bims-mitdis 2021-12-26 papers

bims-mitdis

Biomed News

on Mitochondrial disorders

Issue of 2021‒12‒26
thirty-six papers selected by
Catalina Vasilescu
University of Helsinki

ATAD3A has a scaffolding role regulating mitochondria inner membrane structure and protein assembly.
Maintaining mitochondrial ribosome function: The role of ribosome rescue and recycling factors.
Protein Quality Control at the Mitochondrial Surface.
The Dynamin-Related Protein 1 is Decreased and the Mitochondrial Network is Altered in Friedreich's Ataxia Cardiomyopathy.
The use of soft X-ray tomography to explore mitochondrial structure and function.
Forecasting stroke-like episodes and outcomes in mitochondrial disease.
Saccharomyces cerevisiae as a Tool for Studying Mutations in Nuclear Genes Involved in Diseases Caused by Mitochondrial DNA Instability.
Development of Leigh syndrome with a high probability of cardiac manifestations in infantile-onset patients with m.14453G>A.
Mitochondrial Phenotypes in Parkinson's Diseases-A Focus on Human iPSC-Derived Dopaminergic Neurons.
A minimal motif for sequence recognition by mitochondrial transcription factor A (TFAM).
Emerging role of mitophagy in myoblast differentiation and skeletal muscle remodeling.
Differential effects of mTOR inhibition and dietary ketosis in a mouse model of subacute necrotizing encephalomyelopathy.
Role of Mitochondrial Protein Import in Age-Related Neurodegenerative and Cardiovascular Diseases.
Inactivity of Peptidase ClpP Causes Primary Accumulation of Mitochondrial Disaggregase ClpX with Its Interacting Nucleoid Proteins, and of mtDNA.
Implications of Membrane Binding by the Fe-S Cluster-Containing N-Terminal Domain in the Drosophila Mitochondrial Replicative DNA Helicase.
Mitochondrial neurogastrointestinal encephalomyopathy: Clinical and biochemical impact of allogeneic stem cell transplantation in a Greek patient with one novel TYMP mutation.
Disruption of the TCA cycle reveals an ATF4-dependent integration of redox and amino acid metabolism.
A novel MRPS34 gene mutation with combined OXPHOS deficiency in an adult patient with Leigh syndrome.
Characterization of a Novel Splicing Variant in Acylglycerol Kinase (AGK) Associated with Fatal Sengers Syndrome.
Astroglial ER-mitochondria calcium transfer mediates endocannabinoid-dependent synaptic integration.
A roadmap for the characterization of energy metabolism in human cardiomyocytes derived from induced pluripotent stem cells.
Clinical Diagnosis and Treatment of Leigh Syndrome Based on SURF1: Genotype and Phenotype.
Measuring hypertrophy in neonatal rat primary cardiomyocytes and human iPSC-derived cardiomyocytes.
Therapeutic Potential of Emerging NAD+-Increasing Strategies for Cardiovascular Diseases.
Valine tRNA levels and availability regulate complex I assembly in leukaemia.
Mitochondrial dysfunction and mitochondrial therapies in heart failure.
PDIA3 inhibits mitochondrial respiratory function in brain endothelial cells and C. elegans through STAT3 signaling and decreases survival after OGD.
BNIP3L/NIX-mediated mitophagy: molecular mechanisms and implications for human disease.
Activation mechanism of PINK1.
Vitamin B12 deficiency is associated with narcolepsy.
GFAT2 mediates cardiac hypertrophy through HBP-O-GlcNAcylation-Akt pathway.
Directly Reprogrammed Human Neurons to Understand Age-Related Energy Metabolism Impairment and Mitochondrial Dysfunction in Healthy Aging and Neurodegeneration.
Post-translational modifications on mitochondrial metabolic enzymes in cancer.
Allele-specific targeting of mutant ataxin-3 by antisense oligonucleotides in SCA3-iPSC-derived neurons.
Automated reanalysis application to assist in detecting novel gene-disease associations after genome sequencing.
Acetyl-CoA production by specific metabolites promotes cardiac repair after myocardial infarction via histone acetylation.

Cell Rep. 2021 Dec 21. pii: S2211-1247(21)01635-1. [Epub ahead of print]37(12): 110139

ATAD3A has a scaffolding role regulating mitochondria inner membrane structure and protein assembly.

Tania Arguello, Susana Peralta, Hana Antonicka, Gabriel Gaidosh, Francisca Diaz, Ya-Ting Tu, Sofia Garcia, Ramin Shiekhattar, Antonio Barrientos, Carlos T Moraes.

  The ATPase Family AAA Domain Containing 3A (ATAD3A), is a mitochondrial inner membrane protein conserved in metazoans. ATAD3A has been associated with several mitochondrial functions, including nucleoid organization, cholesterol metabolism, and mitochondrial translation. To address its primary role, we generated a neuronal-specific conditional knockout (Atad3 nKO) mouse model, which developed a severe encephalopathy by 5 months of age. Pre-symptomatic mice showed aberrant mitochondrial cristae morphogenesis in the cortex as early as 2 months. Using a multi-omics approach in the CNS of 2-to-3-month-old mice, we found early alterations in the organelle membrane structure. We also show that human ATAD3A associates with different components of the inner membrane, including OXPHOS complex I, Letm1, and prohibitin complexes. Stochastic Optical Reconstruction Microscopy (STORM) shows that ATAD3A is regularly distributed along the inner mitochondrial membrane, suggesting a critical structural role in inner mitochondrial membrane and its organization, most likely in an ATPase-dependent manner.

Keywords:  ATAD3; cardiolipin; cristae; inner membrane; mitochondria

DOI:  https://doi.org/10.1016/j.celrep.2021.110139
RNA Biol. 2021 Dec 20. 1-15

Maintaining mitochondrial ribosome function: The role of ribosome rescue and recycling factors.

Franziska Nadler, Elena Lavdovskaia, Ricarda Richter-Dennerlein.

  The universally conserved process of protein biosynthesis is crucial for maintaining cellular homoeostasis and in eukaryotes, mitochondrial translation is essential for aerobic energy production. Mitochondrial ribosomes (mitoribosomes) are highly specialized to synthesize 13 core subunits of the oxidative phosphorylation (OXPHOS) complexes. Although the mitochondrial translation machinery traces its origin from a bacterial ancestor, it has acquired substantial differences within this endosymbiotic environment. The cycle of mitoribosome function proceeds through the conserved canonical steps of initiation, elongation, termination and mitoribosome recycling. However, when mitoribosomes operate in the context of limited translation factors or on aberrant mRNAs, they can become stalled and activation of rescue mechanisms is required. This review summarizes recent advances in the understanding of protein biosynthesis in mitochondria, focusing especially on the mechanistic and physiological details of translation termination, and mitoribosome recycling and rescue.

Keywords:  Mitochondrial ribosome (mitoribosome); mitoribosome recycling; mitoribosome rescue; mitoribosome-associated quality control (mtRQC); translation termination

DOI:  https://doi.org/10.1080/15476286.2021.2015561
Front Cell Dev Biol. 2021 ;9 795685

Protein Quality Control at the Mitochondrial Surface.

Fabian den Brave, Arushi Gupta, Thomas Becker.

  Mitochondria contain two membranes, the outer and inner membrane. The outer membrane fulfills crucial functions for the communication of mitochondria with the cellular environment like exchange of lipids via organelle contact sites, the transport of metabolites and the formation of a signaling platform in apoptosis and innate immunity. The translocase of the outer membrane (TOM complex) forms the entry gate for the vast majority of precursor proteins that are produced on cytosolic ribosomes. Surveillance of the functionality of outer membrane proteins is critical for mitochondrial functions and biogenesis. Quality control mechanisms remove defective and mistargeted proteins from the outer membrane as well as precursor proteins that clog the TOM complex. Selective degradation of single proteins is also an important mode to regulate mitochondrial dynamics and initiation of mitophagy pathways. Whereas inner mitochondrial compartments are equipped with specific proteases, the ubiquitin-proteasome system is a central player in protein surveillance on the mitochondrial surface. In this review, we summarize our current knowledge about the molecular mechanisms that govern quality control of proteins at the outer mitochondrial membrane.

Keywords:  Cdc48; TOM complex; mitochondria; protein quality control; protein sorting

DOI:  https://doi.org/10.3389/fcell.2021.795685
Int J Biochem Cell Biol. 2021 Dec 16. pii: S1357-2725(21)00218-1. [Epub ahead of print] 106137

The Dynamin-Related Protein 1 is Decreased and the Mitochondrial Network is Altered in Friedreich's Ataxia Cardiomyopathy.

Bojjibabu Chidipi, Mariana Burgos Angulo, Syed Islamuddin Shah, Michelle Rieser, Ganim Ullah, Thomas V McDonald, Sami F Noujaim.

