bims-mitdis 2021-09-19 papers

bims-mitdis

Biomed News

on Mitochondrial disorders

Issue of 2021–09–19
35 papers selected by
Catalina Vasilescu, University of Helsinki

Mitochondrial Nucleic Acid as a Driver of Pathogenic Type I Interferon Induction in Mendelian Disease.
Targeting Adaptive Cellular Responses To Mitochondrial Bioenergetic Deficiencies In Human Disease.
Decreased Mitochondrial Membrane Potential Activates the Mitochondrial Unfolded Protein Response.
A role for mitochondrial DNA in cellular proteostasis.
Mitochondrial disease, mitophagy, and cellular distress in methylmalonic acidemia.
Preclinical and clinical evidence of NAD+ precursors in health, disease, and ageing.
Mapping Activity-Dependent Quasi-stationary States of Mitochondrial Membranes with Graphene-Induced Energy Transfer Imaging.
Activation of mTORC1 and c-Jun by Prohibitin1 loss in Schwann cells may link mitochondrial dysfunction to demyelination.
Leaked Mitochondrial C1QBP Inhibits Activation of the DNA Sensor cGAS.
Sirtuin 3 regulates mitochondrial protein acetylation and metabolism in tubular epithelial cells during renal fibrosis.
HDAC6: A Key Link Between Mitochondria and Development of Peripheral Neuropathy.
Mitochondrial enzyme GPT2 regulates metabolic mechanisms required for neuron growth and motor function in vivo.
Genetic screening reveals phospholipid metabolism as a key regulator of the biosynthesis of the redox-active lipid coenzyme Q.
Correction to 'DNA polymerase gamma mutations that impair holoenzyme stability cause catalytic subunit depletion'.
Dynamin-related protein 1 regulates substrate oxidation in skeletal muscle by stabilizing cellular and mitochondrial calcium dynamics.
The recurrent missense mutation p.(Arg367Trp) in YARS1 causes a distinct neurodevelopmental phenotype.
Homeostatic control of nuclear-encoded mitochondrial gene expression by the histone variant H2A.Z is essential for neuronal survival.
Leigh syndrome-like MRI changes in a patient with biallelic HPDL variants treated with ketogenic diet.
Autophagy-competent mitochondrial translation elongation factor TUFM inhibits caspase-8-mediated apoptosis.
Mitochondrial contact site and cristae organizing system (MICOS) machinery supports heme biosynthesis by enabling optimal performance of ferrochelatase.
Molecular mechanisms of dietary restriction promoting health and longevity.
A de novo mutation in mitochondrial ATPsynthase subunit α causes a life threatening disease in neonates which heals in infancy.
Increased fidelity of protein synthesis extends lifespan.
Mitochondrial disease: Replace or edit?
Mitochondrial-encoded MOTS-c prevents pancreatic islet destruction in autoimmune diabetes.
Characterization of variants of uncertain significance in isovaleryl-CoA dehydrogenase identified through newborn screening: An approach for faster analysis.
Cristae-dependent quality control of the mitochondrial genome.
Viola: a structural variant signature extractor with user-defined classifications.
Herding cats: Label-based approaches in protein translocation through nanopore sensors for single-molecule protein sequence analysis.
Mitochondrial-derived peptides and exercise.
Whole-genome sequencing as a first-tier diagnostic framework for rare genetic diseases.
Identifying digenic disease genes via machine learning in the Undiagnosed Diseases Network.
RNA splicing programs define tissue compartments and cell types at single cell resolution.
Local adaptation and archaic introgression shape global diversity at human structural variant loci.
Metabolic Changes of Hepatocytes in NAFLD.

Front Immunol. 2021 ;12 729763

Mitochondrial Nucleic Acid as a Driver of Pathogenic Type I Interferon Induction in Mendelian Disease.

Alice Lepelley, Timothy Wai, Yanick J Crow.

  The immune response to viral infection involves the recognition of pathogen-derived nucleic acids by intracellular sensors, leading to type I interferon (IFN), and downstream IFN-stimulated gene, induction. Ineffective discrimination of self from non-self nucleic acid can lead to autoinflammation, a phenomenon implicated in an increasing number of disease states, and well highlighted by the group of rare genetic disorders referred to as the type I interferonopathies. To understand the pathogenesis of these monogenic disorders, and polyfactorial diseases associated with pathogenic IFN upregulation, such as systemic lupus erythematosus and dermatomyositis, it is important to define the self-derived nucleic acid species responsible for such abnormal IFN induction. Recently, attention has focused on mitochondria as a novel source of immunogenic self nucleic acid. Best appreciated for their function in oxidative phosphorylation, metabolism and apoptosis, mitochondria are double membrane-bound organelles that represent vestigial bacteria in the cytosol of eukaryotic cells, containing their own DNA and RNA enclosed within the inner mitochondrial membrane. There is increasing recognition that a loss of mitochondrial integrity and compartmentalization can allow the release of mitochondrial nucleic acid into the cytosol, leading to IFN induction. Here, we provide recent insights into the potential of mitochondrial-derived DNA and RNA to drive IFN production in Mendelian disease. Specifically, we summarize current understanding of how nucleic acids are detected as foreign when released into the cytosol, and then consider the findings implicating mitochondrial nucleic acid in type I interferonopathy disease states. Finally, we discuss the potential for IFN-driven pathology in primary mitochondrial disorders.

Keywords:  autoinflammation; innate immunity; mitochondria; mitochondrial disease; mtDNA; mtRNA; type I interferon; type I interferonopathy

DOI:  https://doi.org/10.3389/fimmu.2021.729763
FEBS J. 2021 Sep 12.

Targeting Adaptive Cellular Responses To Mitochondrial Bioenergetic Deficiencies In Human Disease.

Christopher F Bennett, Conor T Ronayne, Pere Puigserver.

  Mitochondrial dysfunction is increasingly appreciated as a central contributor to human disease. Oxidative metabolism at the mitochondrial respiratory chain produces ATP and is intricately tied to redox homeostasis and biosynthetic pathways. Metabolic stress arising from genetic mutations in mitochondrial genes and environmental factors such as malnutrition or overnutrition is perceived by the cell and leads to adaptive and maladaptive responses that can underlie pathology. Here, we will outline cellular sensors that react to alterations in energy production, organellar redox, and metabolites stemming from mitochondrial disease (MD) mutations. MD is a heterogenous group of disorders primarily defined by defects in mitochondrial oxidative phosphorylation from nuclear or mitochondrial-encoded gene mutations. Pre-clinical therapies that improve fitness of MD mouse models have been recently identified. Targeting metabolic/energetic deficiencies, maladaptive signaling processes, and hyper-oxygenation of tissues are all strategies aside from direct genetic approaches that hold therapeutic promise. A further mechanistic understanding of these curative processes as well as the identification of novel targets will significantly impact mitochondrial biology and disease research.

