bims-mitdis Biomed News
on Mitochondrial Disorders
Issue of 2021‒02‒28
forty-three papers selected by
Catalina Vasilescu
University of Helsinki

  1. Mol Neurodegener. 2021 Feb 25. 16(1): 12
      Inherited optic neuropathies are the most common mitochondrial diseases, leading to neurodegeneration involving the irreversible loss of retinal ganglion cells, optic nerve degeneration and central visual loss. Importantly, properly regulated mitochondrial dynamics are critical for maintaining cellular homeostasis, and are further regulated by MIEF1 (mitochondrial elongation factor 1) which encodes for MID51 (mitochondrial dynamics protein 51), an outer mitochondrial membrane protein that acts as an adaptor protein to regulate mitochondrial fission. However, dominant mutations in MIEF1 have not been previously linked to any human disease. Using targeted sequencing of genes involved in mitochondrial dynamics, we report the first heterozygous variants in MIEF1 linked to disease, which cause an unusual form of late-onset progressive optic neuropathy characterized by the initial loss of peripheral visual fields. Pathogenic MIEF1 variants linked to optic neuropathy do not disrupt MID51's localization to the outer mitochondrial membrane or its oligomerization, but rather, significantly disrupt mitochondrial network dynamics compared to wild-type MID51 in high spatial and temporal resolution confocal microscopy live imaging studies. Together, our study identifies dominant MIEF1 mutations as a cause for optic neuropathy and further highlights the important role of properly regulated mitochondrial dynamics in neurodegeneration.
    Keywords:  Dominant optic atrophy (DOA); Inherited optic neuropathy (ION); MIEF1; Mid51; Mitochondria dynamics; Mitochondrial disease; Neurodegeneration; Peripheral visual field
  2. Nat Rev Neurol. 2021 Feb 23.
      Next-generation sequencing (NGS) has increased our understanding of the molecular basis of many primary mitochondrial diseases (PMDs). Despite this progress, many patients with suspected PMD remain without a genetic diagnosis, which restricts their access to in-depth genetic counselling, reproductive options and clinical trials, in addition to hampering efforts to understand the underlying disease mechanisms. Although they represent a considerable improvement over their predecessors, current methods for sequencing the mitochondrial and nuclear genomes have important limitations, and molecular diagnostic techniques are often manual and time consuming. However, recent advances in genomics and transcriptomics offer realistic solutions to these challenges. In this Review, we discuss the current genetic testing approach for PMDs and the opportunities that exist for increased use of whole-genome NGS of nuclear and mitochondrial DNA (mtDNA) in the clinical environment. We consider the possible role for long-read approaches in sequencing of mtDNA and in the identification of novel nuclear genomic causes of PMDs. We examine the expanding applications of RNA sequencing, including the detection of cryptic variants that affect splicing and gene expression and the interpretation of rare and novel mitochondrial transfer RNA variants.
  3. Surv Ophthalmol. 2021 Feb 18. pii: S0039-6257(21)00060-6. [Epub ahead of print]
      Cellular function and survival are critically dependent on the proper functionality of the mitochondrion. Neurodegenerative cellular processes including cellular adenosine triphosphate production, intermediary metabolism control, and apoptosis regulation are all mitochondrially mediated. The A to G transition at position 3243 in the mitochondrial MTTL1 gene that encodes for the leucine transfer RNA (m.3243A>G) causes a variety of diseases including maternally inherited loss of hearing and diabetes syndrome (MIDD), mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes syndrome (MELAS). Ophthalmological findings-including posterior sub-capsular cataract, ptosis, external ophthalmoplegia, and pigmentary retinopathy- have all been associated with the m.3243A>G variant. Pigmentary retinopathy is, however, the most common ocular finding, occurring in 38% to 86% of cases. To date, little is known about the pathogenesis, natural history, and heteroplasmic and phenotypic correlations of m.3243A>G associated pigmentary retinopathy. We summarize the current understanding of mitochondrial genetics and pathogenesis of some associated diseases. We then review the pathophysiology, histology, clinical features, treatment and important ocular and systemic phenotypic manifestations of m.3243A>G variant associated retinopathy. Mitochondrial diseases require a multidisciplinary team approach to ensure effective treatment, regular follow-ups, and accurate genetic counseling.