  Friedreich ataxia is an autosomal recessive congenital neurodegenerative disease caused by a deficiency in the frataxin protein and is often diagnosed in young adulthood. An expansion of guanine-adenine-adenine repeats in the first intron of the FXN gene leads to decreased frataxin expression. Frataxin plays an essential role in mitochondrial metabolism. Most Friedreich ataxia patients are diagnosed with left ventricular hypertrophic cardiomyopathy, and 60% of patients die with hypertrophic cardiomyopathy. However, the mitochondrial anatomy in Friedreich ataxia hypertrophic cardiomyopathy is still poorly understood. We investigated mitochondrial fission, fusion, and function using biochemical, microscopy, and computational stochastic analysis in human induced pluripotent stem cell derived cardiomyocytes from a patient with Friedreich ataxia hypertrophic cardiomyopathy and a healthy individual. We found a significantly higher mitochondrial footprint, decreased mitochondrial fission protein dynamin-related protein, and mitochondrial fission rate over fusion with more giant mitochondrial clusters in human induced pluripotent stem cell derived cardiomyocytes from a patient with Friedreich ataxia hypertrophic cardiomyopathy, compared to an unaffected individual. We also found significantly depolarized mitochondrial membrane potential and higher reactive oxygen species levels in Friedreich ataxia human induced pluripotent stem cell cardiomyocytes. Our results show that frataxin's depletion may dampen the mitochondrial fission machinery by reducing dynamin-related protein1. The loss of mitochondrial fission might lead to elevated reactive oxygen species and depolarized mitochondrial membrane potential, which may cause oxidative damage in Friedreich ataxia hypertrophic cardiomyopathy. Further investigations are needed to identify the mechanism of downregulating dynamin-related protein1 due to the frataxin deficiency in Friedreich ataxia hypertrophic cardiomyopathy.

Keywords:  DRP1; Friedreich ataxia; hypertrophic cardiomyopathy; mitochondrial fusion and fission

DOI:  https://doi.org/10.1016/j.biocel.2021.106137
Mol Metab. 2021 Dec 20. pii: S2212-8778(21)00279-9. [Epub ahead of print] 101421

The use of soft X-ray tomography to explore mitochondrial structure and function.

Valentina Loconte, Kate L White.

  Mitochondria are cellular organelles responsible for energy production, and dysregulation of the mitochondrial network is associated with many disease states. To fully characterize the mitochondrial network's structure and function, a three-dimensional whole cell mapping technique is required. This review highlights the use of soft X-ray tomography (SXT) as a relatively high-throughput approach to quantify mitochondrial structure and function under multiple cellular conditions. The use of SXT opens the door for mapping cellular rearrangements during critical processes such as insulin secretion, stem cell differentiation, or disease progression. SXT also provides unique information such as biochemical compositions or molecular densities of organelles and allows for unbiased, label-free imaging of intact whole cells. Mapping mitochondria in the context of the near-native cellular environment will reveal more information regarding mitochondrial network functions within the cell.

Keywords:  Structural biology; cell mapping; mitochondria; spatial biology; tomography

DOI:  https://doi.org/10.1016/j.molmet.2021.101421
Brain. 2021 Dec 20. pii: awab353. [Epub ahead of print]

Forecasting stroke-like episodes and outcomes in mitochondrial disease.

Yi Shiau Ng, Nichola Z Lax, Alasdair P Blain, Daniel Erskine, Mark R Baker, Tuomo Polvikoski, Rhys H Thomas, Christopher M Morris, Ming Lai, Roger G Whittaker, Alasdair Gebbels, Amy Winder, Julie Hall, Catherine Feeney, Maria Elena Farrugia, Claire Hirst, Mark Roberts, Charlotte Lawthom, Alexia Chrysostomou, Kevin Murphy, Tracey Baird, Paul Maddison, Callum Duncan, Joanna Poulton, Victoria Nesbitt, Michael G Hanna, Robert D S Pitceathly, Robert W Taylor, Emma L Blakely, Andrew M Schaefer, Doug M Turnbull, Robert McFarland, Gráinne S Gorman.

  In this retrospective, multicentre, observational cohort study, we sought to determine the clinical, radiological, EEG, genetics and neuropathological characteristics of mitochondrial stroke-like episodes and to identify associated risk predictors. Between January 1998 and June 2018, we identified 111 patients with genetically-determined mitochondrial disease who developed stroke-like episodes. Post-mortem cases of mitochondrial disease (n = 26) were identified from Newcastle Brain Tissue Resource. The primary outcome was to interrogate the clinic-radio-pathological correlates and prognostic indicators of stroke-like episode in patients with mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes syndrome. The secondary objective was to develop a multivariable prediction model to forecast stroke-like episode risk. The most common genetic cause of stroke-like episodes was the m.3243A>G variant in MT-TL1 (n = 66), followed by recessive pathogenic POLG variants (n = 22), and 11 other rarer pathogenic mitochondrial DNA (mtDNA) variants (n = 23). The age of first stroke-like episode was available for 105 patients (mean [SD] age: 31.8 [16.1]); a total of 35 patients (32%) presented with their first stroke-like episode ≥40 years of age. The median interval (interquartile range) between first and second stroke-like episodes was 1.33 (2.86) years; 43% of patients developed recurrent stroke-like episodes within 12 months. Clinico-radiological, electrophysiological and neuropathological findings of stroke-like episodes were consistent with the hallmarks of medically refractory epilepsy. Patients with POLG-related stroke-like episodes demonstrated more fulminant disease trajectories than cases of m.3243A>G and other mtDNA pathogenic variants, in terms of the frequency of refractory status epilepticus, rapidity of progression and overall mortality. In multivariate analysis, baseline factors of body mass index, age-adjusted blood m.3243A>G heteroplasmy, sensorineural hearing loss and serum lactate were significantly associated with risk of stroke-like episodes in patients with the m.3243A>G variant. These factors informed the development of a prediction model to assess the risk of developing stroke-like episodes that demonstrated good overall discrimination (area under the curve = 0.87, 95% CI 0.82-0.93; c-statistic = 0.89). Significant radiological and pathological features of neurodegeneration was more evident in patients harbouring pathogenic mtDNA variants compared with POLG: brain atrophy on cranial MRI (90% vs 44%, p < 0.001) and reduced mean brain weight [SD] (1044 g [148] vs 1304 g [142], p = 0.005). Our findings highlight the often idiosyncratic clinical, radiological and EEG characteristics of mitochondrial stroke-like episodes. Early recognition of seizures and aggressive instigation of treatment may help circumvent or slow neuronal loss and abate increasing disease burden. The risk-prediction model for the m.3243A>G variant can help inform more tailored genetic counselling and prognostication in routine clinical practice.

Keywords:  MELAS; mitochondrial DNA (mtDNA); neuropathology; prognostic modelling; seizures

DOI:  https://doi.org/10.1093/brain/awab353
Genes (Basel). 2021 Nov 24. pii: 1866. [Epub ahead of print]12(12):

Saccharomyces cerevisiae as a Tool for Studying Mutations in Nuclear Genes Involved in Diseases Caused by Mitochondrial DNA Instability.

Alexandru Ionut Gilea, Camilla Ceccatelli Berti, Martina Magistrati, Giulia di Punzio, Paola Goffrini, Enrico Baruffini, Cristina Dallabona.

  Mitochondrial DNA (mtDNA) maintenance is critical for oxidative phosphorylation (OXPHOS) since some subunits of the respiratory chain complexes are mitochondrially encoded. Pathological mutations in nuclear genes involved in the mtDNA metabolism may result in a quantitative decrease in mtDNA levels, referred to as mtDNA depletion, or in qualitative defects in mtDNA, especially in multiple deletions. Since, in the last decade, most of the novel mutations have been identified through whole-exome sequencing, it is crucial to confirm the pathogenicity by functional analysis in the appropriate model systems. Among these, the yeast Saccharomyces cerevisiae has proved to be a good model for studying mutations associated with mtDNA instability. This review focuses on the use of yeast for evaluating the pathogenicity of mutations in six genes, MPV17/SYM1, MRM2/MRM2, OPA1/MGM1, POLG/MIP1, RRM2B/RNR2, and SLC25A4/AAC2, all associated with mtDNA depletion or multiple deletions. We highlight the techniques used to construct a specific model and to measure the mtDNA instability as well as the main results obtained. We then report the contribution that yeast has given in understanding the pathogenic mechanisms of the mutant variants, in finding the genetic suppressors of the mitochondrial defects and in the discovery of molecules able to improve the mtDNA stability.