Keywords:  Mitochondrial dysfunction; hypoxia; mTORC1; metabolism; mitochondrial disease; mitochondrial signaling; oxidative stress; reactive oxygen species; redox homeostasis

DOI:  https://doi.org/10.1111/febs.16195
MicroPubl Biol. 2021 ;2021

Decreased Mitochondrial Membrane Potential Activates the Mitochondrial Unfolded Protein Response.

Brandon J Berry, Tyrone O Nieves, Andrew P Wojtovich.

Mitochondria are ATP-producing organelles that also signal throughout the cell. Mitochondrial protein homeostasis is regulated through membrane potential-dependent protein import and quality control signaling. The mitochondrial unfolded protein response (UPRmt) is a specific program that responds to imbalances in nuclear and mitochondrial gene expression. Mounting evidence suggests that the electrochemical gradient that powers mitochondrial function, the mitochondrial membrane potential (Δψm), is a core regulator of the UPRmt. Here we tested this notion directly by pharmacologically dissipating Δψm and monitoring UPRmt activation. We found that chemical dissipation of Δψm using FCCP indeed activated UPRmt dose-dependently in C. elegans assayed by the HSP-60::GFP reporter strain.

DOI: https://doi.org/10.17912/micropub.biology.000445
Nat Rev Genet. 2021 Sep 13.

A role for mitochondrial DNA in cellular proteostasis.

Caroline Barranco.

DOI: https://doi.org/10.1038/s41576-021-00418-9
Cell Mol Life Sci. 2021 Sep 15.

Mitochondrial disease, mitophagy, and cellular distress in methylmalonic acidemia.

Alessandro Luciani, Matthew C S Denley, Larissa P Govers, Vincenzo Sorrentino, D Sean Froese.

  Mitochondria-the intracellular powerhouse in which nutrients are converted into energy in the form of ATP or heat-are highly dynamic, double-membraned organelles that harness a plethora of cellular functions that sustain energy metabolism and homeostasis. Exciting new discoveries now indicate that the maintenance of this ever changing and functionally pleiotropic organelle is particularly relevant in terminally differentiated cells that are highly dependent on aerobic metabolism. Given the central role in maintaining metabolic and physiological homeostasis, dysregulation of the mitochondrial network might therefore confer a potentially devastating vulnerability to high-energy requiring cell types, contributing to a broad variety of hereditary and acquired diseases. In this Review, we highlight the biological functions of mitochondria-localized enzymes from the perspective of understanding-and potentially reversing-the pathophysiology of inherited disorders affecting the homeostasis of the mitochondrial network and cellular metabolism. Using methylmalonic acidemia as a paradigm of complex mitochondrial dysfunction, we discuss how mitochondrial directed-signaling circuitries govern the homeostasis and physiology of specialized cell types and how these may be disturbed in disease. This Review also provides a critical analysis of affected tissues, potential molecular mechanisms, and novel cellular and animal models of methylmalonic acidemia which are being used to develop new therapeutic options for this disease. These insights might ultimately lead to new therapeutics, not only for methylmalonic acidemia, but also for other currently intractable mitochondrial diseases, potentially transforming our ability to regulate homeostasis and health.

Keywords:  Cell damage; Inherited metabolic diseases; Metabolism; Mitochondria; Mitophagy; Oxidative stress

DOI:  https://doi.org/10.1007/s00018-021-03934-3
Mech Ageing Dev. 2021 Sep 10. pii: S0047-6374(21)00139-1. [Epub ahead of print] 111567

Preclinical and clinical evidence of NAD+ precursors in health, disease, and ageing.

Ole Kristian Reiten, Martin Andreas Wilvang, Sarah J Mitchell, Zeping Hu, Evandro F Fang.

  NAD+ is a fundamental molecule in human life and health as it participates in energy metabolism, cell signalling, mitochondrial homeostasis, and in dictating cell survival or death. Emerging evidence from preclinical and human studies indicates an age-dependent reduction of cellular NAD+, possibly due to reduced synthesis and increased consumption. In preclinical models, NAD+ repletion extends healthspan and / or lifespan and mitigates several conditions, such as premature ageing diseases and neurodegenerative diseases. These findings suggest that NAD+ replenishment through NAD+ precursors has great potential as a therapeutic target for ageing and age-predisposed diseases, such as Alzheimer's disease. Here, we provide an updated review on the biological activity, safety, and possible side effects of NAD+ precursors in preclinical and clinical studies. Major NAD+ precursors focused on by this review are nicotinamide riboside (NR), nicotinamide mononucleotide (NMN), and the new discovered dihydronicotinamide riboside (NRH). In summary, NAD+ precursors have an exciting therapeutic potential for ageing, metabolic and neurodegenerative diseases.

Keywords:  Alzheimer’s disease; NAD(+); ageing; healthspan

DOI:  https://doi.org/10.1016/j.mad.2021.111567
Nano Lett. 2021 Sep 14.

Mapping Activity-Dependent Quasi-stationary States of Mitochondrial Membranes with Graphene-Induced Energy Transfer Imaging.

Sufi O Raja, Alexey I Chizhik, Christoph F Schmidt, Jörg Enderlein, Arindam Ghosh.

  Graphene-induced energy transfer (GIET) was recently introduced for sub-nanometric axial localization of fluorescent molecules. GIET relies on near-field energy transfer from an optically excited fluorophore to a single sheet of graphene. Recently, we demonstrated its potential by determining the distance between two leaflets of supported lipid bilayers. Here, we use GIET imaging for mapping quasi-stationary states of the inner and outer mitochondrial membranes before and during adenosine triphosphate (ATP) synthesis. We trigger the ATP synthesis state in vitro by activating mitochondria with precursor molecules. Our results demonstrate that the inner membrane approaches the outer membrane, while the outer membrane does not show any measurable change in average axial position upon activation. The inter-membrane space is reduced by ∼2 nm. This direct experimental observation of the subtle dynamics of mitochondrial membranes and the change in intermembrane distance upon activation is relevant for our understanding of mitochondrial function.

Keywords:  GIET; IM-OM distance; hyperosmotic shock; quasi-stationary states

DOI:  https://doi.org/10.1021/acs.nanolett.1c02672
Elife. 2021 Sep 14. pii: e66278. [Epub ahead of print]10

Activation of mTORC1 and c-Jun by Prohibitin1 loss in Schwann cells may link mitochondrial dysfunction to demyelination.

Gustavo Della Flora Nunes, Emma R Wilson, Edward Hurley, Bin He, Bert W O'Malley, Yannick Poitelon, Lawrence Wrabetz, M Laura Feltri.