    Keywords:  A3243G variant retinopathy; Mitochondria; and systemic implications; heteroplasmy; pathogenesis; prognosis
  4. EMBO J. 2021 Feb 23. e107165
      Mitochondria contain an autonomous and spatially segregated genome. The organizational unit of their genome is the nucleoid, which consists of mitochondrial DNA (mtDNA) and associated architectural proteins. Here, we show that phase separation is the primary physical mechanism for assembly and size control of the mitochondrial nucleoid (mt-nucleoid). The major mtDNA-binding protein TFAM spontaneously phase separates in vitro via weak, multivalent interactions into droplets with slow internal dynamics. TFAM and mtDNA form heterogenous, viscoelastic structures in vitro, which recapitulate the dynamics and behavior of mt-nucleoids in vivo. Mt-nucleoids coalesce into larger droplets in response to various forms of cellular stress, as evidenced by the enlarged and transcriptionally active nucleoids in mitochondria from patients with the premature aging disorder Hutchinson-Gilford Progeria Syndrome (HGPS). Our results point to phase separation as an evolutionarily conserved mechanism of genome organization.
    Keywords:  TFAM; biomolecular condensate; genome organization; mitochondrial genome; phase separation
  5. Aging Cell. 2021 Feb 24. e13321
      One of the hallmarks of aging is an accumulation of cells with defects in oxidative phosphorylation (OXPHOS) due to mutations of mitochondrial DNA (mtDNA). Rapidly dividing tissues maintained by stem cells, such as the colonic epithelium, are particularly susceptible to accumulation of OXPHOS defects over time; however, the effects on the stem cells are unknown. We have crossed a mouse model in which intestinal stem cells are labelled with EGFP (Lgr5-EGFP-IRES-creERT2) with a model of accelerated mtDNA mutagenesis (PolgAmut/mut ) to investigate the effect of OXPHOS dysfunction on colonic stem cell proliferation. We show that a reduction in complex I protein levels is associated with an increased rate of stem cell cycle re-entry. These changes in stem cell homeostasis could have significant implications for age-associated intestinal pathogenesis.
    Keywords:  aging; colon; complex I; mitochondria; stem cells
  6. Int J Biochem Cell Biol. 2021 Feb 18. pii: S1357-2725(21)00035-2. [Epub ahead of print] 105951
      Mitochondria are highly dynamic organelles, which undergo frequent structural and metabolic changes to fulfil cellular demands. To facilitate these processes several proteins are required to regulate mitochondrial shape and interorganellar communication. These proteins include the classical mitochondrial fusion (MFN1, MFN2, and OPA1) and fission proteins (DRP1, MFF, FIS1 etc.) as well as several other proteins that are directly or indirectly involved in these processes (e.g. YME1L, OMA1, INF2, GDAP1, MIC13, etc.). During the last two decades, inherited genetic defects in mitochondrial fusion and fission proteins have emerged as an important class of neurodegenerative human disease with variable onset ranging from infancy to adulthood. So far, no causal treatment strategies are available for these disorders. In this review, we provide an overview about the current knowledge on mitochondrial dynamics under physiological conditions. Moreover, we describe human diseases, which are associated with genetic defects in these pathways.