Keywords:  MPV17/SYM1; MRM2/MRM2; OPA1/MGM1; POLG/MIP1; RRM2B/RNR2; SLC25A4 (ANT1)/AAC2; diseases associated with mtDNA deletions; drug repurposing; mtDNA depletion syndromes; yeast model

DOI:  https://doi.org/10.3390/genes12121866
Mitochondrion. 2021 Dec 18. pii: S1567-7249(21)00172-0. [Epub ahead of print]

Development of Leigh syndrome with a high probability of cardiac manifestations in infantile-onset patients with m.14453G>A.

Masaru Shimura, Takanori Onuki, Yohei Sugiyama, Tetsuro Matsuhashi, Tomohiro Ebihara, Takuya Fushimi, Makiko Tajika, Keiko Ichimoto, Ayako Matsunaga, Tomoko Tsuruoka, Kazuhiro R Nitta, Atsuko Imai-Okazaki, Yukiko Yatsuka, Yoshihito Kishita, Akira Ohtake, Yasushi Okazaki, Kei Murayama.

  The m.14453G>A mutation in MT-ND6 has been described in a few patients with mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes or Leigh syndrome.However, the clinical spectrum and molecular characteristics are unclear.Here, we present four infantile-onset patients with m.14453G>A-associated Leigh syndrome. All four patients had brainstem lesions with basal ganglia lesions, and two patients had cardiac manifestations. Decreased ND6 protein expression and immunoreactivity were observed in patient-derived samples. There was no clear correlation between heteroplasmy levels and onset age or between heteroplasmy levels and phenotype; however, infantile onset was associated with Leigh syndrome.

Keywords:  Leigh syndrome; Wolff-Parkinson-White syndrome; brainstem lesion; hypertrophic cardiomyopathy; mitochondrial NADH-ubiquinone oxidoreductase chain 6 gene

DOI:  https://doi.org/10.1016/j.mito.2021.12.005
Cells. 2021 Dec 07. pii: 3436. [Epub ahead of print]10(12):

Mitochondrial Phenotypes in Parkinson's Diseases-A Focus on Human iPSC-Derived Dopaminergic Neurons.

Leonie M Heger, Rachel M Wise, J Tabitha Hees, Angelika B Harbauer, Lena F Burbulla.

  Established disease models have helped unravel the mechanistic underpinnings of pathological phenotypes in Parkinson's disease (PD), the second most common neurodegenerative disorder. However, these discoveries have been limited to relatively simple cellular systems and animal models, which typically manifest with incomplete or imperfect recapitulation of disease phenotypes. The advent of induced pluripotent stem cells (iPSCs) has provided a powerful scientific tool for investigating the underlying molecular mechanisms of both familial and sporadic PD within disease-relevant cell types and patient-specific genetic backgrounds. Overwhelming evidence supports mitochondrial dysfunction as a central feature in PD pathophysiology, and iPSC-based neuronal models have expanded our understanding of mitochondrial dynamics in the development and progression of this devastating disorder. The present review provides a comprehensive assessment of mitochondrial phenotypes reported in iPSC-derived neurons generated from PD patients' somatic cells, with an emphasis on the role of mitochondrial respiration, morphology, and trafficking, as well as mitophagy and calcium handling in health and disease. Furthermore, we summarize the distinguishing characteristics of vulnerable midbrain dopaminergic neurons in PD and report the unique advantages and challenges of iPSC disease modeling at present, and for future mechanistic and therapeutic applications.

Keywords:  Parkinson’s disease; dopaminergic neurons; iPSC; mitochondria

DOI:  https://doi.org/10.3390/cells10123436
Nucleic Acids Res. 2021 Dec 20. pii: gkab1230. [Epub ahead of print]

A minimal motif for sequence recognition by mitochondrial transcription factor A (TFAM).

Woo Suk Choi, Miguel Garcia-Diaz.

Mitochondrial transcription factor A (TFAM) plays a critical role in mitochondrial transcription initiation and mitochondrial DNA (mtDNA) packaging. Both functions require DNA binding, but in one case TFAM must recognize a specific promoter sequence, while packaging requires coating of mtDNA by association with non sequence-specific regions. The mechanisms by which TFAM achieves both sequence-specific and non sequence-specific recognition have not yet been determined. Existing crystal structures of TFAM bound to DNA allowed us to identify two guanine-specific interactions that are established between TFAM and the bound DNA. These interactions are observed when TFAM is bound to both specific promoter sequences and non-sequence specific DNA. These interactions are established with two guanine bases separated by 10 random nucleotides (GN10G). Our biochemical results demonstrate that the GN10G consensus is essential for transcriptional initiation and contributes to facilitating TFAM binding to DNA substrates. Furthermore, we report a crystal structure of TFAM in complex with a non sequence-specific sequence containing a GN10G consensus. The structure reveals a unique arrangement in which TFAM bridges two DNA substrates while maintaining the GN10G interactions. We propose that the GN10G consensus is key to facilitate the interaction of TFAM with DNA.

DOI: https://doi.org/10.1093/nar/gkab1230
Semin Cell Dev Biol. 2021 Dec 16. pii: S1084-9521(21)00308-6. [Epub ahead of print]

Emerging role of mitophagy in myoblast differentiation and skeletal muscle remodeling.

Fasih Ahmad Rahman, Joe Quadrilatero.

  Mitochondrial turnover in the form of mitophagy is emerging as a central process in maintaining cellular function. The degradation of damaged mitochondria through mitophagy is particularly important in cells/tissues that exhibit high energy demands. Skeletal muscle is one such tissue that requires precise turnover of mitochondria in several conditions in order to optimize energy production and prevent bioenergetic crisis. For instance, the formation of skeletal muscle (i.e., myogenesis) is accompanied by robust turnover of low-functioning mitochondria to eventually allow the formation of high-functioning mitochondria. In mature skeletal muscle, alterations in mitophagy-related signaling occur during exercise, aging, and various disease states. Nonetheless, several questions regarding the direct role of mitophagy in various skeletal muscle conditions remain unknown. Furthermore, given the heterogenous nature of skeletal muscle with respect to various cellular and molecular properties, and the plasticity in these properties in various conditions, the involvement and characterization of mitophagy requires more careful consideration in this tissue. Therefore, this review will highlight the known mechanisms of mitophagy in skeletal muscle, and discuss their involvement during myogenesis and various skeletal muscle conditions. This review also provides important considerations for the accurate measurement of mitophagy and interpretation of data in skeletal muscle.

Keywords:  Aging; Atrophy; Autophagy; Cancer; Differentiation; Fiber type; Mitochondria; Mitochondrial network; Mitophagy; Myoblasts; Myogenesis; Regeneration; Remodeling; Skeletal muscle

DOI:  https://doi.org/10.1016/j.semcdb.2021.11.026
Neurobiol Dis. 2021 Dec 20. pii: S0969-9961(21)00343-0. [Epub ahead of print]163 105594

Differential effects of mTOR inhibition and dietary ketosis in a mouse model of subacute necrotizing encephalomyelopathy.

Rebecca Bornstein, Katerina James, Julia Stokes, Kyung Yeon Park, Ernst-Bernhard Kayser, John Snell, Angela Bard, Yihan Chen, Franck Kalume, Simon C Johnson.

  Genetic mitochondrial diseases are the most frequent cause of inherited metabolic disorders and one of the most prevalent causes of heritable neurological disease. Leigh syndrome is the most common clinical presentation of pediatric mitochondrial disease, typically appearing in the first few years of life, and involving severe multisystem pathologies. Clinical care for Leigh syndrome patients is difficult, complicated by the wide range of symptoms including characteristic progressive CNS lesion, metabolic sequelae, and epileptic seizures, which can be intractable to standard management. While no proven therapies yet exist for the underlying mitochondrial disease, a ketogenic diet has led to some reports of success in managing mitochondrial epilepsies, with ketosis reducing seizure risk and severity. The impact of ketosis on other aspects of disease progression in Leigh syndrome has not been studied, however, and a rigorous study of the impact of ketosis on seizures in mitochondrial disease is lacking. Conversely, preclinical efforts have identified the intracellular nutrient signaling regulator mTOR as a promising therapeutic target, with data suggesting the benefits are mediated by metabolic changes. mTOR inhibition alleviates epilepsies arising from defects in TSC, an mTOR regulator, but the therapeutic potential of mTOR inhibition in seizures related to primary mitochondrial dysfunction is unknown. Given that ketogenic diet is used clinically in the setting of mitochondrial disease, and mTOR inhibition is in clinical trials for intractable pediatric epilepsies of diverse causal origins, a direct experimental assessment of their effects is imperative. Here, we define the impact of dietary ketosis on survival and CNS disease in the Ndufs4(KO) mouse model of Leigh syndrome and the therapeutic potential of both dietary ketosis and mTOR inhibition on seizures in this model. These data provide timely insight into two important clinical interventions.