  Schwann cell (SC) mitochondria are quickly emerging as an important regulator of myelin maintenance in the peripheral nervous system (PNS). However, the mechanisms underlying demyelination in the context of mitochondrial dysfunction in the PNS are incompletely understood. We recently showed that conditional ablation of the mitochondrial protein Prohibitin 1 (PHB1) in SCs causes a severe and fast progressing demyelinating peripheral neuropathy in mice, but the mechanism that causes failure of myelin maintenance remained unknown. Here, we report that mTORC1 and c-Jun are continuously activated in the absence of Phb1, likely as part of the SC response to mitochondrial damage. Moreover, we demonstrate that these pathways are involved in the demyelination process, and that inhibition of mTORC1 using rapamycin partially rescues the demyelinating pathology. Therefore, we propose that mTORC1 and c-Jun may play a critical role as executioners of demyelination in the context of perturbations to SC mitochondria.

Keywords:  mouse; neuroscience

DOI:  https://doi.org/10.7554/eLife.66278
J Immunol. 2021 Sep 15. pii: ji2100392. [Epub ahead of print]

Leaked Mitochondrial C1QBP Inhibits Activation of the DNA Sensor cGAS.

Kun Song, Yakun Wu, Bishi Fu, Lingyan Wang, Wenzhuo Hao, Fang Hua, Yiwen Sun, Martin E Dorf, Shitao Li.

Cytosolic DNA from pathogens activates the DNA sensor cyclic GMP-AMP (cGAMP) synthase (cGAS) that produces the second messenger, cGAMP. cGAMP triggers a signal cascade leading to type I IFN expression. Host DNA is normally restricted in the cellular compartments of the nucleus and mitochondria. Recent studies have shown that DNA virus infection triggers mitochondrial stress, leading to the release of mitochondrial DNA to the cytosol and activation of cGAS; however, the regulatory mechanism of mitochondrial DNA-mediated cGAS activation is not well elucidated. In this study, we analyzed cGAS protein interactome in mouse RAW264.7 macrophages and found that cGAS interacted with C1QBP. C1QBP predominantly localized in the mitochondria and leaked into the cytosol during DNA virus infection. The leaked C1QBP bound the NTase domain of cGAS and inhibited cGAS enzymatic activity in cells and in vitro. Overexpression of the cytosolic form of C1QBP inhibited cytosolic DNA-elicited innate immune responses and promoted HSV-1 infection. By contrast, deficiency of C1QBP led to the elevated innate immune responses and impaired HSV-1 infection. Taken together, our study suggests that C1QBP is a novel cGAS inhibitor hidden in the mitochondria.

DOI: https://doi.org/10.4049/jimmunol.2100392
Cell Death Dis. 2021 Sep 13. 12(9): 847

Sirtuin 3 regulates mitochondrial protein acetylation and metabolism in tubular epithelial cells during renal fibrosis.

Yu Zhang, Ping Wen, Jing Luo, Hao Ding, Hongdi Cao, Weichun He, Ke Zen, Yang Zhou, Junwei Yang, Lei Jiang.

Proximal tubular epithelial cells (TECs) demand high energy and rely on mitochondrial oxidative phosphorylation as the main energy source. However, this is disturbed in renal fibrosis. Acetylation is an important post-translational modification for mitochondrial metabolism. The mitochondrial protein NAD+-dependent deacetylase sirtuin 3 (SIRT3) regulates mitochondrial metabolic function. Therefore, we aimed to identify the changes in the acetylome in tubules from fibrotic kidneys and determine their association with mitochondria. We found that decreased SIRT3 expression was accompanied by increased acetylation in mitochondria that have separated from TECs during the early phase of renal fibrosis. Sirt3 knockout mice were susceptible to hyper-acetylated mitochondrial proteins and to severe renal fibrosis. The activation of SIRT3 by honokiol ameliorated acetylation and prevented renal fibrosis. Analysis of the acetylome in separated tubules using LC-MS/MS showed that most kidney proteins were hyper-acetylated after unilateral ureteral obstruction. The increased acetylated proteins with 26.76% were mitochondrial proteins which were mapped to a broad range of mitochondrial pathways including fatty acid β-oxidation, the tricarboxylic acid cycle (TCA cycle), and oxidative phosphorylation. Pyruvate dehydrogenase E1α (PDHE1α), which is the primary link between glycolysis and the TCA cycle, was hyper-acetylated at lysine 385 in TECs after TGF-β1 stimulation and was regulated by SIRT3. Our findings showed that mitochondrial proteins involved in regulating energy metabolism were acetylated and targeted by SIRT3 in TECs. The deacetylation of PDHE1α by SIRT3 at lysine 385 plays a key role in metabolic reprogramming associated with renal fibrosis.

DOI: https://doi.org/10.1038/s41419-021-04134-4
Front Mol Neurosci. 2021 ;14 684714

HDAC6: A Key Link Between Mitochondria and Development of Peripheral Neuropathy.

Krystal English, Michelle Craig Barton.

  Peripheral neuropathy, which is the result of nerve damage from lesions or disease, continues to be a major health concern due to the common manifestation of neuropathic pain. Most investigations into the development of peripheral neuropathy focus on key players such as voltage-gated ion channels or glutamate receptors. However, emerging evidence points to mitochondrial dysfunction as a major player in the development of peripheral neuropathy and resulting neuropathic pain. Mitochondrial dysfunction in neuropathy includes altered mitochondrial transport, mitochondrial metabolism, as well as mitochondrial dynamics. The mechanisms that lead to mitochondrial dysfunction in peripheral neuropathy are poorly understood, however, the Class IIb histone deacetylase (HDAC6), may play an important role in the process. HDAC6 is a key regulator in multiple mechanisms of mitochondrial dynamics and may contribute to mitochondrial dysregulation in peripheral neuropathy. Accumulating evidence shows that HDAC6 inhibition is strongly associated with alleviating peripheral neuropathy and neuropathic pain, as well as mitochondrial dysfunction, in in vivo and in vitro models of peripheral neuropathy. Thus, HDAC6 inhibitors are being investigated as potential therapies for multiple peripheral neuropathic disorders. Here, we review emerging studies and integrate recent advances in understanding the unique connection between peripheral neuropathy and mitochondrial dysfunction through HDAC6-mediated interactions.

Keywords:  chronic pain; histone deacetylase 6; mitochondria; mitochondrial dysfunction; neuropathic pain; peripheral neuropathy

DOI:  https://doi.org/10.3389/fnmol.2021.684714
Hum Mol Genet. 2021 Sep 14. pii: ddab269. [Epub ahead of print]

Mitochondrial enzyme GPT2 regulates metabolic mechanisms required for neuron growth and motor function in vivo.

Ozan Baytas, Shawn M Davidson, Ralph J DeBerardinis, Eric M Morrow.

