mike A Nalls, Daniel Vitale, Shannon Ballard, Yue A Qi, Daniel M Ramos, Kailyn M Anderson, Julia Stadler, Priyanka Narayan, Jason Papademetriou, Luke Reilly, Matthew P Nelson, Sanya Aggarwal, Leah U Rosen, Peter Kirwan, Venkat Pisupati, Steven L Coon, Sonja W Scholz, Theresa Priebe, Miriam Öttl, Jian Dong, Marieke Meijer, Lara J M Janssen, Vanessa S Lourenco, Rik van der Kant, Dennis Crusius, Dominik Paquet, Ana-Caroline Raulin, Guojun Bu, Aaron Held, Brian J Wainger, Rebecca M C Gabriele, Jackie M Casey, Selina Wray, Dad Abu-Bonsrah, Clare L Parish, Melinda S Beccari, Don W Cleveland, Emmy Li, Indigo V L Rose, Martin Kampmann, Carles Calatayud Aristoy, Patrik Verstreken, Laurin Heinrich, Max Y Chen, Birgitt Schüle, Dan Dou, Erika L F Holzbaur, Maria Clara Zanellati, Richa Basundra, Mohanish Deshmukh, Sarah Cohen, Richa Khanna, Malavika Raman, Zachary S Nevin, Madeline Matia, Jonas Van Lent, Vincent Timmerman, Bruce R Conklin, Katherine Johnson Chase, Ke Zhang, Salome Funes, Daryl A Bosco, Lena Erlebach, Marc Welzer, Deborah Kronenberg-Versteeg, Guochang Lyu, Ernest Arenas, Elena Coccia, Lily Sarrafha, Tim Ahfeldt, John C Marioni, William C Skarnes, Mark R Cookson, Michael E Ward, Florian T Merkle.

  Human induced pluripotent stem cell (iPSC) lines are a powerful tool for studying development and disease, but the considerable phenotypic variation between lines makes it challenging to replicate key findings and integrate data across research groups. To address this issue, we sub-cloned candidate human iPSC lines and deeply characterized their genetic properties using whole genome sequencing, their genomic stability upon CRISPR-Cas9-based gene editing, and their phenotypic properties including differentiation to commonly used cell types. These studies identified KOLF2.1J as an all-around well-performing iPSC line. We then shared KOLF2.1J with groups around the world who tested its performance in head-to-head comparisons with their own preferred iPSC lines across a diverse range of differentiation protocols and functional assays. On the strength of these findings, we have made KOLF2.1J and its gene-edited derivative clones readily accessible to promote the standardization required for large-scale collaborative science in the stem cell field.

Keywords:  CRISPR; differentiation; iPSC; karyotype; p53; pluripotent; reference; single-cell; stem cell; whole-genome

DOI:  https://doi.org/10.1016/j.stem.2022.11.004
Redox Biol. 2022 Nov 19. pii: S2213-2317(22)00305-6. [Epub ahead of print]58 102533

Mitochondria-originated redox signalling regulates KLF-1 to promote longevity in Caenorhabditis elegans.

Johannes Cw Hermeling, Marija Herholz, Linda Baumann, Estela Cepeda Cores, Aleksandra Zečić, Thorsten Hoppe, Jan Riemer, Aleksandra Trifunovic.

Alternations of redox metabolism have been associated with the extension of lifespan in roundworm Caenorhabditis elegans, caused by moderate mitochondrial dysfunction, although the underlying signalling cascades are largely unknown. Previously, we identified transcriptional factor Krüppel-like factor-1 (KLF-1) as the main regulator of cytoprotective longevity-assurance pathways in the C. elegans long-lived mitochondrial mutants. Here, we show that KLF-1 translocation to the nucleus and the activation of the signalling cascade is dependent on the mitochondria-derived hydrogen peroxide (H2O2) produced during late developmental phases where aerobic respiration and somatic mitochondrial biogenesis peak. We further show that mitochondrial-inducible superoxide dismutase-3 (SOD-3), together with voltage-dependent anion channel-1 (VDAC-1), is required for the life-promoting H2O2 signalling that is further regulated by peroxiredoxin-3 (PRDX-3). Increased H2O2 release in the cytoplasm activates the p38 MAPK signalling cascade that induces KLF-1 translocation to the nucleus and the activation of transcription of C. elegans longevity-promoting genes, including cytoprotective cytochrome P450 oxidases. Taken together, our results underline the importance of redox-regulated signalling as the key regulator of longevity-inducing pathways in C. elegans, and position precisely timed mitochondria-derived H2O2 in the middle of it.