    Keywords:  Alzheimer’s disease; OXPHOS; Parkinson’s disease; cristae; mitochondrial dynamics; mitochondriopathy
  7. J Neurochem. 2020 Aug 16.
      Mitochondria are essential for neuronal function. They produce ATP to meet energy demands, regulate homeostasis of ion levels such as calcium and regulate reactive oxygen species that cause oxidative cellular stress. Mitochondria have also been shown to regulate protein synthesis within themselves, as well as within the nucleus, and also influence synaptic plasticity. These roles are especially important for neurons, which have higher energy demands and greater susceptibility to stress. Dysfunction of mitochondria has been associated with several neurodegenerative diseases, including Parkinson's disease, Alzheimer's disease, Huntington's disease, Glaucoma and Amyotrophic Lateral Sclerosis. The focus of this review is on how and why mitochondrial function is linked to the pathology of Parkinson's disease (PD). Many of the PD-linked genetic mutations which have been identified result in dysfunctional mitochondria, through a wide-spread number of mechanisms. In this review, we describe how susceptible neurons are predisposed to be vulnerable to the toxic events that occur during the neurodegenerative process of PD, and how mitochondria are central to these pathways. We also discuss ways in which proteins linked with familial PD control mitochondrial function, both physiologically and pathologically, along with their implications in genome-wide association studies and risk assessment. Finally, we review potential strategies for disease modification through mitochondrial enhancement. Ultimately, agents capable of both improving and/or restoring mitochondrial function, either alone, or in conjunction with other disease-modifying agents may halt or slow the progression of neurodegeneration in Parkinson's disease.
    Keywords:  Parkinson's disease; animal models; cell and molecular mechanisms; genetic / familial Parkinson's disease; human studies; mitochondria; mitochondria enhancers and small molecules
  8. J Gene Med. 2021 Feb 24. e3328
      BACKGROUND: Mutations in mitochondrial tRNA (mt-tRNA) genes are associated with hypertension, but their pathogenic mechanisms remain poorly understood.METHODS: Here, two Han Chinese families with maternally transmitted hypertension were interviewed. The mitochondrial DNA (mtDNA) mutations of matrilineal relatives were screened by PCR-Sanger sequencing. Mitochondrial ATP, membrane potential, and ROS were also analyzed in polymononuclear leukocytes (PMNs) carrying these mt-tRNA mutations. Additionally, the levels of oxidative-stress related biomarkers (MDA, SOD, GSH-Px and 8-OHdG) were analyzed.
    RESULTS: Nine of 13 adult matrilineal relatives of these pedigrees exhibited a wide range of severity of hypertension. The age at onset of hypertension was 30-62 years, (average 46). Mutational screening of mitochondrial genomes revealed tRNAArg T10410C and T10454C mutations. In fact, the m.T10454C and m.T10410C mutations occurred at conserved bases of TΨC-loop and acceptor arm of tRNAArg (positions 55 and 6), which are critical for tRNAArg post-transcriptional modification. Thus, the defects in tRNA modification may cause failure in tRNA metabolism, impairing mitochondrial translation. Biochemical analysis revealed that m.T10454C or m.T10410C mutation significantly reduced mitochondrial ATP and membrane potential, and increased ROS production in mutant cell lines (all P<0.05). In addition, the levels of MDA and 8-OHdG in hypertensive patients markedly increased, whereas those of SOD and GSH-Px decreased (all P<0.05).
    CONCLUSIONS: These findings demonstrate that m.T10410C and m.T10454C mutations affect the structure and function of tRNAArg and consequently alter mitochondrial function and lead to oxidative stress, which are involved in the pathogenesis of maternally inherited hypertension.
    Keywords:  Chinese family; hypertension; mtDNA mutations; tRNA metabolism; tRNAArg
  9. Curr Drug Targets. 2021 Feb 22.
      The neuron is high energy utilizing tissue. The rate of neuronal cell respiration is higher than in other cells. The cellular respiration occurs with mitochondria. Healthy production and functions of mitochondria play a key role in the maintenances of healthy neurons. In pathological conditions such as neurodegenerative diseases, healthy mitochondria help to alleviate pathological events in neuronal cells. Conversely, mitochondrial dysfunction promotes the acceleration of the neurodegenerative process. Furthermore, glial-derived mitochondria contribute to multiple roles in the regulation of healthy neuron functions. It also supports releasing of the neurotransmitters; generation of the impulses, regulation of the membrane potential and molecular dynamics; controlling of the axonal transport; controlling of the mitochondrial fission and fusion functions in the peripheral as well as the central nervous system. Moreover, it plays a key role in the regeneration process of neuronal cells. Therefore, healthy mitochondria can provide a healthy environment for neuronal cell function and can treat neurodegenerative disorders. In this review, we explore the current view of healthy mitochondria and their role in healthy neuronal functions.