The metabolic needs for postnatal growth of the human nervous system are vast. Recessive loss-of-function mutations in the mitochondrial enzyme glutamate pyruvate transaminase 2 (GPT2) in humans cause postnatal undergrowth of brain, and cognitive and motor disability. We demonstrate that GPT2 governs critical metabolic mechanisms in neurons required for neuronal growth and survival. These metabolic processes include neuronal alanine synthesis and anaplerosis, the replenishment of tricarboxylic acid (TCA) cycle intermediates. We performed metabolomics across postnatal development in Gpt2-null mouse brain to identify the trajectory of dysregulated metabolic pathways: alterations in alanine occur earliest; followed by reduced TCA cycle intermediates and reduced pyruvate; followed by elevations in glycolytic intermediates and amino acids. Neuron-specific deletion of GPT2 in mice is sufficient to cause motor abnormalities and death pre-weaning, a phenotype identical to the germline Gpt2-null mouse. Alanine biosynthesis is profoundly impeded in Gpt2-null neurons. Exogenous alanine is necessary for Gpt2-null neuronal survival in vitro, but is not needed for Gpt2-null astrocytes. Dietary alanine supplementation in Gpt2-null mice enhances animal survival, and improves the metabolic profile of Gpt2-null brain, but does not alone appear to correct motor function. In surviving Gpt2-null animals, we observe smaller upper and lower motor neurons in vivo. We also observe selective death of lower motor neurons in vivo with worsening motor behavior with age. In conclusion, these studies of the pathophysiology of GPT2 Deficiency have identified metabolic mechanisms required for neuronal growth and that potentially underlie selective neuronal vulnerabilities in motor neurons.

DOI: https://doi.org/10.1093/hmg/ddab269
Redox Biol. 2021 Sep 08. pii: S2213-2317(21)00286-X. [Epub ahead of print]46 102127

Genetic screening reveals phospholipid metabolism as a key regulator of the biosynthesis of the redox-active lipid coenzyme Q.

Anita Ayer, Daniel J Fazakerley, Cacang Suarna, Ghassan J Maghzal, Diba Sheipouri, Kevin J Lee, Michelle C Bradley, Lucía Fernández-Del-Rio, Sergey Tumanov, Stephanie My Kong, Jelske N van der Veen, Andrian Yang, Joshua W K Ho, Steven G Clarke, David E James, Ian W Dawes, Dennis E Vance, Catherine F Clarke, René L Jacobs, Roland Stocker.

  Mitochondrial energy production and function rely on optimal concentrations of the essential redox-active lipid, coenzyme Q (CoQ). CoQ deficiency results in mitochondrial dysfunction associated with increased mitochondrial oxidative stress and a range of pathologies. What drives CoQ deficiency in many of these pathologies is unknown, just as there currently is no effective therapeutic strategy to overcome CoQ deficiency in humans. To date, large-scale studies aimed at systematically interrogating endogenous systems that control CoQ biosynthesis and their potential utility to treat disease have not been carried out. Therefore, we developed a quantitative high-throughput method to determine CoQ concentrations in yeast cells. Applying this method to the Yeast Deletion Collection as a genome-wide screen, 30 genes not known previously to regulate cellular concentrations of CoQ were discovered. In combination with untargeted lipidomics and metabolomics, phosphatidylethanolamine N-methyltransferase (PEMT) deficiency was confirmed as a positive regulator of CoQ synthesis, the first identified to date. Mechanistically, PEMT deficiency alters mitochondrial concentrations of one-carbon metabolites, characterized by an increase in the S-adenosylmethionine to S-adenosylhomocysteine (SAM-to-SAH) ratio that reflects mitochondrial methylation capacity, drives CoQ synthesis, and is associated with a decrease in mitochondrial oxidative stress. The newly described regulatory pathway appears evolutionary conserved, as ablation of PEMT using antisense oligonucleotides increases mitochondrial CoQ in mouse-derived adipocytes that translates to improved glucose utilization by these cells, and protection of mice from high-fat diet-induced insulin resistance. Our studies reveal a previously unrecognized relationship between two spatially distinct lipid pathways with potential implications for the treatment of CoQ deficiencies, mitochondrial oxidative stress/dysfunction, and associated diseases.

Keywords:  Coenzyme Q; Insulin resistance; Mitochondria; PEMT; Reactive oxygen species; S-adenosylhomocysteine; S-adenosylmethionine

DOI:  https://doi.org/10.1016/j.redox.2021.102127
Nucleic Acids Res. 2021 Sep 14. pii: gkab837. [Epub ahead of print]

Correction to 'DNA polymerase gamma mutations that impair holoenzyme stability cause catalytic subunit depletion'.

Pedro Silva-Pinheiro, Carlos Pardo-Hernández, Aurelio Reyes, Lisa Tilokani, Anup Mishra, Raffaele Cerutti, Shuaifeng Li, Dieu-Hien Rozsivalova, Sebastian Valenzuela, Sukru A Dogan, Bradley Peter, Patricio Fernández-Silva, Aleksandra Trifunovic, Julien Prudent, Michal Minczuk, Laurence Bindoff, Bertil Macao, Massimo Zeviani, Maria Falkenberg, Carlo Viscomi.

DOI: https://doi.org/10.1093/nar/gkab837
J Biol Chem. 2021 Sep 13. pii: S0021-9258(21)00998-4. [Epub ahead of print] 101196

Dynamin-related protein 1 regulates substrate oxidation in skeletal muscle by stabilizing cellular and mitochondrial calcium dynamics.

William T King, Christopher L Axelrod, Elizabeth R M Zunica, Robert C Noland, Gangarao Davuluri, Hisashi Fujioka, Bernard Tandler, Kathryn Pergola, Gerlinda E Hermann, Richard C Rogers, Sandra López-Domènech, Wagner S Dantas, Krisztian Stadler, Charles L Hoppel, John P Kirwan.

  Mitochondria undergo continuous cycles of fission and fusion to promote inheritance, regulate quality control, and mitigate organelle stress. More recently, this process of mitochondrial dynamics has been demonstrated to be highly sensitive to nutrient supply, ultimately conferring bioenergetic plasticity to the organelle. However, whether regulators of mitochondrial dynamics play a causative role in nutrient regulation remains unclear. In this study, we generated a cellular loss-of-function model for dynamin-related protein 1 (DRP1), the primary regulator of outer membrane mitochondrial fission. Loss of DRP1 (shDRP1) resulted in extensive ultrastructural and functional remodeling of mitochondria, characterized by pleomorphic enlargement, increased electron density of the matrix, and defective NADH and succinate oxidation. Despite increased mitochondrial size and volume, shDRP1 cells exhibited reduced cellular glucose uptake and mitochondrial fatty acid oxidation. Untargeted transcriptomic profiling revealed severe downregulation of genes required for cellular and mitochondrial calcium homeostasis, inhibition of ATP-stimulated calcium flux, and impaired substrate oxidation stimulated by calcium levels. The insights obtained herein suggest that DRP1 regulates fatty acid oxidation by altering whole-cell and mitochondrial calcium dynamics. These findings are relevant to the targetability of mitochondrial fission and have clinical relevance in the identification of treatments for fission-related pathologies such as hereditary neuropathies, inborn errors in metabolism, cancer, and chronic diseases.

Keywords:  calcium signaling; dynamin-related protein 1; mitochondrial dynamics; skeletal muscle; β-oxidation

DOI:  https://doi.org/10.1016/j.jbc.2021.101196
J Mol Med (Berl). 2021 Sep 18.