DOI: https://doi.org/10.1016/j.redox.2022.102533
Stem Cell Res. 2022 Nov 22. pii: S1873-5061(22)00329-4. [Epub ahead of print]65 102980

Generation of a homozygous FIS1 knockout human embryonic stem cell line GIBHe015-B by CRISPR/Cas9 system.

Mingquan Wang, Jun Tang, Tiancheng Zhou, Yuchan Mai, Yanling Zhu.

The mitochondrial fission protein 1 (FIS1) is essential for mitochondrial division or fission and has been determined to mediate mitochondrial and peroxisomal fission. Other studies also found that FIS1 functions as an essential component of the mitophagy and apoptosis pathways in mammalian cells, suggesting that FIS1 has multiple important roles. Here, we generated homozygous FIS1 knockout human embryonic stem cells (hESCs) using the CRISPR/Cas9 system. This cell line exhibits normal karyotype, pluripotency, and trilineage differentiation potential, which could provide a useful cellular resource for exploring the functions of FIS1 and their implications in human health and diseases.

DOI: https://doi.org/10.1016/j.scr.2022.102980
Mol Reprod Dev. 2022 Nov 29.

Profiling of mitochondrial heteroplasmy in single human oocytes by next-generation sequencing.

Valentina Russo, Massimo Ancora, Valentina Gatta, Massimiliano Orsini, Giuseppe Prencipe, Alessia Peserico, Alessia Colosimo, Mohammad El Khatib, Annunziata Mauro, Chiara Di Berardino, Silvia Scialabba, Gian Mario Tiboni, Maurilia Marcacci, Cesare Cammà, Barbara Barboni.

  Mitochondrial DNA (mtDNA) plays a crucial role in the development of a competent oocyte. Indeed, mtDNA alterations may predispose to chromosome nondisjunction, resulting in infertility due to a reduced vitality and quality of oocytes and embryos. In this methods paper, the multiple displacement amplification approach was applied in combination with next-generation sequencing (NGS) to amplify and sequence, in single-end, the entire mtDNA of single human oocytes to directly construct genomic NGS libraries, and subsequently, to highlight and quantify the mutations they presented. The bioinformatic workflow was carried out with a specific ad hoc developed in-house software. This approach proved to be sensitive and specific, also highlighting the mutations present in heteroplasmy, showing deletion, insertion or substitution mutations in the genes involved in the respiratory chain, even if the found variants were benign or of uncertain meaning. The analysis of mtDNA mutations in the oocyte could provide a better understanding of specific genetic abnormalities and of their possible effect on oocyte developmental competence. This study shows how this approach, based on a massive parallel sequencing of clonally amplified DNA molecules, allows to sequence the entire mitochondrial genome of single oocytes in a short time and with a single analytical run and to verify mtDNA mutations.

Keywords:  heteroplasmic mutations; human oocyte; mitochondrial DNA; next-generation sequencing

DOI:  https://doi.org/10.1002/mrd.23655
Cell Discov. 2022 Nov 29. 8(1): 128

Loss of function of CMPK2 causes mitochondria deficiency and brain calcification.

Miao Zhao, Hui-Zhen Su, Yi-Heng Zeng, Yuan Sun, Xin-Xin Guo, Yun-Lu Li, Chong Wang, Zhi-Yuan Zhao, Xue-Jing Huang, Kai-Jun Lin, Zi-Ling Ye, Bi-Wei Lin, Shunyan Hong, Jitan Zheng, Yao-Bin Liu, Xiang-Ping Yao, Dehao Yang, Ying-Qian Lu, Hai-Zhu Chen, Erwei Zuo, Guang Yang, Hong-Tao Wang, Chen-Wei Huang, Xiao-Hong Lin, Zhidong Cen, Lu-Lu Lai, Yan-Ke Zhang, Xi Li, Tianmin Lai, Jingjing Lin, Dan-Dan Zuo, Min-Ting Lin, Chia-Wei Liou, Qing-Xia Kong, Chuan-Zhu Yan, Zhi-Qi Xiong, Ning Wang, Wei Luo, Cui-Ping Zhao, Xuewen Cheng, Wan-Jin Chen.