Keywords:  Epilepsy; Ketogenic diet; Ketosis; Mitochondrial disease; Seizure; mTOR

DOI:  https://doi.org/10.1016/j.nbd.2021.105594
Cells. 2021 Dec 14. pii: 3528. [Epub ahead of print]10(12):

Role of Mitochondrial Protein Import in Age-Related Neurodegenerative and Cardiovascular Diseases.

Andrey Bogorodskiy, Ivan Okhrimenko, Dmitrii Burkatovskii, Philipp Jakobs, Ivan Maslov, Valentin Gordeliy, Norbert A Dencher, Thomas Gensch, Wolfgang Voos, Joachim Altschmied, Judith Haendeler, Valentin Borshchevskiy.

  Mitochondria play a critical role in providing energy, maintaining cellular metabolism, and regulating cell survival and death. To carry out these crucial functions, mitochondria employ more than 1500 proteins, distributed between two membranes and two aqueous compartments. An extensive network of dedicated proteins is engaged in importing and sorting these nuclear-encoded proteins into their designated mitochondrial compartments. Defects in this fundamental system are related to a variety of pathologies, particularly engaging the most energy-demanding tissues. In this review, we summarize the state-of-the-art knowledge about the mitochondrial protein import machinery and describe the known interrelation of its failure with age-related neurodegenerative and cardiovascular diseases.

Keywords:  Alzheimer’s disease; Parkinson’s disease; TERT; age-related diseases; cardiolipin; cardiovascular disease; mitochondria; mitochondrial protein import

DOI:  https://doi.org/10.3390/cells10123528
Cells. 2021 Nov 29. pii: 3354. [Epub ahead of print]10(12):

Inactivity of Peptidase ClpP Causes Primary Accumulation of Mitochondrial Disaggregase ClpX with Its Interacting Nucleoid Proteins, and of mtDNA.

Jana Key, Sylvia Torres-Odio, Nina C Bach, Suzana Gispert, Gabriele Koepf, Marina Reichlmeir, A Phillip West, Holger Prokisch, Peter Freisinger, William G Newman, Stavit Shalev, Stephan A Sieber, Ilka Wittig, Georg Auburger.

  Biallelic pathogenic variants in CLPP, encoding mitochondrial matrix peptidase ClpP, cause a rare autosomal recessive condition, Perrault syndrome type 3 (PRLTS3). It is characterized by primary ovarian insufficiency and early sensorineural hearing loss, often associated with progressive neurological deficits. Mouse models showed that accumulations of (i) its main protein interactor, the substrate-selecting AAA+ ATPase ClpX, (ii) mitoribosomes, and (iii) mtDNA nucleoids are the main cellular consequences of ClpP absence. However, the sequence of these events and their validity in human remain unclear. Here, we studied global proteome profiles to define ClpP substrates among mitochondrial ClpX interactors, which accumulated consistently in ClpP-null mouse embryonal fibroblasts and brains. Validation work included novel ClpP-mutant patient fibroblast proteomics. ClpX co-accumulated in mitochondria with the nucleoid component POLDIP2, the mitochondrial poly(A) mRNA granule element LRPPRC, and tRNA processing factor GFM1 (in mouse, also GRSF1). Only in mouse did accumulated ClpX, GFM1, and GRSF1 appear in nuclear fractions. Mitoribosomal accumulation was minor. Consistent accumulations in murine and human fibroblasts also affected multimerizing factors not known as ClpX interactors, namely, OAT, ASS1, ACADVL, STOM, PRDX3, PC, MUT, ALDH2, PMPCB, UQCRC2, and ACADSB, but the impact on downstream metabolites was marginal. Our data demonstrate the primary impact of ClpXP on the assembly of proteins with nucleic acids and show nucleoid enlargement in human as a key consequence.

Keywords:  ClpB; ERAL1; HARS2; LARS2; Parkinson’s disease; TWNK; ataxia; leukodystrophy

DOI:  https://doi.org/10.3390/cells10123354
Front Genet. 2021 ;12 790521

Implications of Membrane Binding by the Fe-S Cluster-Containing N-Terminal Domain in the Drosophila Mitochondrial Replicative DNA Helicase.

Minyoung So, Johnny Stiban, Grzegorz L Ciesielski, Stacy L Hovde, Laurie S Kaguni.

  Recent evidence suggests that iron-sulfur clusters (ISCs) in DNA replicative proteins sense DNA-mediated charge transfer to modulate nuclear DNA replication. In the mitochondrial DNA replisome, only the replicative DNA helicase (mtDNA helicase) from Drosophila melanogaster (Dm) has been shown to contain an ISC in its N-terminal, primase-like domain (NTD). In this report, we confirm the presence of the ISC and demonstrate the importance of a metal cofactor in the structural stability of the Dm mtDNA helicase. Further, we show that the NTD also serves a role in membrane binding. We demonstrate that the NTD binds to asolectin liposomes, which mimic phospholipid membranes, through electrostatic interactions. Notably, membrane binding is more specific with increasing cardiolipin content, which is characteristically high in the mitochondrial inner membrane (MIM). We suggest that the N-terminal domain of the mtDNA helicase interacts with the MIM to recruit mtDNA and initiate mtDNA replication. Furthermore, Dm NUBPL, the known ISC donor for respiratory complex I and a putative donor for Dm mtDNA helicase, was identified as a peripheral membrane protein that is likely to execute membrane-mediated ISC delivery to its target proteins.

Keywords:  NUBPL/Ind1; genome stability; iron-sulfur clusters; liposomes; membrane binding; mitochondria; replicative helicase

DOI:  https://doi.org/10.3389/fgene.2021.790521
Mol Genet Metab Rep. 2022 Mar;30 100829

Mitochondrial neurogastrointestinal encephalomyopathy: Clinical and biochemical impact of allogeneic stem cell transplantation in a Greek patient with one novel TYMP mutation.

A Paisiou, M Rogalidou, R Pons, E Ioannidou, K Dimakou, A Papadopoulou, F M Vaz, G Vessalas, S M I Goorden, J Roelofsen, A Zoetekouw, M M Nieman, E Dimitriou, M Moraitou, I Peristeri, H Michelakakis, A B P van Kuilenburg.

  We describe the case of a Greek female patient with the Classic form of the ultra- rare and fatal autosomal recessive disorder Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) and the impact of allogeneic hematopoietic stem cell transplantation on the biochemical and clinical aspects of the disease. The patient presented at the age of 15 years with severe gastrointestinal symptoms, cachexia, peripheral neuropathy and diffuse leukoencephalopathy. The diagnosis of MNGIE disease was established by the increased levels of thymidine and deoxyuridine in plasma and the complete deficiency of thymidine phosphorylase activity. The novel c.[978dup] (p.Ala327Argfs*?) variant and the previously described variant c.[417 + 1G > A] were identified in TYMP. The donor for the allogeneic hematopoietic stem cell transplantation was her fully compatible sister, a carrier of the disease. The patient had a completely uneventful post- transplant period and satisfactory PB chimerism levels. A marked and rapid decrease in thymidine and deoxyuridine plasma levels and an increase of the thymidine phosphorylase activity to the levels measured in her donor sister was observed and is still present sixteen months post-transplant. Disease symptoms stabilized and some improvement was also observed both in her neurological and gastrointestinal symptoms. Follow up studies will be essential for determining the long term impact of allogeneic hematopoietic stem cell transplantation in our patient.

Keywords:  AHSCT, allogeneic hematopoietic stem cell transplantation;; Allogeneic hematopoietic stem cell transplantation, AHSCT; CSF, cerebrospinal fluid;; GVHD, Graft Versus Host Disease;; HSCT, hematopoietic stem cell transplantation;; MNGIE; MNGIE, mitochondrial neurogastrointestinal encephalomyopathy;; Mitochondrial neurogastrointestinal encephalomyopathy; Mutation analysis; OLT, orthotopic liver transplantation;; PB, peripheral blood;; PLT, platelet;; TP, thymidine phosphorylase;; TPN, total parenteral nutrition;; TYMP, thymidine phosphorylase gene;; VLCFA, very long chain fatty acids; dThd, thymidine;; dUrd, 2′-deoxyuridine;; mtDNA, mitochondrial DNA;

DOI:  https://doi.org/10.1016/j.ymgmr.2021.100829
Elife. 2021 Dec 23. pii: e72593. [Epub ahead of print]10

Disruption of the TCA cycle reveals an ATF4-dependent integration of redox and amino acid metabolism.