The recurrent missense mutation p.(Arg367Trp) in YARS1 causes a distinct neurodevelopmental phenotype.

Luisa Averdunk, Heinrich Sticht, Harald Surowy, Hermann-Josef Lüdecke, Margarete Koch-Hogrebe, Hessa S Alsaif, Kimia Kahrizi, Hamad Alzaidan, Bashayer S Alawam, Mohamed Tohary, Cornelia Kraus, Sabine Endele, Erin Wadman, Julie D Kaplan, Stephanie Efthymiou, Hossein Najmabadi, André Reis, Fowzan S Alkuraya, Dagmar Wieczorek.

  Pathogenic variants in aminoacyl-tRNA synthetases (ARS1) cause a diverse spectrum of autosomal recessive disorders. Tyrosyl tRNA synthetase (TyrRS) is encoded by YARS1 (cytosolic, OMIM*603,623) and is responsible of coupling tyrosine to its specific tRNA. Next to the enzymatic domain, TyrRS has two additional functional domains (N-Terminal TyrRSMini and C-terminal EMAP-II-like domain) which confer cytokine-like functions. Mutations in YARS1 have been associated with autosomal-dominant Charcot-Marie-Tooth (CMT) neuropathy type C and a heterogenous group of autosomal recessive, multisystem diseases. We identified 12 individuals from 6 families with the recurrent homozygous missense variant c.1099C > T;p.(Arg367Trp) (NM_003680.3) in YARS1. This variant causes a multisystem disorder with developmental delay, microcephaly, failure to thrive, short stature, muscular hypotonia, ataxia, brain anomalies, microcytic anemia, hepatomegaly, and hypothyroidism. In silico analyses show that the p.(Arg367Trp) does not affect the catalytic domain responsible of enzymatic coupling, but destabilizes the cytokine-like C-terminal domain. The phenotype associated with p.(Arg367Trp) is distinct from the other biallelic pathogenic variants that reside in different functional domains of TyrRS which all show some common, but also divergent clinical signs [(e.g., p.(Phe269Ser)-retinal anomalies, p.(Pro213Leu)/p.(Gly525Arg)-mild ID, p.(Pro167Thr)-high fatality)]. The diverse clinical spectrum of ARS1-associated disorders is related to mutations affecting the various non-canonical domains of ARS1, and impaired protein translation is likely not the exclusive disease-causing mechanism of YARS1- and ARS1-associated neurodevelopmental disorders. KEY MESSAGES: The missense variant p.(Arg367Trp) in YARS1 causes a distinct multisystem disorder. p.(Arg367Trp) affects a non-canonical domain with cytokine-like functions. Phenotypic heterogeneity associates with the different affected YARS1 domains. Impaired protein translation is likely not the exclusive mechanism of ARS1-associated disorders.

Keywords:  Aminoacyl-tRNA synthetases (ARS1); Functional protein domains; Multisystem diseases; Neurodevelopmental disorders; Novel disease genes; Phenotypic heterogeneity

DOI:  https://doi.org/10.1007/s00109-021-02124-9
Cell Rep. 2021 Sep 14. pii: S2211-1247(21)01151-7. [Epub ahead of print]36(11): 109704

Homeostatic control of nuclear-encoded mitochondrial gene expression by the histone variant H2A.Z is essential for neuronal survival.

Christopher Lowden, Aren Boulet, Nicholas A Boehler, Shavanie Seecharran, Julian Rios Garcia, Nicholas J Lowe, Jiashu Liu, Jonathan L K Ong, Wanzhang Wang, Lingfeng Ma, Arthur H Cheng, Adriano Senatore, D Ashley Monks, Bao-Hua Liu, Scot C Leary, Hai-Ying Mary Cheng.

  Histone variants are crucial regulators of chromatin structure and gene transcription, yet their functions within the brain remain largely unexplored. Here, we show that the H2A histone variant H2A.Z is essential for neuronal survival. Mice lacking H2A.Z in GABAergic neurons or Purkinje cells (PCs) present with a progressive cerebellar ataxia accompanied by widespread degeneration of PCs. Ablation of H2A.Z in other neuronal subtypes also triggers cell death. H2A.Z binds to the promoters of key nuclear-encoded mitochondrial genes to regulate their expression and promote organelle function. Bolstering mitochondrial activity genetically or by organelle transplant enhances the survival of H2A.Z-ablated neurons. Changes in bioenergetic status alter H2A.Z occupancy at the promoters of nuclear-encoded mitochondrial genes, an adaptive response essential for cell survival. Our results highlight that H2A.Z fulfills a key, conserved role in neuronal survival by acting as a transcriptional rheostat to regulate the expression of genes critical to mitochondrial function.

Keywords:  H2A.Z; Purkinje cells; bioenergetics; cerebellar ataxia; epigenetics; histone variants; mitochondria; neurodegeneration; neurons

DOI:  https://doi.org/10.1016/j.celrep.2021.109704
Mol Genet Metab Rep. 2021 Dec;29 100800

Leigh syndrome-like MRI changes in a patient with biallelic HPDL variants treated with ketogenic diet.

Yurika Numata-Uematsu, Mitsugu Uematsu, Toshiyuki Yamamoto, Hirotomo Saitsu, Yu Katata, Yoshitsugu Oikawa, Naoya Saijyo, Takehiko Inui, Kei Murayama, Akira Ohtake, Hitoshi Osaka, Jun-Ichi Takanashi, Shigeo Kure, Ken Inoue.

  Biallelic 4-hydroxyphenylpyruvate dioxygenase-like protein (HPDL) variants were recently reported as a cause of progressive and incurable neurodegenerative diseases ranging from neonatal-onset leukoencephalopathy with severe neurodevelopmental delay to spastic paraplegia. Although the physiological function of HPDL remains unknown, its subcellular localization in the mitochondria has been reported. Here, we report a case of HPDL-related neurological disease that was clinically and neuroimaging compatible with Leigh syndrome, previously unreported, and was treated with a ketogenic diet.

Keywords:  HPDL; HPDL, 4-hydroxyphenylpyruvate dioxygenase-like protein; Ketogenic diet; LS, Leigh syndrome; Leigh syndrome; Leukoencephalopathy; MRS, Magnetic resonance spectroscopy; Mitochondria; PDHC, Pyruvate dehydrogenase complex

DOI:  https://doi.org/10.1016/j.ymgmr.2021.100800
Cell Death Differ. 2021 Sep 12.

Autophagy-competent mitochondrial translation elongation factor TUFM inhibits caspase-8-mediated apoptosis.

Chang-Yong Choi, Mai Tram Vo, John Nicholas, Young Bong Choi.