    Keywords:  Glial cell; membrane potential; mitochondrial fission; mitochondrial fusion; neurodegenerative disorder; neurotransmitter.
  10. Biochim Biophys Acta Mol Basis Dis. 2021 Feb 19. pii: S0925-4439(21)00037-5. [Epub ahead of print] 166104
      Depolarized/damaged mitochondria aggregate at the perinuclear region prior to mitophagy in cells treated with mitochondrial stressors. However, the cellular mechanism(s) by which damaged mitochondria are transported and remain aggregated at the perinuclear region is unknown. Here, we demonstrate that mitofusins (Mfn1/2) are post-translationally modified by SUMO2 (Small Ubiquitin-related Modifier 2) in Human embryonic kidney 293 (Hek293) cells treated with protonophore CCCP and proteasome inhibitor MG132, both known mitochondrial stressors. SUMOylation of Mfn1/2 is not for their proteasomal degradation but facilitate mitochondrial congression at the perinuclear region in CCCP- and MG132-treated cells. Additionally, congressed mitochondria (mito-aggresomes) colocalize with LC3, ubiquitin, and SUMO2 in CCCP-treated cells. Knowing that SUMO functions as a "molecular glue" to facilitate protein-protein interactions, we propose that SUMOylation of Mfn1/2 may congress, glues, and confines damaged mitochondria to the perinuclear region thereby, protectively quarantining them from the heathy mitochondrial network until their removal via mitophagy in cells.
    Keywords:  26S Proteasome; Autophagy; Mitochondria; Mitofusin; Mitophagy; Small Ubiquitin Modifier (SUMO); ubiquitin
  11. Nat Commun. 2021 02 23. 12(1): 1252
      Upon starvation, cells rewire their metabolism, switching from glucose-based metabolism to mitochondrial oxidation of fatty acids, which require the transfer of FAs from lipid droplets (LDs) to mitochondria at mitochondria-LD membrane contact sites (MCSs). However, factors responsible for FA transfer at these MCSs remain uncharacterized. Here, we demonstrate that vacuolar protein sorting-associated protein 13D (VPS13D), loss-of-function mutations of which cause spastic ataxia, coordinates FA trafficking in conjunction with the endosomal sorting complex required for transport (ESCRT) protein tumor susceptibility 101 (TSG101). The VPS13 adaptor-binding domain of VPS13D and TSG101 directly remodels LD membranes in a cooperative manner. The lipid transfer domain of human VPS13D binds glycerophospholipids and FAs in vitro. Depletion of VPS13D, TSG101, or ESCRT-III proteins inhibits FA trafficking from LDs to mitochondria. Our findings suggest that VPS13D mediates the ESCRT-dependent remodeling of LD membranes to facilitate FA transfer at mitochondria-LD contacts.