Dylan Gerard Ryan, Ming Yang, Hiran A Prag, Giovanny Rodriguez Blanco, Efterpi Nikitopoulou, Marc Segarra-Mondejar, Christopher A Powell, Tim Young, Nils Burger, Jan Lj Miljkovic, Michal Minczuk, Michael P Murphy, Alex von Kriegsheim, Christian Frezza.

  The Tricarboxylic Acid Cycle (TCA) cycle is arguably the most critical metabolic cycle in physiology and exists as an essential interface coordinating cellular metabolism, bioenergetics, and redox homeostasis. Despite decades of research, a comprehensive investigation into the consequences of TCA cycle dysfunction remains elusive. Here, we targeted two TCA cycle enzymes, fumarate hydratase (FH) and succinate dehydrogenase (SDH), and combined metabolomics, transcriptomics, and proteomics analyses to fully appraise the consequences of TCA cycle inhibition (TCAi) in murine kidney epithelial cells. Our comparative approach shows that TCAi elicits a convergent rewiring of redox and amino acid metabolism dependent on the activation of ATF4 and the integrated stress response (ISR). Furthermore, we also uncover a divergent metabolic response, whereby acute FHi, but not SDHi, can maintain asparagine levels via reductive carboxylation and maintenance of cytosolic aspartate synthesis. Our work highlights an important interplay between the TCA cycle, redox biology and amino acid homeostasis.

Keywords:  biochemistry; cell biology; chemical biology; mouse

DOI:  https://doi.org/10.7554/eLife.72593
Mol Genet Metab Rep. 2022 Mar;30 100830

A novel MRPS34 gene mutation with combined OXPHOS deficiency in an adult patient with Leigh syndrome.

L Lenzini, M Carecchio, E Iori, A Legati, E Lamantea, A Avogaro, N Vitturi.

We report a novel pathogenic variant (c.223G > C; p.Gly75Arg) in the gene encoding the small mitoribosomal subunit protein mS34 in a long-surviving patient with Leigh Syndrome who was genetically diagnosed at age 34 years. The patient presented with delayed motor milestones and a stepwise motor deterioration during life, along with brain MRI alterations involving the subcortical white matter, deep grey nuclei and in particular the internal globi pallidi, that appeared calcified on CT scan. The novel variant is associated with a reduction of mS34 protein levels and of the OXPHOS complex I and IV subunits in peripheral blood mononuclear cells of the case. This study expands the number of variants that, by affecting the stability of the mitoribosome, may cause an OXPHOS deficiency in Leigh Syndrome and reports, for the first time, an unusual long survival in a patient with a homozygous MRPS34 pathogenic variant.

DOI: https://doi.org/10.1016/j.ymgmr.2021.100830
Int J Mol Sci. 2021 Dec 15. pii: 13484. [Epub ahead of print]22(24):

Characterization of a Novel Splicing Variant in Acylglycerol Kinase (AGK) Associated with Fatal Sengers Syndrome.

Sofia Barbosa-Gouveia, Maria E Vázquez-Mosquera, Emiliano Gonzalez-Vioque, Álvaro Hermida-Ameijeiras, Laura L Valverde, Judith Armstrong-Moron, Maria Del Carmen Fons-Estupiña, Liesbeth T Wintjes, Antonia Kappen, Richard J Rodenburg, Maria L Couce.

  Mitochondrial functional integrity depends on protein and lipid homeostasis in the mitochondrial membranes and disturbances in their accumulation can cause disease. AGK, a mitochondrial acylglycerol kinase, is not only involved in lipid signaling but is also a component of the TIM22 complex in the inner mitochondrial membrane, which mediates the import of a subset of membrane proteins. AGK mutations can alter both phospholipid metabolism and mitochondrial protein biogenesis, contributing to the pathogenesis of Sengers syndrome. We describe the case of an infant carrying a novel homozygous AGK variant, c.518+1G>A, who was born with congenital cataracts, pielic ectasia, critical congenital dilated myocardiopathy, and hyperlactacidemia and died 20 h after birth. Using the patient's DNA, we performed targeted sequencing of 314 nuclear genes encoding respiratory chain complex subunits and proteins implicated in mitochondrial oxidative phosphorylation (OXPHOS). A decrease of 96-bp in the length of the AGK cDNA sequence was detected. Decreases in the oxygen consumption rate (OCR) and the OCR:ECAR (extracellular acidification rate) ratio in the patient's fibroblasts indicated reduced electron flow through the respiratory chain, and spectrophotometry revealed decreased activity of OXPHOS complexes I and V. We demonstrate a clear defect in mitochondrial function in the patient's fibroblasts and describe the possible molecular mechanism underlying the pathogenicity of this novel AGK variant. Experimental validation using in vitro analysis allowed an accurate characterization of the disease-causing variant.

Keywords:  Sengers syndrome; acylglycerol kinase; mitochondrial ATP generation; mitochondrial dysfunction; oxidative phosphorylation machinery

DOI:  https://doi.org/10.3390/ijms222413484
Cell Rep. 2021 Dec 21. pii: S2211-1247(21)01629-6. [Epub ahead of print]37(12): 110133

Astroglial ER-mitochondria calcium transfer mediates endocannabinoid-dependent synaptic integration.

Roman Serrat, Ana Covelo, Vladimir Kouskoff, Sebastien Delcasso, Andrea Ruiz-Calvo, Nicolas Chenouard, Carol Stella, Corinne Blancard, Benedicte Salin, Francisca Julio-Kalajzić, Astrid Cannich, Federico Massa, Marjorie Varilh, Severine Deforges, Laurie M Robin, Diego De Stefani, Arnau Busquets-Garcia, Frederic Gambino, Anna Beyeler, Sandrine Pouvreau, Giovanni Marsicano.

  Intracellular calcium signaling underlies the astroglial control of synaptic transmission and plasticity. Mitochondria-endoplasmic reticulum contacts (MERCs) are key determinants of calcium dynamics, but their functional impact on astroglial regulation of brain information processing is unexplored. We found that the activation of astrocyte mitochondrial-associated type-1 cannabinoid (mtCB1) receptors determines MERC-dependent intracellular calcium signaling and synaptic integration. The stimulation of mtCB1 receptors promotes calcium transfer from the endoplasmic reticulum to mitochondria through a specific molecular cascade, involving the mitochondrial calcium uniporter (MCU). Physiologically, mtCB1-dependent mitochondrial calcium uptake determines the dynamics of cytosolic calcium events in astrocytes upon endocannabinoid mobilization. Accordingly, electrophysiological recordings in hippocampal slices showed that conditional genetic exclusion of mtCB1 receptors or dominant-negative MCU expression in astrocytes blocks lateral synaptic potentiation, through which astrocytes integrate the activity of distant synapses. Altogether, these data reveal an endocannabinoid link between astroglial MERCs and the regulation of brain network functions.

Keywords:  CB1; MERCs; astrocytes; calcium; cannabinoid; lateral synaptic potentiation; mitochondria

DOI:  https://doi.org/10.1016/j.celrep.2021.110133
J Mol Cell Cardiol. 2021 Dec 16. pii: S0022-2828(21)00228-5. [Epub ahead of print]164 136-147

A roadmap for the characterization of energy metabolism in human cardiomyocytes derived from induced pluripotent stem cells.

Giulia Emanuelli, Anna Zoccarato, Christina M Reumiller, Angelos Papadopoulos, Mei Chong, Sabine Rebs, Kai Betteridge, Matteo Beretta, Katrin Streckfuss-Bömeke, Ajay M Shah.

  Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) are an increasingly employed model in cardiac research and drug discovery. As cellular metabolism plays an integral role in determining phenotype, the characterization of the metabolic profile of hiPSC-CM during maturation is crucial for their translational application. In this study we employ a combination of methods including extracellular flux, 13C-glucose enrichment and targeted metabolomics to characterize the metabolic profile of hiPSC-CM during their maturation in culture from 6 weeks, up to 12 weeks. Results show a progressive remodeling of pathways involved in energy metabolism and substrate utilization along with an increase in sarcomere regularity. The oxidative capacity of hiPSC-CM and particularly their ability to utilize fatty acids increased with time. In parallel, relative glucose oxidation was reduced while glutamine oxidation was maintained at similar levels. There was also evidence of increased coupling of glycolysis to mitochondrial respiration, and away from glycolytic branch pathways at later stages of maturation. The rate of glycolysis as assessed by lactate production was maintained at both stages but with significant alterations in proximal glycolytic enzymes such as hexokinase and phosphofructokinase. We observed a progressive maturation of mitochondrial oxidative capacity at comparable levels of mitochondrial content between these time-points with enhancement of mitochondrial network structure. These results show that the metabolic profile of hiPSC-CM is progressively restructured, recapitulating aspects of early post-natal heart development. This would be particularly important to consider when employing these cell model in studies where metabolism plays an important role.