Brain calcification is a critical aging-associated pathology and can cause multifaceted neurological symptoms. Cerebral phosphate homeostasis dysregulation, blood-brain barrier defects, and immune dysregulation have been implicated as major pathological processes in familial brain calcification (FBC). Here, we analyzed two brain calcification families and identified calcification co-segregated biallelic variants in the CMPK2 gene that disrupt mitochondrial functions. Transcriptome analysis of peripheral blood mononuclear cells (PBMCs) isolated from these patients showed impaired mitochondria-associated metabolism pathways. In situ hybridization and single-cell RNA sequencing revealed robust Cmpk2 expression in neurons and vascular endothelial cells (vECs), two cell types with high energy expenditure in the brain. The neurons in Cmpk2-knockout (KO) mice have fewer mitochondrial DNA copies, down-regulated mitochondrial proteins, reduced ATP production, and elevated intracellular inorganic phosphate (Pi) level, recapitulating the mitochondrial dysfunction observed in the PBMCs isolated from the FBC patients. Morphologically, the cristae architecture of the Cmpk2-KO murine neurons was also impaired. Notably, calcification developed in a progressive manner in the homozygous Cmpk2-KO mice thalamus region as well as in the Cmpk2-knock-in mice bearing the patient mutation, thus phenocopying the calcification pathology observed in the patients. Together, our study identifies biallelic variants of CMPK2 as novel genetic factors for FBC; and demonstrates how CMPK2 deficiency alters mitochondrial structures and functions, thereby highlighting the mitochondria dysregulation as a critical pathogenic mechanism underlying brain calcification.

DOI: https://doi.org/10.1038/s41421-022-00475-2
Front Pediatr. 2022 ;10 1032359

Editorial: NGS technologies of rare diseases diagnosis.

María L Couce, Emiliano González-Vioque.



Keywords:  DNA SEQUENCING; exome sequencing; genome sequencing; transcriptome; variants

DOI:  https://doi.org/10.3389/fped.2022.1032359
Brain. 2022 Dec 01. pii: awac453. [Epub ahead of print]

Homozygous COQ7 mutation: a new cause of potentially treatable distal hereditary motor neuropathy.

Arnaud Jacquier, Julian Theuriet, Fanny Fontaine, Valentine Mosbach, Nicolas Lacoste, Shams Ribault, Valérie Risson, Julien Carras, Laurent Coudert, Thomas Simonet, Philippe Latour, Tanya Stojkovic, Juliette Piard, Anne Cosson, Gaëtan Lesca, Françoise Bouhour, Stéphane Allouche, Hélène Puccio, Antoine Pégat, Laurent Schaeffer.

  Distal hereditary motor neuropathy represents a group of motor inherited neuropathies leading to distal weakness. We report a family of two brothers and a sister affected by distal hereditary motor neuropathy in whom a homozygous variant c.3G > T (p.1Met? ) was identified in the COQ7 gene. This gene encodes a protein required for Coenzyme Q10 biosynthesis, a component of the respiratory chain in mitochondria. Mutations of COQ7 were previously associated with severe multi-organ disorders characterized by early childhood onset and developmental delay. Using patient blood sample and fibroblasts derived from a skin biopsy, we investigated the pathogenicity of the variant of unknown significance c.3G > T (p.1Met? ) in the COQ7 gene and the effect of Coenzyme Q10 supplementation in vitro. We showed that this variation leads to a severe decrease in COQ7 protein levels in the patient's fibroblasts, resulting in a decrease in Coenzyme Q10 production, and in the accumulation of 6-demethoxycoenzyme Q10, the COQ7 substrate. Interestingly, such accumulation was also found in the patient's plasma. Normal Coenzyme Q10 and 6-demethoxycoenzyme Q10 levels were restored in vitro by using the Coenzyme Q10 precursor 2,4-dihydroxybenzoic acid, thus bypassing COQ7 requirement. Coenzyme Q10 biosynthesis deficiency is known to impair mitochondrial respiratory chain. Seahorse experiments showed that the patient's cells mainly rely on glycolysis to maintain sufficient ATP production. Consistently, the replacement of glucose by galactose in the culture medium of these cells reduced their proliferation rate. Interestingly, normal proliferation was restored by Coenzyme Q10 supplementation in the culture medium, suggesting a therapeutic avenue for these patients. Altogether, we have identified the first example of recessive distal hereditary motor neuropathy caused by a homozygous variation in the COQ7 gene, which should thus be included in the gene panels used to diagnose peripheral inherited neuropathies. Furthermore, 6-demethoxycoenzyme Q10 accumulation in the blood can be used to confirm the pathogenic nature of the mutation. Finally, supplementation with Coenzyme Q10 or derivatives should be considered to prevent the progression of COQ7-related peripheral inherited neuropathy in diagnosed patients.