  12. J Inherit Metab Dis. 2021 Feb 27.
      Peripheral neuropathy is a known long-term, irreversible complication of long-chain 3-hydroxyacyl-CoA dehydrogenase deficiency (LCHADD) and mitochondrial trifunctional protein deficiency (MTPD), two inherited disorders of mitochondrial long-chain fatty acid oxidation. The underlying pathophysiology of neuropathy is still not fully understood. We report electrophysiological studies and neurological findings in a series of 8 LCHAD-deficient and 11 MTP-deficient patients. The median age at time of the study was 8.0 years (0.5-25 years). The overall prevalence of neuropathy was 58% with neuropathic symptoms being slightly more common in MTPD compared to LCHADD (70% versus 50%, respectively). Onset of neuropathy was significantly earlier in MTPD patients compared to LCHADD patients (median age at onset 4.7 versus 15.3 years, respectively, p=0.047). In four patients, isolated peripheral neuropathy was the first and only presenting symptom, and in all four the diagnosis was missed by newborn screening. About half of the patients (45.5%) had a sensorimotor neuropathy, while 27.3% showed a pure motor form and another 27.3% an isolated sensory form. Despite early diagnosis by newborn screening and early initiation of therapy, peripheral neuropathy cannot be prevented in all patients with LCHADD/MTPD and has severe impact on the life of affected patients. Electrophysiology classifies LCHADD/MTPD neuropathy as axonal with secondary demyelination. A novel observation is that in patients with acute, fulminant onset of neuropathy, symptoms can be partly reversible. Further studies are needed to elucidate the underlying pathophysiology of axonal damage and possible therapeutic targets. This article is protected by copyright. All rights reserved.
    Keywords:  LCHAD; MTP; complication; fatty acid oxidation; long chain 3-hydroxyacyl-CoA dehydrogenase deficiency; mTFP; mitochondrial trifunctional protein deficiency; neuropathy
  13. Nat Metab. 2021 Feb;3(2): 196-210
      Ketone bodies are generated in the liver and allow for the maintenance of systemic caloric and energy homeostasis during fasting and caloric restriction. It has previously been demonstrated that neonatal ketogenesis is activated independently of starvation. However, the role of ketogenesis during the perinatal period remains unclear. Here, we show that neonatal ketogenesis plays a protective role in mitochondrial function. We generated a mouse model of insufficient ketogenesis by disrupting the rate-limiting hydroxymethylglutaryl-CoA synthase 2 enzyme gene (Hmgcs2). Hmgcs2 knockout (KO) neonates develop microvesicular steatosis within a few days of birth. Electron microscopic analysis and metabolite profiling indicate a restricted energy production capacity and accumulation of acetyl-CoA in Hmgcs2 KO mice. Furthermore, acetylome analysis of Hmgcs2 KO cells revealed enhanced acetylation of mitochondrial proteins. These findings suggest that neonatal ketogenesis protects the energy-producing capacity of mitochondria by preventing the hyperacetylation of mitochondrial proteins.
  14. J Hum Genet. 2021 Feb 22.
      MSTO1 is a cytoplasmic protein that modulates mitochondrial dynamics by promoting mitochondrial fusion. Mutations in the MSTO1 gene are responsible for an extremely rare condition characterized by early-onset myopathy and cerebellar ataxia. We report here two siblings from a large Ashkenazi Jewish family, presenting with a progressive neuromuscular disease characterized by ataxia and myopathy. By whole exome sequencing, we found a novel homozygous missense mutation (c.1403T>A, p.Leu468Gln) in MSTO1. Studies performed on fibroblasts from the index patient demonstrated the pathogenic role of the identified variant; we found that MSTO1 protein level was reduced and that mitochondrial network was fragmented or formed enlarged structures. Moreover, patient's cells showed reduced mitochondrial DNA amount. Our report confirms that MSTO1 mutations are typically recessive, and associated with clinical phenotypes characterized by early-onset muscle impairment and ataxia, often with upper motor neuron signs and varied cognitive impairment.