Mitochondria support multiple cell functions, but an accumulation of dysfunctional or excessive mitochondria is detrimental to cells. We previously demonstrated that a defect in the autophagic removal of mitochondria, termed mitophagy, leads to the acceleration of apoptosis induced by herpesvirus productive infection. However, the exact molecular mechanisms underlying activation of mitophagy and regulation of apoptosis remain poorly understood despite the identification of various mitophagy-associated proteins. Here, we report that the mitochondrial translation elongation factor Tu, a mitophagy-associated protein encoded by the TUFM gene, locates in part on the outer membrane of mitochondria (OMM) where it acts as an inhibitor of altered mitochondria-induced apoptosis through its autophagic function. Inducible depletion of TUFM potentiated caspase-8-mediated apoptosis in virus-infected cells with accumulation of altered mitochondria. In addition, TUFM depletion promoted caspase-8 activation induced by treatment with TNF-related apoptosis-inducing ligand in cancer cells, potentially via dysregulation of mitochondrial dynamics and mitophagy. Importantly, we revealed the existence of and structural requirements for autophagy-competent TUFM on the OMM; the GxxxG motif within the N-terminal mitochondrial targeting sequences of TUFM was required for self-dimerization and mitophagy. Furthermore, we found that autophagy-competent TUFM was subject to ubiquitin-proteasome-mediated degradation but stabilized upon mitophagy or autophagy activation. Moreover, overexpression of autophagy-competent TUFM could inhibit caspase-8 activation. These studies extend our knowledge of mitophagy regulation of apoptosis and could provide a novel strategic basis for targeted therapy of cancer and viral diseases.

DOI: https://doi.org/10.1038/s41418-021-00868-y
Redox Biol. 2021 Sep 10. pii: S2213-2317(21)00284-6. [Epub ahead of print]46 102125

Mitochondrial contact site and cristae organizing system (MICOS) machinery supports heme biosynthesis by enabling optimal performance of ferrochelatase.

Jonathan V Dietz, Mathilda M Willoughby, Robert B Piel, Teresa A Ross, Iryna Bohovych, Hannah G Addis, Jennifer L Fox, William N Lanzilotta, Harry A Dailey, James A Wohlschlegel, Amit R Reddi, Amy E Medlock, Oleh Khalimonchuk.

  Heme is an essential cofactor required for a plethora of cellular processes in eukaryotes. In metazoans the heme biosynthetic pathway is typically partitioned between the cytosol and mitochondria, with the first and final steps taking place in the mitochondrion. The pathway has been extensively studied and its biosynthetic enzymes structurally characterized to varying extents. Nevertheless, understanding of the regulation of heme synthesis and factors that influence this process in metazoans remains incomplete. Therefore, we investigated the molecular organization as well as the physical and genetic interactions of the terminal pathway enzyme, ferrochelatase (Hem15), in the yeast Saccharomyces cerevisiae. Biochemical and genetic analyses revealed dynamic association of Hem15 with Mic60, a core component of the mitochondrial contact site and cristae organizing system (MICOS). Loss of MICOS negatively impacts Hem15 activity, affects the size of the Hem15 high-mass complex, and results in accumulation of reactive and potentially toxic tetrapyrrole precursors that may cause oxidative damage. Restoring intermembrane connectivity in MICOS-deficient cells mitigates these cytotoxic effects. These data provide new insights into how heme biosynthetic machinery is organized and regulated, linking mitochondrial architecture-organizing factors to heme homeostasis.

Keywords:  Ferrochelatase; Heme; MICOS; Mitochondria; Yeast

DOI:  https://doi.org/10.1016/j.redox.2021.102125
Nat Rev Mol Cell Biol. 2021 Sep 13.

Molecular mechanisms of dietary restriction promoting health and longevity.

Cara L Green, Dudley W Lamming, Luigi Fontana.

Dietary restriction with adequate nutrition is the gold standard for delaying ageing and extending healthspan and lifespan in diverse species, including rodents and non-human primates. In this Review, we discuss the effects of dietary restriction in these mammalian model organisms and discuss accumulating data that suggest that dietary restriction results in many of the same physiological, metabolic and molecular changes responsible for the prevention of multiple ageing-associated diseases in humans. We further discuss how different forms of fasting, protein restriction and specific reductions in the levels of essential amino acids such as methionine and the branched-chain amino acids selectively impact the activity of AKT, FOXO, mTOR, nicotinamide adenine dinucleotide (NAD+), AMP-activated protein kinase (AMPK) and fibroblast growth factor 21 (FGF21), which are key components of some of the most important nutrient-sensing geroprotective signalling pathways that promote healthy longevity.

DOI: https://doi.org/10.1038/s41580-021-00411-4
Eur J Hum Genet. 2021 Sep 17.

A de novo mutation in mitochondrial ATPsynthase subunit α causes a life threatening disease in neonates which heals in infancy.

Massimo Zeviani.

DOI: https://doi.org/10.1038/s41431-021-00965-z
Cell Metab. 2021 Sep 08. pii: S1550-4131(21)00417-4. [Epub ahead of print]

Increased fidelity of protein synthesis extends lifespan.

Victoria Eugenia Martinez-Miguel, Celia Lujan, Tristan Espie-Caullet, Daniel Martinez-Martinez, Saul Moore, Cassandra Backes, Suam Gonzalez, Evgeniy R Galimov, André E X Brown, Mario Halic, Kazunori Tomita, Charalampos Rallis, Tobias von der Haar, Filipe Cabreiro, Ivana Bjedov.

  Loss of proteostasis is a fundamental process driving aging. Proteostasis is affected by the accuracy of translation, yet the physiological consequence of having fewer protein synthesis errors during multi-cellular organismal aging is poorly understood. Our phylogenetic analysis of RPS23, a key protein in the ribosomal decoding center, uncovered a lysine residue almost universally conserved across all domains of life, which is replaced by an arginine in a small number of hyperthermophilic archaea. When introduced into eukaryotic RPS23 homologs, this mutation leads to accurate translation, as well as heat shock resistance and longer life, in yeast, worms, and flies. Furthermore, we show that anti-aging drugs such as rapamycin, Torin1, and trametinib reduce translation errors, and that rapamycin extends further organismal longevity in RPS23 hyperaccuracy mutants. This implies a unified mode of action for diverse pharmacological anti-aging therapies. These findings pave the way for identifying novel translation accuracy interventions to improve aging.

Keywords:  RPS23; aging; archaea; mTOR; protein synthesis; proteostasis; ribosome; translation; translation accuracy; translation fidelity

DOI:  https://doi.org/10.1016/j.cmet.2021.08.017
Science. 2021 Sep 10. 373(6560): 1200-1201

Mitochondrial disease: Replace or edit?

Eli Y Adashi, Donald S Rubenstein, Jim A Mossman, Eric A Schon, I Glenn Cohen.

[Figure: see text].

DOI: https://doi.org/10.1126/science.abg0491
Cell Rep. 2021 Sep 14. pii: S2211-1247(21)01173-6. [Epub ahead of print]36(11): 109724

Mitochondrial-encoded MOTS-c prevents pancreatic islet destruction in autoimmune diabetes.

Byung Soo Kong, Se Hee Min, Changhan Lee, Young Min Cho.