Keywords:  COQ7; Coenzyme Q10; distal hereditary motor neuropathy

DOI:  https://doi.org/10.1093/brain/awac453
Cell Signal. 2022 Nov 24. pii: S0898-6568(22)00298-4. [Epub ahead of print] 110536

Lin28a induced mitochondrial dysfunction in human granulosa cells via suppressing LARS2 expression.

Jing Chen, Weimin Liu.

  Granulosa cells surround the oocytes as a component of ovarian follicles and produce sex steroids and growth factors to support oocyte development. Mitochondria is one of the multiple factors regulating granulosa cell function by modulating bioenergetic pathways and maintaining cells' metabolic needs. Lin28a was reported to regulate the primordial germ cell development in the ovary and affect the fertility rate in females. However, whether Lin28a modulated mitochondria function in granulosa cells to regulate steroidogenesis remains a further exploration. In this study, we utilized immortal human granulosa cells (HGrC1) to overexpress or suppress the protein level of Lin28a. Results showed that overexpression of Lin28a could decrease the estrogen level, ATP content, mitochondrial membrane potential and Glutathione (GSH) level, while silencing Lin28a caused the opposite effect. Further, we found that overexpression of LARS2, a mitochondrial leucyl-tRNA synthetase, could increase the estrogen level, ATP content, mitochondrial membrane potential and GSH level while silencing LARS2 caused adverse results. Overexpression of LARS2 reversed Lin28a-induced estrogen downregulation and mitochondrial dysfunction. Moreover, overexpression of LARS2 increased the mRNA level of Pgc1α and Nrf2, which were involved in mitochondrial biogenesis. Besides, Lin28a could directly bind to the mRNA of Lars2 to suppress its translation. Taken together, overexpression of Lin28a caused mitochondrial dysfunction in granulosa cells via suppressing LARS2 expression. This study can provide new insights into how Lin28a regulates mitochondrial function in granulosa cells and influences female fertility.

Keywords:  Estrogen; Granulosa cells; LARS2; Lin28a; Mitochondrial dysfunction

DOI:  https://doi.org/10.1016/j.cellsig.2022.110536
Cell Genom. 2022 May;2(5):

Benchmarking challenging small variants with linked and long reads.

Justin Wagner, Nathan D Olson, Lindsay Harris, Ziad Khan, Jesse Farek, Medhat Mahmoud, Ana Stankovic, Vladimir Kovacevic, Byunggil Yoo, Neil Miller, Jeffrey A Rosenfeld, Bohan Ni, Samantha Zarate, Melanie Kirsche, Sergey Aganezov, Michael C Schatz, Giuseppe Narzisi, Marta Byrska-Bishop, Wayne Clarke, Uday S Evani, Charles Markello, Kishwar Shafin, Xin Zhou, Arend Sidow, Vikas Bansal, Peter Ebert, Tobias Marschall, Peter Lansdorp, Vincent Hanlon, Carl-Adam Mattsson, Alvaro Martinez Barrio, Ian T Fiddes, Chunlin Xiao, Arkarachai Fungtammasan, Chen-Shan Chin, Aaron M Wenger, William J Rowell, Fritz J Sedlazeck, Andrew Carroll, Marc Salit, Justin M Zook.