  15. J Biol Chem. 2021 Feb 18. pii: S0021-9258(21)00210-6. [Epub ahead of print] 100437
      Mitochondria maintain a distinct pool of ribosomal machinery, including tRNAs and tRNAs activating enzymes, like mitochondrial tyrosyl-tRNA synthetase (YARS2). Mutations in YARS2 which typically lead to the impairment of mitochondrial protein synthesis, have been linked to an array of human diseases including optic neuropathy. However, the lack of YARS2 mutation animal model makes us difficult to elucidate the pathophysiology underlying YARS2 deficiency. To explore this system, we generated YARS2 knockout (KO) HeLa cells and zebrafish using CRISPR/Cas9 technology. We observed the aberrant tRNATyr aminoacylation overall and reductions in the levels in mitochondrion- and nucleus-encoding subunits of oxidative phosphorylation system (OXPHOS), which were especially pronounced effects in the subunits of complex I and complex IV. These deficiencies manifested the decreased levels of intact supercomplexes overall. Immunoprecipitation assays showed that YARS2 bound to specific subunits of complex I and complex IV, suggesting the posttranslational stabilization of OXPHOS. Furthermore, YARS2 ablation caused defects in the stability and activities of OXPHOS complexes. These biochemical defects could be rescued by the overexpression of YARS2 cDNA in the YARS2KO cells. In zebrafish, the yars2KO larva conferred deficient COX activities in the retina, abnormal mitochondrial morphology and numbers in the photoreceptor and retinal ganglion cells. The zebrafish further exhibited the retinal defects affecting both rods and cones. Vision defects in yars2KO zebrafish recapitulated the clinical phenotypes in the optic neuropathy patients carrying the YARS2 mutations. Our findings highlighted the critical role of YARS2 in the stability and activity of OXPHOS and its pathological consequence in vision impairments.
    Keywords:  Mitochondrial tyrosyl-tRNA synthetase; animal disease model; oxidative phosphorylation; retina; vision function
  16. Commun Biol. 2021 Feb 24. 4(1): 248
      βA3/A1-crystallin, a lens protein that is also expressed in astrocytes, is produced as βA3 and βA1-crystallin isoforms by leaky ribosomal scanning. In a previous human proteome high-throughput array, we found that βA3/A1-crystallin interacts with protein tyrosine phosphatase 1B (PTP1B), a key regulator of glucose metabolism. This prompted us to explore possible roles of βA3/A1-crystallin in metabolism of retinal astrocytes. We found that βA1-crystallin acts as an uncompetitive inhibitor of PTP1B, but βA3-crystallin does not. Loss of βA1-crystallin in astrocytes triggers metabolic abnormalities and inflammation. In CRISPR/cas9 gene-edited βA1-knockdown (KD) mice, but not in βA3-knockout (KO) mice, the streptozotocin (STZ)-induced diabetic retinopathy (DR)-like phenotype is exacerbated. Here, we have identified βA1-crystallin as a regulator of PTP1B; loss of this regulation may be a new mechanism by which astrocytes contribute to DR. Interestingly, proliferative diabetic retinopathy (PDR) patients showed reduced βA1-crystallin and higher levels of PTP1B in the vitreous humor.
  17. FASEB J. 2021 Mar;35(3): e21362
      Friedreich ataxia (FRDA) is a neurodegenerative disease resulting from a severe decrease of frataxin (FXN). Most patients carry a GAA repeat expansion in both alleles of the FXN gene, whereas a small fraction of them are compound heterozygous for the expansion and a point mutation in the other allele. FXN is involved in the mitochondrial biogenesis of the FeS-clusters. Distinctive feature of FRDA patient cells is an impaired cellular respiration, likely due to a deficit of key redox cofactors working as electrons shuttles through the respiratory chain. However, a definite relationship between FXN levels, FeS-clusters assembly dysregulation and bioenergetics failure has not been established. In this work, we performed a comparative analysis of the mitochondrial phenotype of cell lines from FRDA patients, either homozygous for the expansion or compound heterozygotes for the G130V mutation. We found that, in healthy cells, FXN and two key proteins of the FeS-cluster assembly machinery are enriched in mitochondrial cristae, the dynamic subcompartment housing the respiratory chain. On the contrary, FXN widely redistributes to the matrix in FRDA cells with defects in respiratory supercomplexes assembly and altered respiratory function. We propose that this could be relevant for the early mitochondrial defects afflicting FRDA cells and that perturbation of mitochondrial morphodynamics could in turn be critical in terms of disease mechanisms.