Keywords:  Cardiac cell models; Energy metabolism; Metabolic maturation; Metabolic shift; iPSC-derived cardiomyocytes

DOI:  https://doi.org/10.1016/j.yjmcc.2021.12.001
Antioxidants (Basel). 2021 Dec 05. pii: 1950. [Epub ahead of print]10(12):

Clinical Diagnosis and Treatment of Leigh Syndrome Based on SURF1: Genotype and Phenotype.

Inn-Chi Lee, Kuo-Liang Chiang.

  SURF1 encodes the assembly factor for maintaining the antioxidant of cytochrome c oxidase (COX) stability in the human electron respiratory chain. Mutations in SURF1 can cause Leigh syndrome (LS), a subacute neurodegenerative encephalopathy, characterized by early onset (infancy), grave prognosis, and predominant symptoms presenting in the basal ganglia, thalamus, brainstem, cerebellum, and peripheral nerves. To date, more than sixty different SURF1 mutations have been found to cause SURF1-associated LS; however, the relationship between genotype and phenotype is still unclear. Most SURF1-associated LS courses present as typical LS and cause early mortality (before the age of ten years). However, 10% of the cases present with atypical courses with milder symptoms and increased life expectancy. One reason for this inconsistency may be due to specific duplications or mutations close to the C-terminus of the SURF1 protein appearing to cause less protein decay. Furthermore, the treatment for SURF1-associated LS is unsatisfactory. A ketogenic diet is most often prescribed and has proven to be effective. Supplementing with coenzyme Q and other cofactors is also a common treatment option; however, the results are inconsistent. Importantly, anti-epileptic drugs such as valproate-which cause mitochondrial dysfunction-should be avoided in patients with SURF1-associated LS presenting with seizures.

Keywords:  Leigh syndrome; complex IV assembly; mitochondrial disorders

DOI:  https://doi.org/10.3390/antiox10121950
Methods. 2021 Dec 18. pii: S1046-2023(21)00281-4. [Epub ahead of print]

Measuring hypertrophy in neonatal rat primary cardiomyocytes and human iPSC-derived cardiomyocytes.

Kyla Bourque, Cara Hawey, Jace Jones-Tabah, Darlaine Pétrin, Ryan D Martin, Yi Ling Sun, Terence E Hébert.

  In the heart, left ventricular hypertrophy is initially an adaptive mechanism that increases wall thickness to preserve normal cardiac output and function in the face of coronary artery disease or hypertension. Cardiac hypertrophy develops in response to pressure and volume overload but can also be seen in inherited cardiomyopathies. As the wall thickens, it becomes stiffer impairing the distribution of oxygenated blood to the rest of the body. With complex cellular signalling and transcriptional networks involved in the establishment of the hypertrophic state, several model systems have been developed to better understand the molecular drivers of disease. Immortalized cardiomyocyte cell lines, primary rodent and larger animal models have all helped understand the pathological mechanisms underlying cardiac hypertrophy. Induced pluripotent stem cell-derived cardiomyocytes are also used and have the additional benefit of providing access to human samples with direct disease relevance as when generated from patients suffering from hypertrophic cardiomyopathies. Here, we briefly review in vitro and in vivo model systems that have been used to model hypertrophy and provide detailed methods to isolate primary neonatal rat cardiomyocytes as well as to generate cardiomyocytes from human iPSCs. We also describe how to model hypertrophy in a "dish" using gene expression analysis and immunofluorescence combined with automated high-content imaging.

Keywords:  Hypertrophy; Imaging; Induced pluripotent stem cells; Primary neonatal cardiomyocytes

DOI:  https://doi.org/10.1016/j.ymeth.2021.12.006
Antioxidants (Basel). 2021 Dec 03. pii: 1939. [Epub ahead of print]10(12):

Therapeutic Potential of Emerging NAD+-Increasing Strategies for Cardiovascular Diseases.

Noemi Rotllan, Mercedes Camacho, Mireia Tondo, Elena M G Diarte-Añazco, Marina Canyelles, Karen Alejandra Méndez-Lara, Sonia Benitez, Núria Alonso, Didac Mauricio, Joan Carles Escolà-Gil, Francisco Blanco-Vaca, Josep Julve.

  Cardiovascular diseases are the leading cause of death worldwide. Aging and/or metabolic stress directly impact the cardiovascular system. Over the last few years, the contributions of altered nicotinamide adenine dinucleotide (NAD+) metabolism to aging and other pathological conditions closely related to cardiovascular diseases have been intensively investigated. NAD+ bioavailability decreases with age and cardiometabolic conditions in several mammalian tissues. Compelling data suggest that declining tissue NAD+ is commonly related to mitochondrial dysfunction and might be considered as a therapeutic target. Thus, NAD+ replenishment by either genetic or natural dietary NAD+-increasing strategies has been recently demonstrated to be effective for improving the pathophysiology of cardiac and vascular health in different experimental models, as well as human health, to a lesser extent. Here, we review and discuss recent experimental evidence illustrating that increasing NAD+ bioavailability, particularly by the use of natural NAD+ precursors, may offer hope for new therapeutic strategies to prevent and treat cardiovascular diseases.

Keywords:  COVID-19; aneurysm; animal models; atherosclerosis; cardiomyopathy; chemotherapy; clinical trials; diabetes; heart failure; ischemia/reperfusion; macrophage; mitochondria; myocarditis; niacin; niacinamide; niagen; niaspan; tryptophan; vitamin B3

DOI:  https://doi.org/10.3390/antiox10121939
Nature. 2021 Dec 22.

Valine tRNA levels and availability regulate complex I assembly in leukaemia.

Palaniraja Thandapani, Andreas Kloetgen, Matthew T Witkowski, Christina Glytsou, Anna K Lee, Eric Wang, Jingjing Wang, Sarah E LeBoeuf, Kleopatra Avrampou, Thales Papagiannakopoulos, Aristotelis Tsirigos, Iannis Aifantis.

Although deregulation of transfer RNA (tRNA) biogenesis promotes the translation of pro-tumorigenic mRNAs in cancers1,2, the mechanisms and consequences of tRNA deregulation in tumorigenesis are poorly understood. Here we use a CRISPR-Cas9 screen to focus on genes that have been implicated in tRNA biogenesis, and identify a mechanism by which altered valine tRNA biogenesis enhances mitochondrial bioenergetics in T cell acute lymphoblastic leukaemia (T-ALL). Expression of valine aminoacyl tRNA synthetase is transcriptionally upregulated by NOTCH1, a key oncogene in T-ALL, underlining a role for oncogenic transcriptional programs in coordinating tRNA supply and demand. Limiting valine bioavailability through restriction of dietary valine intake disrupted this balance in mice, resulting in decreased leukaemic burden and increased survival in vivo. Mechanistically, valine restriction reduced translation rates of mRNAs that encode subunits of mitochondrial complex I, leading to defective assembly of complex I and impaired oxidative phosphorylation. Finally, a genome-wide CRISPR-Cas9 loss-of-function screen in differential valine conditions identified several genes, including SLC7A5 and BCL2, whose genetic ablation or pharmacological inhibition synergized with valine restriction to reduce T-ALL growth. Our findings identify tRNA deregulation as a critical adaptation in the pathogenesis of T-ALL and provide a molecular basis for the use of dietary approaches to target tRNA biogenesis in blood malignancies.

DOI: https://doi.org/10.1038/s41586-021-04244-1
Pharmacol Res. 2021 Dec 17. pii: S1043-6618(21)00622-8. [Epub ahead of print]175 106038

Mitochondrial dysfunction and mitochondrial therapies in heart failure.

Chennan Wu, Zhen Zhang, Weidong Zhang, Xia Liu.

  Cardiovascular diseases remain the leading cause of death worldwide in the last decade, accompanied by immense health and economic burdens. Heart failure (HF), as the terminal stage of many cardiovascular diseases, is a common, intractable, and costly medical condition. Despite significant improvements in pharmacologic and device therapies over the years, life expectancy for this disease remains poor. Current therapies have not reversed the trends in morbidity and mortality as expected. Thus, there is an urgent need for novel potential therapeutic agents. Although the pathophysiology of the failing heart is extraordinarily complex, targeting mitochondrial dysfunction can be an effective approach for potential treatment. Increasing evidence has shown that mitochondrial abnormalities, including altered metabolic substrate utilization, impaired mitochondrial oxidative phosphorylation (OXPHOS), increased reactive oxygen species (ROS) formation, and aberrant mitochondrial dynamics, are closely related to HF. Here, we reviewed the findings on the role of mitochondrial dysfunction in HF, along with novel mitochondrial therapeutics and their pharmacological effects.