DOI: https://doi.org/10.1016/j.celrep.2021.109724
Mol Genet Metab. 2021 Aug 30. pii: S1096-7192(21)00776-9. [Epub ahead of print]

Characterization of variants of uncertain significance in isovaleryl-CoA dehydrogenase identified through newborn screening: An approach for faster analysis.

Olivia M D'Annibale, Erik A Koppes, Ahmad N Alodaib, Catherine Kochersperger, Anuradha Karunanidhi, Al-Walid Mohsen, Jerry Vockley.

   INTRODUCTION: Clinical standard of care for newborn screening (NBS) is acylcarnitine metabolites quantitation by tandem mass spectrometry (MS/MS) from dried blood spots. Follow up sequencing often results in identification of one or more variants of uncertain significance (VUS). Isovaleric acidemia (IVA) is an autosomal recessive inborn error of metabolism caused by deficiency of isovaleryl-CoA dehydrogenase (IVDH) in the Leu catabolism pathway. Many IVD mutations are characterized as VUS complicating IVA clinical diagnoses and treatment. We present a testing platform approach to confirm the functional implication of VUS identified in newborns with IVA applicable to multiple inborn errors of metabolism identified by NBS.
METHODS: An IVD null HEK293T cell culture model was generated by using a dual sgRNA CRISPR/Cas9 genome-editing strategy targeting IVD exons 2-3. Clonal cell lines were confirmed by a combination of genomic breakpoint sequencing and droplet digital PCR. The IVD null model had no IVDH antigen signal and 96% reduction in IVDH enzyme activity. The IVD null model was transfected with vectors containing control or variant IVD and functional assays were performed to determine variant pathogenicity.
RESULTS: c.149G > C (p.Arg50Pro; precursor numbering), c.986T > C (p.Met329Thr), and c.1010G > A (p.Arg337Gln), c.1179del394 f. mutant proteins had reduced IVDH protein and activity. c.932C > T (p.Ala311Val), c.707C > T (p.Thr236Ile), and c.1232G > A (p.Arg411Gln) had stable IVDH protein, but no enzyme activity. c.521T > G (p.Val174Gly) had normal IVDH protein and activity. IVD variant transfection results confirmed results from IVA fibroblasts containing the same variants.
CONCLUSIONS: We have developed an IVD null HEK293T cell line to rapidly allow determination of VUS pathogenicity following identification of novel alleles by clinical sequencing following positive NBS results for suspected IVA. We suggest similar models can be generated via genome-editing for high throughput assessment of VUS function for a multitude of inborn errors of metabolism and can ideally supplement NBS programs.

Keywords:  Isovaleric acidemia; Isovaleryl-CoA dehydrogenase; Newborn screening; Organic acidemia; Variants of uncertain significance

DOI:  https://doi.org/10.1016/j.ymgme.2021.08.012
Sci Adv. 2021 Sep 03. 7(36): eabi8886

Cristae-dependent quality control of the mitochondrial genome.

Christopher Jakubke, Rodaria Roussou, Andreas Maiser, Christina Schug, Felix Thoma, David Bunk, David Hörl, Heinrich Leonhardt, Peter Walter, Till Klecker, Christof Osman.

[Figure: see text].

DOI: https://doi.org/10.1126/sciadv.abi8886
Bioinformatics. 2021 Sep 17. pii: btab662. [Epub ahead of print]

Viola: a structural variant signature extractor with user-defined classifications.

Itsuki Sugita, Shohei Matsuyama, Hiroki Dobashi, Daisuke Komura, Shumpei Ishikawa.

: Here, we present Viola, a Python package that provides structural variant (SV; large scale genome DNA variations that can result in disease, e.g., cancer) signature analytical functions and utilities for custom SV classification, merging multi-SV-caller output files, and SV annotation. We demonstrate that Viola can extract biologically meaningful SV signatures from publicly available SV data for cancer and we evaluate the computational time necessary for annotation of the data.
AVAILABILITY: Viola is available on pip (https://pypi.org/project/Viola-SV/) and the source code is on GitHub (https://github.com/dermasugita/Viola-SV).
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DOI: https://doi.org/10.1093/bioinformatics/btab662
iScience. 2021 Sep 24. 24(9): 103032

Herding cats: Label-based approaches in protein translocation through nanopore sensors for single-molecule protein sequence analysis.

Keisuke Motone, Nicolas Cardozo, Jeff Nivala.

  Proteins carry out life's essential functions. Comprehensive proteome analysis technologies are thus required for a full understanding of the operating principles of biological systems. While current proteomics techniques suffer from limitations in sensitivity and/or throughput, nanopore technology has the potential to enable de novo protein identification through single-molecule sequencing. However, a significant barrier to achieving this goal is controlling protein/peptide translocation through the nanopore sensor for processive strand analysis. Here, we review recent approaches that use a range of techniques, from oligonucleotide conjugation to molecular motors, aimed at driving protein strands and peptides through protein nanopores. We further discuss site-specific protein conjugation chemistry that could be combined with these translocation approaches as future directions to achieve single-molecule protein detection and sequencing of native proteins.

Keywords:  Biochemistry; Bioorganic chemistry; Proteomics

DOI:  https://doi.org/10.1016/j.isci.2021.103032
Biochim Biophys Acta Gen Subj. 2021 Sep 11. pii: S0304-4165(21)00170-7. [Epub ahead of print] 130011

Mitochondrial-derived peptides and exercise.

Jonathan S T Woodhead, Troy L Merry.

  Acute exercise, and in particular aerobic exercise, increases skeletal muscle energy demand causing mitochondrial stress, and mitochondrial-related adaptations which are a hallmark of exercise training. Given that mitochondria are central players in the exercise response, it is imperative that they have networks that can communicate their status both intra- and inter-cellularly. Peptides encoded by short open-reading frames within mitochondrial DNA, mitochondrial-derived peptides (MDPs), have been suggested to form a newly recognised branch of this retrograde signalling cascade that contribute to coordinating the adaptive response to regular exercise. Here we summarise the recent evidence that acute high intensity exercise in humans can increase concentrations of the MDPs humanin and MOTS-c in skeletal muscle and plasma, and speculate on the mechanisms controlling MDP responses to exercise stress. Evidence that exercise training results in chronic changes in MDP expression within tissues and the circulation is conflicting and may depend on the mode, duration, intensity of training plan and participant characteristics. Further research is required to define the effect of these variables on MDPs and to determine whether MDPs other than MOTS-c have exercise mimetic properties. MOTS-c treatment of young and aged mice improves exercise capacity/performance and leads to adaptions that are similar to that of being physically active (weight loss, increased antioxidant capacity and improved insulin sensitivity), however, studies utilising a MOTS-c inactivating genetic variant or combination of exercise + MOTS-c treatment in mice suggest that there are distinct and overlapping pathways through which exercise and MOTS-c evoke metabolic benefits. Overall, MOTS-c, and potentially other MDPs, may be exercise-sensitive myokines and further work is required to define inter- and intra-tissue targets in an exercise context.