    Keywords:  FeS-cluster assembly; mitochondria; mitochondrial morphology; respiration
  18. Proc Natl Acad Sci U S A. 2021 Mar 02. pii: e2018342118. [Epub ahead of print]118(9):
      Duchenne muscular dystrophy (DMD) is an X-linked recessive disorder characterized by progressive muscle degeneration and weakness due to mutations in the dystrophin gene. The symptoms of DMD share similarities with those of accelerated aging. Recently, hydrogen sulfide (H2S) supplementation has been suggested to modulate the effects of age-related decline in muscle function, and metabolic H2S deficiencies have been implicated in affecting muscle mass in conditions such as phenylketonuria. We therefore evaluated the use of sodium GYY4137 (NaGYY), a H2S-releasing molecule, as a possible approach for DMD treatment. Using the dys-1(eg33) Caenorhabditis elegans DMD model, we found that NaGYY treatment (100 µM) improved movement, strength, gait, and muscle mitochondrial structure, similar to the gold-standard therapeutic treatment, prednisone (370 µM). The health improvements of either treatment required the action of the kinase JNK-1, the transcription factor SKN-1, and the NAD-dependent deacetylase SIR-2.1. The transcription factor DAF-16 was required for the health benefits of NaGYY treatment, but not prednisone treatment. AP39 (100 pM), a mitochondria-targeted H2S compound, also improved movement and strength in the dys-1(eg33) model, further implying that these improvements are mitochondria-based. Additionally, we found a decline in total sulfide and H2S-producing enzymes in dystrophin/utrophin knockout mice. Overall, our results suggest that H2S deficit may contribute to DMD pathology, and rectifying/overcoming the deficit with H2S delivery compounds has potential as a therapeutic approach to DMD treatment.
    Keywords:  C. elegans; hydrogen sulfide; mitochondria; mouse; muscle
  19. Nature. 2021 Feb 24.
      Mitochondrial DNA double-strand breaks (mtDSBs) are toxic lesions that compromise the integrity of mitochondrial DNA (mtDNA) and alter mitochondrial function1. Communication between mitochondria and the nucleus is essential to maintain cellular homeostasis; however, the nuclear response to mtDSBs remains unknown2. Here, using mitochondrial-targeted transcription activator-like effector nucleases (TALENs)1,3,4, we show that mtDSBs activate a type-I interferon response that involves the phosphorylation of STAT1 and activation of interferon-stimulated genes. After the formation of breaks in the mtDNA, herniation5 mediated by BAX and BAK releases mitochondrial RNA into the cytoplasm and triggers a RIG-I-MAVS-dependent immune response. We further investigated the effect of mtDSBs on interferon signalling after treatment with ionizing radiation and found a reduction in the activation of interferon-stimulated genes when cells that lack mtDNA are exposed to gamma irradiation. We also show that mtDNA breaks synergize with nuclear DNA damage to mount a robust cellular immune response. Taken together, we conclude that cytoplasmic accumulation of mitochondrial RNA is an intrinsic immune surveillance mechanism for cells to cope with mtDSBs, including breaks produced by genotoxic agents.
  20. Biochim Biophys Acta Gen Subj. 2021 Feb 23. pii: S0304-4165(21)00044-1. [Epub ahead of print] 129886
      BACKGROUND: In most sexually reproducing organisms, mitochondrial DNA (mtDNA) is inherited maternally.SCOPE OF REVIEW: In this review, we summarise recent knowledge on how paternal mitochondria and their mtDNA are selectively eliminated from embryos.