Keywords:  Energy metabolism; Heart failure; Mitochondrial dynamics; Mitochondrial dysfunction; Oxidative phosphorylation

DOI:  https://doi.org/10.1016/j.phrs.2021.106038
Cell Commun Signal. 2021 Dec 18. 19(1): 119

PDIA3 inhibits mitochondrial respiratory function in brain endothelial cells and C. elegans through STAT3 signaling and decreases survival after OGD.

Matt P Keasey, V Razskazovskiy, C Jia, E D Peterknecht, P C Bradshaw, T Hagg.

  BACKGROUND: Protein disulfide isomerase A3 (PDIA3, also named GRP58, ER-60, ERp57) is conserved across species and mediates protein folding in the endoplasmic reticulum. PDIA3 is, reportedly, a chaperone for STAT3. However, the role of PDIA3 in regulating mitochondrial bioenergetics and STAT3 phosphorylation at serine 727 (S727) has not been described.METHODS: Mitochondrial respiration was compared in immortalized human cerebral microvascular cells (CMEC) wild type or null for PDIA3 and in whole organism C. Elegans WT or null for pdi-3 (worm homologue). Mitochondrial morphology and cell signaling pathways in PDIA3-/- and WT cells were assessed. PDIA3-/- cells were subjected to oxygen-glucose deprivation (OGD) to determine the effects of PDIA3 on cell survival after injury.
RESULTS: We show that PDIA3 gene deletion using CRISPR-Cas9 in cultured CMECs leads to an increase in mitochondrial bioenergetic function. In C. elegans, gene deletion or RNAi knockdown of pdi-3 also increased respiratory rates, confirming a conserved role for this gene in regulating mitochondrial bioenergetics. The PDIA3-/- bioenergetic phenotype was reversed by overexpression of WT PDIA3 in cultured PDIA3-/- CMECs. PDIA3-/- and siRNA knockdown caused an increase in phosphorylation of the S727 residue of STAT3, which is known to promote mitochondrial bioenergetic function. Increased respiration in PDIA3-/- CMECs was reversed by a STAT3 inhibitor. In PDIA3-/- CMECs, mitochondrial membrane potential and reactive oxygen species production, but not mitochondrial mass, was increased, suggesting an increased mitochondrial bioenergetic capacity. Finally, PDIA3-/- CMECs were more resistant to oxygen-glucose deprivation, while STAT3 inhibition reduced the protective effect.
CONCLUSIONS: We have discovered a novel role for PDIA3 in suppressing mitochondrial bioenergetic function by inhibiting STAT3 S727 phosphorylation.

Keywords:  Mitochondria; PDIA3; STAT3

DOI:  https://doi.org/10.1186/s12964-021-00794-z
Cell Death Dis. 2021 Dec 20. 13(1): 14

BNIP3L/NIX-mediated mitophagy: molecular mechanisms and implications for human disease.

Yue Li, Wanqing Zheng, Yangyang Lu, Yanrong Zheng, Ling Pan, Xiaoli Wu, Yang Yuan, Zhe Shen, Shijia Ma, Xingxian Zhang, Jiaying Wu, Zhong Chen, Xiangnan Zhang.

Mitophagy is a highly conserved cellular process that maintains the mitochondrial quantity by eliminating dysfunctional or superfluous mitochondria through autophagy machinery. The mitochondrial outer membrane protein BNIP3L/Nix serves as a mitophagy receptor by recognizing autophagosomes. BNIP3L is initially known to clear the mitochondria during the development of reticulocytes. Recent studies indicated it also engages in a variety of physiological and pathological processes. In this review, we provide an overview of how BNIP3L induces mitophagy and discuss the biological functions of BNIP3L and its regulation at the molecular level. We further discuss current evidence indicating the involvement of BNIP3L-mediated mitophagy in human disease, particularly in cancer and neurological disorders.

DOI: https://doi.org/10.1038/s41419-021-04469-y
Nature. 2021 Dec 21.

Activation mechanism of PINK1.

Zhong Yan Gan, Sylvie Callegari, Simon A Cobbold, Thomas R Cotton, Michael J Mlodzianoski, Alexander F Schubert, Niall D Geoghegan, Kelly L Rogers, Andrew Leis, Grant Dewson, Alisa Glukhova, David Komander.

Mutations in the protein kinase PINK1 lead to defects in mitophagy and cause autosomal recessive early onset Parkinson's Disease (EOPD)1,2. PINK1 has many unique features that enable it to phosphorylate ubiquitin and the ubiquitin-like domain of Parkin3-9. Structural analysis of PINK1 from diverse insect species10-12 with and without ubiquitin provided snapshots of distinct structural states yet did not explain how PINK1 is activated. We here elucidate the activation mechanism of PINK1 by crystallography and cryo-EM. A crystal structure of unphosphorylated Pediculus humanus corporis (Ph) PINK1 resolves a previously omitted N-terminal helix revealing how unphosphorylated yet active PINK1 is oriented on mitochondria. We further reveal a 2.35 Å cryo-EM structure of a symmetric PhPINK1 dimer trapped during the process of trans-autophosphorylation, and a 3.1 Å cryo-EM structure of phosphorylated PhPINK1 in the process of undergoing a conformational change to become an active ubiquitin kinase. Structures and phosphorylation studies further identify a role for regulatory PINK1 oxidation. Together, our work delineates the complete activation mechanism of PINK1, illuminates how PINK1 interacts with the mitochondrial outer membrane, and reveals how PINK1 activity may be modulated by mitochondrial reactive oxygen species.

DOI: https://doi.org/10.1038/s41586-021-04340-2
Clin Neurol Neurosurg. 2021 Dec 18. pii: S0303-8467(21)00626-0. [Epub ahead of print]212 107097

Vitamin B12 deficiency is associated with narcolepsy.

Chaofan Geng, Zhenzhen Yang, Pengfei Xu, Hongju Zhang.

  BACKGROUND: Narcolepsy can be defined as a sleep disorder. However, whether changes in the serum vitamin B12 levels are involved in the pathophysiological mechanism of narcolepsy remains unclear. Our study aimed to assess whether vitamin B12 levels are independently related to the occurrence of narcolepsy.METHODS: The serum folate, vitamin B12, and homocysteine levels of 40 patients with narcolepsy and 40 age- and gender-matched healthy controls (HC) were retrospectively analyzed. According to the results of the univariate logistic analysis, a multiple logistic regression model was constructed to predict the independent influencing indicators.
RESULTS: Serum folic acid and vitamin B12 levels in the narcolepsy group were significantly reduced. Moreover, through the sex subgroup, males in the narcolepsy group had lower serum vitamin B12 levels. Multivariate logistic regression revealed serum vitamin B12 to be independently associated with narcolepsy (p < 0.05; odds ratio=0.97; 95% confidence interval: 0.95-0.98).
CONCLUSION: Decreased serum vitamin B12 levels are independently associated with the development of narcolepsy, which illustrates the complex relationship between vitamin B12 and narcolepsy. Future studies should explore whether vitamin B12 supplementation can improve the symptoms of patients.

Keywords:  Folic acid; Homocysteine; Narcolepsy; Pathophysiology; Vitamin B12

DOI:  https://doi.org/10.1016/j.clineuro.2021.107097
iScience. 2021 Dec 17. 24(12): 103517

GFAT2 mediates cardiac hypertrophy through HBP-O-GlcNAcylation-Akt pathway.

Akihito Ishikita, Shouji Matsushima, Soichiro Ikeda, Kosuke Okabe, Ryohei Nishimura, Tomonori Tadokoro, Nobuyuki Enzan, Taishi Yamamoto, Masashi Sada, Yoshitomo Tsutsui, Ryo Miyake, Masataka Ikeda, Tomomi Ide, Shintaro Kinugawa, Hiroyuki Tsutsui.

  Molecular mechanisms mediating cardiac hypertrophy by glucose metabolism are incompletely understood. Hexosamine biosynthesis pathway (HBP), an accessory pathway of glycolysis, is known to be involved in the attachment of O-linked N-acetylglucosamine motif (O-GlcNAcylation) to proteins, a post-translational modification. We here demonstrate that glutamine-fructose-6-phosphate amidotransferase 2 (GFAT2), a critical HBP enzyme, is a major isoform of GFAT in the heart and is increased in response to several hypertrophic stimuli, including isoproterenol (ISO). Knockdown of GFAT2 suppresses ISO-induced cardiomyocyte hypertrophy, accompanied by suppression of Akt O-GlcNAcylation and activation. Knockdown of GFAT2 does not affect anti-hypertrophic effect by Akt inhibition. Administration of glucosamine, a substrate of HBP, induces protein O-GlcNAcylation, Akt activation, and cardiomyocyte hypertrophy. In mice, 6-diazo-5-oxo-L-norleucine, an inhibitor of GFAT, attenuates ISO-induced protein O-GlcNAcylation, Akt activation, and cardiac hypertrophy. Our results demonstrate that GFAT2 mediates cardiomyocyte hypertrophy by HBP-O-GlcNAcylation-Akt pathway and could be a critical therapeutic target of cardiac hypertrophy.