Genome in a Bottle benchmarks are widely used to help validate clinical sequencing pipelines and develop variant calling and sequencing methods. Here we use accurate linked and long reads to expand benchmarks in 7 samples to include difficult-to-map regions and segmental duplications that are challenging for short reads. These benchmarks add more than 300,000 SNVs and 50,000 insertions or deletions (indels) and include 16% more exonic variants, many in challenging, clinically relevant genes not covered previously, such as PMS2. For HG002, we include 92% of the autosomal GRCh38 assembly while excluding regions problematic for benchmarking small variants, such as copy number variants, that should not have been in the previous version, which included 85% of GRCh38. It identifies eight times more false negatives in a short read variant call set relative to our previous benchmark. We demonstrate that this benchmark reliably identifies false positives and false negatives across technologies, enabling ongoing methods development.

DOI: https://doi.org/10.1016/j.xgen.2022.100128
J Am Coll Cardiol. 2022 Dec 06. pii: S0735-1097(22)07044-9. [Epub ahead of print]80(23): 2220-2223

Targeting Mitochondrial Calcium Handling to Treat Atrial Fibrillation.

Niels Voigt, Christoph Maack, Julius Ryan D Pronto.



Keywords:  atrial arrhythmias; atrial fibrillation; calcium; diabetic cardiomyopathy; metabolism; mitochondria

DOI:  https://doi.org/10.1016/j.jacc.2022.09.043
Nat Commun. 2022 Dec 02. 13(1): 7414

Nuclear localization of mitochondrial TCA cycle enzymes modulates pluripotency via histone acetylation.

Wei Li, Qi Long, Hao Wu, Yanshuang Zhou, Lifan Duan, Hao Yuan, Yingzhe Ding, Yile Huang, Yi Wu, Jinyu Huang, Delong Liu, Baodan Chen, Jian Zhang, Juntao Qi, Shiwei Du, Linpeng Li, Yang Liu, Zifeng Ruan, Zihuang Liu, Zichao Liu, Yifan Zhao, Jianghuan Lu, Junwei Wang, Wai-Yee Chan, Xingguo Liu.

Pluripotent stem cells hold great promise in regenerative medicine and developmental biology studies. Mitochondrial metabolites, including tricarboxylic acid (TCA) cycle intermediates, have been reported to play critical roles in pluripotency. Here we show that TCA cycle enzymes including Pdha1, Pcb, Aco2, Cs, Idh3a, Ogdh, Sdha and Mdh2 are translocated to the nucleus during somatic cell reprogramming, primed-to-naive transition and totipotency acquisition. The nuclear-localized TCA cycle enzymes Pdha1, Pcb, Aco2, Cs, Idh3a promote somatic cell reprogramming and primed-to-naive transition. In addition, nuclear-localized TCA cycle enzymes, particularly nuclear-targeted Pdha1, facilitate the 2-cell program in pluripotent stem cells. Mechanistically, nuclear Pdha1 increases the acetyl-CoA and metabolite pool in the nucleus, leading to chromatin remodeling at pluripotency genes by enhancing histone H3 acetylation. Our results reveal an important role of mitochondrial TCA cycle enzymes in the epigenetic regulation of pluripotency that constitutes a mitochondria-to-nucleus retrograde signaling mode in different states of pluripotent acquisition.

DOI: https://doi.org/10.1038/s41467-022-35199-0
Cell Stress. 2022 Aug;6(8): 72-75

Cardiac PI3K p110α attenuation delays aging and extends lifespan.

Mahmoud Abdellatif, Tobias Eisenberg, Alexander Martin Heberle, Kathrin Thedieck, Guido Kroemer, Simon Sedej.

  Phosphoinositide 3-kinase (PI3K) is a key component of the insulin signaling pathway that controls cellular me-tabolism and growth. Loss-of-function mutations in PI3K signaling and other downstream effectors of the insulin signaling pathway extend the lifespan of various model organisms. However, the pro-longevity effect appears to be sex-specific and young mice with reduced PI3K signaling have increased risk of cardiac disease. Hence, it remains elusive as to whether PI3K inhibition is a valid strategy to delay aging and extend healthspan in humans. We recently demonstrated that reduced PI3K activity in cardiomyocytes delays cardiac growth, causing subnormal contractility and cardiopulmonary functional capacity, as well as increased risk of mortality at young age. In stark contrast, in aged mice, experi-mental attenuation of PI3K signaling reduced the age-dependent decline in cardiac function and extended maximal lifespan, suggesting a biphasic effect of PI3K on cardiac health and survival. The cardiac anti-aging effects of reduced PI3K activity coincided with enhanced oxida-tive phosphorylation and required increased autophagic flux. In humans, explanted failing hearts showed in-creased PI3K signaling, as indicated by increased phos-phorylation of the serine/threonine-protein kinase AKT. Hence, late-life cardiac-specific targeting of PI3K might have a therapeutic potential in cardiac aging and related diseases.