Keywords:  Cellular signalling; Hormesis; Mitochondria; Muscle; Physical activity; ROS

DOI:  https://doi.org/10.1016/j.bbagen.2021.130011
Exp Biol Med (Maywood). 2021 Sep 15. 15353702211040046

Whole-genome sequencing as a first-tier diagnostic framework for rare genetic diseases.

Haseeb Nisar, Bilal Wajid, Samiah Shahid, Faria Anwar, Imran Wajid, Asia Khatoon, Mian Usman Sattar, Saima Sadaf.

  Rare diseases affect nearly 300 million people globally with most patients aged five or less. Traditional diagnostic approaches have provided much of the diagnosis; however, there are limitations. For instance, simply inadequate and untimely diagnosis adversely affects both the patient and their families. This review advocates the use of whole genome sequencing in clinical settings for diagnosis of rare genetic diseases by showcasing five case studies. These examples specifically describe the utilization of whole genome sequencing, which helped in providing relief to patients via correct diagnosis followed by use of precision medicine.

Keywords:  Rare genetic disease; national health systems; next generation sequencing; precision medicine; whole genome sequencing; whole-exome sequencing

DOI:  https://doi.org/10.1177/15353702211040046
Am J Hum Genet. 2021 Sep 10. pii: S0002-9297(21)00318-9. [Epub ahead of print]

Identifying digenic disease genes via machine learning in the Undiagnosed Diseases Network.

Undiagnosed Diseases Network

  Rare diseases affect millions of people worldwide, and discovering their genetic causes is challenging. More than half of the individuals analyzed by the Undiagnosed Diseases Network (UDN) remain undiagnosed. The central hypothesis of this work is that many of these rare genetic disorders are caused by multiple variants in more than one gene. However, given the large number of variants in each individual genome, experimentally evaluating combinations of variants for potential to cause disease is currently infeasible. To address this challenge, we developed the digenic predictor (DiGePred), a random forest classifier for identifying candidate digenic disease gene pairs by features derived from biological networks, genomics, evolutionary history, and functional annotations. We trained the DiGePred classifier by using DIDA, the largest available database of known digenic-disease-causing gene pairs, and several sets of non-digenic gene pairs, including variant pairs derived from unaffected relatives of UDN individuals. DiGePred achieved high precision and recall in cross-validation and on a held-out test set (PR area under the curve > 77%), and we further demonstrate its utility by using digenic pairs from the recent literature. In contrast to other approaches, DiGePred also appropriately controls the number of false positives when applied in realistic clinical settings. Finally, to enable the rapid screening of variant gene pairs for digenic disease potential, we freely provide the predictions of DiGePred on all human gene pairs. Our work enables the discovery of genetic causes for rare non-monogenic diseases by providing a means to rapidly evaluate variant gene pairs for the potential to cause digenic disease.

Keywords:  UDN; Undiagnosed Diseases Network; clinical prediction; digenic disease; machine learning; oligogenic disease; rare disease

DOI:  https://doi.org/10.1016/j.ajhg.2021.08.010
Elife. 2021 Sep 13. pii: e70692. [Epub ahead of print]10

RNA splicing programs define tissue compartments and cell types at single cell resolution.

Tabula Sapiens Consortium

  The extent splicing is regulated at single-cell resolution has remained controversial due to both available data and methods to interpret it. We apply the SpliZ, a new statistical approach, to detect cell-type-specific splicing in >110K cells from 12 human tissues. Using 10x data for discovery, 9.1% of genes with computable SpliZ scores are cell-type-specifically spliced, including ubiquitously expressed genes MYL6 and RPS24. These results are validated with RNA FISH, single-cell PCR, and Smart-seq2. SpliZ analysis reveals 170 genes with regulated splicing during human spermatogenesis, including examples conserved in mouse and mouse lemur. The SpliZ allows model-based identification of subpopulations indistinguishable based on gene expression, illustrated by subpopulation-specific splicing of classical monocytes involving an ultraconserved exon in SAT1. Together, this analysis of differential splicing across multiple organs establishes that splicing is regulated cell-type-specifically.

Keywords:  computational biology; genetics; genomics; human; mouse; systems biology

DOI:  https://doi.org/10.7554/eLife.70692
Elife. 2021 Sep 16. pii: e67615. [Epub ahead of print]10

Local adaptation and archaic introgression shape global diversity at human structural variant loci.

Stephanie M Yan, Rachel M Sherman, Dylan J Taylor, Divya R Nair, Andrew N Bortvin, Michael C Schatz, Rajiv C McCoy.

  Large genomic insertions and deletions are a potent source of functional variation, but are challenging to resolve with short-read sequencing, limiting knowledge of the role of such structural variants (SVs) in human evolution. Here, we used a graph-based method to genotype long-read-discovered SVs in short-read data from diverse human genomes. We then applied an admixture-aware method to identify 220 SVs exhibiting extreme patterns of frequency differentiation-a signature of local adaptation. The top two variants traced to the immunoglobulin heavy chain locus, tagging a haplotype that swept to near fixation in certain Southeast Asian populations, but is rare in other global populations. Further investigation revealed evidence that the haplotype traces to gene flow from Neanderthals, corroborating the role of immune-related genes as prominent targets of adaptive introgression. Our study demonstrates how recent technical advances can help resolve signatures of key evolutionary events that remained obscured within technically challenging regions of the genome.

Keywords:  evolutionary biology; genetics; genomics; human

DOI:  https://doi.org/10.7554/eLife.67615
Front Physiol. 2021 ;12 710420

Metabolic Changes of Hepatocytes in NAFLD.

Qianrang Lu, Xinyao Tian, Hao Wu, Jiacheng Huang, Mengxia Li, Zhibin Mei, Lin Zhou, Haiyang Xie, Shusen Zheng.

  Nonalcoholic fatty liver disease (NAFLD) is often accompanied by systemic metabolic disorders such as hyperglycemia, insulin resistance, and obesity. The relationship between NAFLD and systemic metabolic disorders has been well reviewed before, however, the metabolic changes that occur in hepatocyte itself have not been discussed. In NAFLD, many metabolic pathways have undergone significant changes in hepatocyte, such as enhanced glycolysis, gluconeogenesis, lactate production, tricarboxylic acid (TCA) cycle, and decreased ketone body production, mitochondrial respiration, and adenosine triphosphate (ATP) synthesis, which play a role in compensating or exacerbating disease progression, and there is close and complex interaction existed between these metabolic pathways. Among them, some metabolic pathways can be the potential therapeutic targets for NAFLD. A detailed summary of the metabolic characteristics of hepatocytes in the context of NAFLD helps us better understand the pathogenesis and outcomes of the disease.

Keywords:  Insulin resistance; Metabolism; Mitochondrial dysfunction; NAFLD; WARBURG effect

DOI:  https://doi.org/10.3389/fphys.2021.710420