Keywords:  Cell biology; Classification Description: Cellular physiology; Molecular physiology

DOI:  https://doi.org/10.1016/j.isci.2021.103517
Oxid Med Cell Longev. 2021 ;2021 5586052

Directly Reprogrammed Human Neurons to Understand Age-Related Energy Metabolism Impairment and Mitochondrial Dysfunction in Healthy Aging and Neurodegeneration.

Camila Gudenschwager, Isadora Chavez, Cesar Cardenas, Christian Gonzalez-Billault.

Brain aging is characterized by several molecular and cellular changes grouped as the hallmarks or pillars of aging, including organelle dysfunction, metabolic and nutrition-sensor changes, stem cell attrition, and macromolecular damages. Separately and collectively, these features degrade the most critical neuronal function: transmission of information in the brain. It is widely accepted that aging is the leading risk factor contributing to the onset of the most prevalent pathological conditions that affect brain functions, such as Alzheimer's, Parkinson's, and Huntington's disease. One of the limitations in understanding the molecular mechanisms involved in those diseases is the lack of an appropriate cellular model that recapitulates the "aged" context in human neurons. The advent of the cellular reprogramming of somatic cells, i.e., dermal fibroblasts, to obtain directly induced neurons (iNs) and induced pluripotent stem cell- (iPSC-) derived neurons is technical sound advances that could open the avenues to understand better the contribution of aging toward neurodegeneration. In this review, we will summarize the commonalities and singularities of these two approaches for the study of brain aging, with an emphasis on the role of mitochondrial dysfunction and redox biology. We will address the evidence showing that iNs retain age-related features in contrast to iPSC-derived neurons that lose the aging signatures during the reprogramming to pluripotency, rendering iNs a powerful strategy to deepen our knowledge of the processes driving normal cellular function decline and neurodegeneration in a human adult model. We will finally discuss the potential utilization of these novel technologies to understand the differential contribution of genetic and epigenetic factors toward neuronal aging, to identify and develop new drugs and therapeutic strategies.

DOI: https://doi.org/10.1155/2021/5586052
Free Radic Biol Med. 2021 Dec 17. pii: S0891-5849(21)01116-3. [Epub ahead of print]179 11-23

Post-translational modifications on mitochondrial metabolic enzymes in cancer.

Yunhua Peng, Huadong Liu, Jiankang Liu, Jiangang Long.

  Mitochondrion is the powerhouse of the cell. The research of nearly a century has expanded our understanding of mitochondrion, far beyond the view that mitochondrion is an important energy generator of cells. During the initiation, growth and survival of tumor cells, significant mitochondrial metabolic changes have taken place in the important enzymes of respiratory chain and tricarboxylic acid cycle, mitochondrial biogenesis and dynamics, oxidative stress regulation and molecular signaling. Therefore, mitochondrial metabolic proteins are the key mediators of tumorigenesis. Post-translational modification is the molecular switch that regulates protein function. Understanding how these mitochondria-related post-translational modification function during tumorigenesis will bring new ideas for the next generation of cancer treatment.

Keywords:  Metabolism; Mitochondrial biogenesis; Mitophagy; OXPHOS; Post-translational modification; TCA cycle

DOI:  https://doi.org/10.1016/j.freeradbiomed.2021.12.264
Mol Ther Nucleic Acids. 2022 Mar 08. 27 99-108

Allele-specific targeting of mutant ataxin-3 by antisense oligonucleotides in SCA3-iPSC-derived neurons.

Stefan Hauser, Jacob Helm, Melanie Kraft, Milena Korneck, Jeannette Hübener-Schmid, Ludger Schöls.

  Spinocerebellar ataxia type 3 (SCA3) is caused by an expanded polyglutamine stretch in ataxin-3. While wild-type ataxin-3 has important functions, e.g., as a deubiquitinase, downregulation of mutant ataxin-3 is likely to slow down the course of this fatal disease. We established a screening platform with human neurons of patients and controls derived from induced pluripotent stem cells to test antisense oligonucleotides (ASOs) for their effects on ataxin-3 expression. We identified an ASO that suppressed mutant and wild-type ataxin-3 levels by >90% after a singular treatment. Next, we screened pairs of ASOs designed to selectively target the mutant or the wild-type allele by taking advantage of a SNP (c.987G > C) in ATXN3 that is present in most SCA3 patients. We found ASOmut4 to reduce levels of mutant ataxin-3 by 80% after 10 days while leaving expression of wild-type ataxin-3 largely unaffected. In a long-term study we proved this effect to last for about 4 weeks after a single treatment without signs of neurotoxicity. This study provides proof of principle that allele-specific lowering of poly(Q)-expanded ataxin-3 by selective ASOs is feasible and long lasting, with sparing of wild-type ataxin-3 expression in a human cell culture model that is genetically identical to SCA3 patients.

Keywords:  ASO; MJD; Machado-Joseph disease; SCA3; SNP; allele-specific targeting; antisense oligonucleotides; iPSC-derived neurons; spinocerebellar ataxia type 3

DOI:  https://doi.org/10.1016/j.omtn.2021.11.015
Genet Med. 2021 Nov 27. pii: S1098-3600(21)05401-0. [Epub ahead of print]

Automated reanalysis application to assist in detecting novel gene-disease associations after genome sequencing.

Nana E Mensah, Ataf H Sabir, Andrew Bond, Wendy Roworth, Melita Irving, Angela C Davies, Joo Wook Ahn.

  PURPOSE: This study aimed to investigate whether a bioinformatics application can streamline genome reanalysis and yield new diagnoses for patients with rare diseases.METHODS: We developed TierUp to identify variants in new disease genes for unresolved rare disease cases recruited to the 100,000 Genomes Project, all of whom underwent genome sequencing. TierUp uses the NHS Genomic Medicine Service bioinformatics infrastructure by securely accessing case details from the Clinical Interpretation Portal application programming interface and by querying the curated PanelApp database for novel gene-disease associations. We applied TierUp to 948 cases, and a subset of variants were reclassified according to the American College of Medical Genetics and Genomics/Association of Molecular Pathology guidelines.
RESULTS: A rare form of spondylometaphyseal dysplasia was diagnosed through TierUp reanalysis, and an additional 4 variants have been reported to date. From a total of 564,441 variants across patients, TierUp highlighted 410 variants present in novel disease genes in under 77 minutes, successfully expediting an important reanalysis strategy.
CONCLUSION: TierUp supports claims that automation can reduce the time taken to reanalyze variants and increase the diagnostic yield from molecular testing. Clinical services should leverage bioinformatics expertise to develop tools that enable routine reanalysis. In addition, services must also explore the ethical, legal, and health economic considerations raised by automation.

Keywords:  Automated variant reanalysis; Automated variant reclassification; Variant reanalysis; Variant reassessment; Variant reclassification

DOI:  https://doi.org/10.1016/j.gim.2021.11.021
Elife. 2021 Dec 23. pii: e60311. [Epub ahead of print]10

Acetyl-CoA production by specific metabolites promotes cardiac repair after myocardial infarction via histone acetylation.

Ienglam Lei, Shuo Tian, Wenbin Gao, Liu Liu, Yijing Guo, Paul Tang, Eugene Chen, Zhong Wang.

  Myocardial infarction (MI) is accompanied by severe energy deprivation and extensive epigenetic changes. However, how energy metabolism and chromatin modifications are interlinked during MI and heart repair has been poorly explored. Here, we examined the effect of different carbon sources that are involved in the major metabolic pathways of acetyl-CoA synthesis on myocardial infarction and found that elevation of acetyl-CoA by sodium octanoate (8C) significantly improved heart function in ischemia reperfusion (I/R) rats. Mechanistically, 8C reduced I/R injury by promoting histone acetylation which in turn activated the expression of antioxidant genes and inhibited cardiomyocyte (CM) apoptosis. Furthermore, we elucidated that 8C-promoted histone acetylation and heart repair were carried out by metabolic enzyme medium-chain acyl-CoA dehydrogenase (MCAD) and histone acetyltransferase Kat2a, suggesting that 8C dramatically improves cardiac function mainly through metabolic acetyl-CoA-mediated histone acetylation. Therefore, our study uncovers an interlinked metabolic/epigenetic network comprising 8C, acetyl-CoA, MCAD, and Kat2a to combat heart injury.

Keywords:  cell biology; mouse

DOI:  https://doi.org/10.7554/eLife.60311