Keywords:  IGF1; PI3K; aging; autophagy; cardiomyopathy; heart failure; insulin signaling; mitochondrial dysfunction

DOI:  https://doi.org/10.15698/cst2022.08.270
Trends Cell Biol. 2022 Nov 24. pii: S0962-8924(22)00252-5. [Epub ahead of print]

Cellular functions of cGAS-STING signaling.

Chen Chen, Pinglong Xu.

  Cyclic GMP-AMP (cGAMP) synthase (cGAS) senses misplaced genomic, mitochondrial, and microbial double-stranded DNA (dsDNA) to synthesize 2'3'-cGAMP that mobilizes stimulator of interferon genes (STING) to unleash innate immune responses, constituting a ubiquitous and effective surveillance system against tissue damage and pathogen invasion. However, imbalanced cGAS-STING signaling tethers considerably in infectious, autoimmune, malignant, fibrotic, and neurodegenerative diseases. Recently, multifaceted roles for cGAS-STING signaling at the cellular scale have emerged; these include autophagy, translation, metabolism homeostasis, cellular condensation, DNA damage repair, senescence, and cell death. These dominances adaptively shape cellular physiologies and impact disease pathogenesis. However, understanding how DNA sensing-initiated responses trigger these diverse cellular processes remains an outstanding challenge. In this review we discuss recent developments of cellular physiological states controlled by cGAS-STING machinery, as well as their disease relevance and underlying mechanisms, canonical or noncanonical. Ultimately, exploiting these cellular functions and mechanisms may represent promising targets for disease therapeutics.

Keywords:  autophagy; cGAMP; cGAS-STING; condensation; innate immunity; metabolism; organelle; pathogenesis; senescence; translation

DOI:  https://doi.org/10.1016/j.tcb.2022.11.001
Nat Metab. 2022 Nov 28.

Mitochondrial RNA stimulates beige adipocyte development in young mice.

Anh Cuong Hoang, László Sasi-Szabó, Tibor Pál, Tamás Szabó, Victoria Diedrich, Annika Herwig, Kathrin Landgraf, Antje Körner, Tamás Röszer.

Childhood obesity is a serious public health crisis and a critical factor that determines future obesity prevalence. Signals affecting adipocyte development in early postnatal life have a strong potential to trigger childhood obesity; however, these signals are still poorly understood. We show here that mitochondrial (mt)RNA efflux stimulates transcription of nuclear-encoded genes for mitobiogenesis and thermogenesis in adipocytes of young mice and human infants. While cytosolic mtRNA is a potential trigger of the interferon (IFN) response, young adipocytes lack such a response to cytosolic mtRNA due to the suppression of IFN regulatory factor (IRF)7 expression by vitamin D receptor signalling. Adult and obese adipocytes, however, strongly express IRF7 and mount an IFN response to cytosolic mtRNA. In turn, suppressing IRF7 expression in adult adipocytes restores mtRNA-induced mitobiogenesis and thermogenesis and eventually mitigates obesity. Retrograde mitochondrion-to-nucleus signalling by mtRNA is thus a mechanism to evoke thermogenic potential during early adipocyte development and to protect against obesity.

DOI: https://doi.org/10.1038/s42255-022-00683-w
Cell. 2022 Nov 22. pii: S0092-8674(22)01378-2. [Epub ahead of print]

Genome-wide data from medieval German Jews show that the Ashkenazi founder event pre-dated the 14th century.

Shamam Waldman, Daniel Backenroth, Éadaoin Harney, Stefan Flohr, Nadia C Neff, Gina M Buckley, Hila Fridman, Ali Akbari, Nadin Rohland, Swapan Mallick, Iñigo Olalde, Leo Cooper, Ariel Lomes, Joshua Lipson, Jorge Cano Nistal, Jin Yu, Nir Barzilai, Inga Peter, Gil Atzmon, Harry Ostrer, Todd Lencz, Yosef E Maruvka, Maike Lämmerhirt, Alexander Beider, Leonard V Rutgers, Virginie Renson, Keith M Prufer, Stephan Schiffels, Harald Ringbauer, Karin Sczech, Shai Carmi, David Reich.

  We report genome-wide data from 33 Ashkenazi Jews (AJ), dated to the 14th century, obtained following a salvage excavation at the medieval Jewish cemetery of Erfurt, Germany. The Erfurt individuals are genetically similar to modern AJ, but they show more variability in Eastern European-related ancestry than modern AJ. A third of the Erfurt individuals carried a mitochondrial lineage common in modern AJ and eight carried pathogenic variants known to affect AJ today. These observations, together with high levels of runs of homozygosity, suggest that the Erfurt community had already experienced the major reduction in size that affected modern AJ. The Erfurt bottleneck was more severe, implying substructure in medieval AJ. Overall, our results suggest that the AJ founder event and the acquisition of the main sources of ancestry pre-dated the 14th century and highlight late medieval genetic heterogeneity no longer present in modern AJ.

Keywords:  Ashkenazi Jews; IBD sharing; admixture; ancient DNA; demographic inference; founder event; mitochondrial DNA; pathogenic variants; population structure; runs of homozygosity

DOI:  https://doi.org/10.1016/j.cell.2022.11.002
Am J Hum Genet. 2022 Dec 01. pii: S0002-9297(22)00464-5. [Epub ahead of print]109(12): 2105-2109

A minimal role for synonymous variation in human disease.

Ryan S Dhindsa, Quanli Wang, Dimitrios Vitsios, Oliver S Burren, Fengyuan Hu, James E DiCarlo, Leonid Kruglyak, Daniel G MacArthur, Matthew E Hurles, Slavé Petrovski.

Synonymous mutations change the DNA sequence of a gene without affecting the amino acid sequence of the encoded protein. Although some synonymous mutations can affect RNA splicing, translational efficiency, and mRNA stability, studies in human genetics, mutagenesis screens, and other experiments and evolutionary analyses have repeatedly shown that most synonymous variants are neutral or only weakly deleterious, with some notable exceptions. Based on a recent study in yeast, there have been claims that synonymous mutations could be as important as nonsynonymous mutations in causing disease, assuming the yeast findings hold up and translate to humans. Here, we argue that there is insufficient evidence to overturn the large, coherent body of knowledge establishing the predominant neutrality of synonymous variants in the human genome.

DOI: https://doi.org/10.1016/j.ajhg.2022.10.016
Mol Cell. 2022 Nov 21. pii: S1097-2765(22)01066-8. [Epub ahead of print]

Profiling lariat intermediates reveals genetic determinants of early and late co-transcriptional splicing.

Yi Zeng, Benjamin J Fair, Huilin Zeng, Aiswarya Krishnamohan, Yichen Hou, Johnathon M Hall, Alexander J Ruthenburg, Yang I Li, Jonathan P Staley.

  Long introns with short exons in vertebrate genes are thought to require spliceosome assembly across exons (exon definition), rather than introns, thereby requiring transcription of an exon to splice an upstream intron. Here, we developed CoLa-seq (co-transcriptional lariat sequencing) to investigate the timing and determinants of co-transcriptional splicing genome wide. Unexpectedly, 90% of all introns, including long introns, can splice before transcription of a downstream exon, indicating that exon definition is not obligatory for most human introns. Still, splicing timing varies dramatically across introns, and various genetic elements determine this variation. Strong U2AF2 binding to the polypyrimidine tract predicts early splicing, explaining exon definition-independent splicing. Together, our findings question the essentiality of exon definition and reveal features beyond intron and exon length that are determinative for splicing timing.

Keywords:  CoLa-seq; GC content; U2AF; branch point; co-transcriptional splicing; exon definition; intron definition; lariat RNAs; modeling; polypyrimidine tract

DOI:  https://doi.org/10.1016/j.molcel.2022.11.004