    MAJOR CONCLUSIONS: Studies based on Caenorhabditis elegans have revealed that paternal mitochondria and their mtDNA are selectively degraded in embryos via mitophagy. Thus, mitophagy functions as the mechanisms of maternal inheritance of mtDNA. The mitophagy of paternal mitochondria is conserved in other species, and the underlying molecular mechanisms have begun to be elucidated. In addition to mitophagy, autophagy-independent digestion of paternal mtDNA before and after fertilization serves as another mechanism for maternal inheritance of mtDNA.
    GENERAL SIGNIFICANCE: Maternal inheritance of mtDNA is strictly controlled via multistep mechanisms. These studies also demonstrate a physiological role of mitophagy during animal development.
    Keywords:  Allophagy; Fertilization; Maternal inheritance; Mitochondria; Mitochondrial DNA; Mitophagy
  21. Ann Clin Transl Neurol. 2021 Feb 27.
      OBJECTIVE: Mitochondrial DNA mutations are associated with an increased risk of heart disease. Whether an increased prevalence of cardiovascular disease is present in patients presenting with mitochondrial abnormalities on skeletal muscle biopsy remains unknown. This study was designed to determine the prevalence of cardiac conduction disease and structural heart disease in patients presenting with mitochondrial abnormalities on skeletal muscle biopsy.METHODS: This is a retrospective cohort study of 103 patients with mitochondrial abnormalities on skeletal muscle biopsy who were referred for evaluation of muscle weakness at a single tertiary care referral center from 2012 to 2018. Of these patients, 59 (57.3%) had an electrocardiogram available and were evaluated for the presence of conduction disease. An echocardiogram was available in 43 patients (42%) who were evaluated for the presence of structural heart disease. The prevalence of cardiac disease was compared to control cohort populations (Framingham and the Atherosclerosis Risk in Communities, ARIC cohorts).
    RESULTS: Mitochondrial abnormalities associated with cardiac conduction disease (defined as QRS duration ≥ 120 msec) were present in 8.9%, versus 2.0% (p < 0.001) in the Framingham population and 2.6% (p = 0.003) in the ARIC cohort. LV systolic dysfunction (LVEF ≤ 50%) was present in 11.6%, versus 3.6% (p < 0.01) in the Framingham and 3% (p < 0.01) in the ARIC populations. Left ventricular hypertrophy was present in 28.6%, versus 13.6% (p < 0.02) in the Framingham and 10.4% (p < 0.001) in the ARIC populations.
    INTERPRETATION: Given the increased prevalence of cardiovascular disease, patients with mitochondrial abnormalities on skeletal muscle biopsy should undergo routine cardiac screening with physical exam, electrocardiography, and cardiac imaging.
  22. iScience. 2021 Feb 19. 24(2): 102090
      Human pluripotent stem cells (hPSCs) have a unique metabolic signature for maintenance of pluripotency, self-renewal, and survival. Although hPSCs could be potentially used in regenerative medicine, the prohibitive cost associated with large-scale cell culture presents a major barrier to the clinical application of hPSC. Moreover, without a fully characterized metabolic signature, hPSC culture conditions are not optimized. Here, we performed detailed amino acid profiling and found that tryptophan (TRP) plays a key role in the proliferation with maintenance of pluripotency. In addition, metabolome analyses revealed that intra- and extracellular kynurenine (KYN) is decreased under TRP-supplemented conditions, whereas N-formylkynurenine (NFK), the upstream metabolite of KYN, is increased thereby contributing to proliferation promotion. Taken together, we demonstrate that TRP is indispensable for survival and proliferation of hPSCs. A deeper understanding of TRP metabolism will enable cost-effective large-scale production of hPSCs, leading to advances in regenerative medicine.
    Keywords:  Cell Biology; Metabolomics; Stem Cell Research
  23. Biochim Biophys Acta Mol Basis Dis. 2021 Feb 19. pii: S0925-4439(21)00035-1. [Epub ahead of print] 166102
      Mitophagy is defective in several neurodegenerative diseases, including Ataxia Telangiectasia (A-T). However, the molecular mechanism underlying defective mitophagy in A-T is unknown. Literature indicates that damaged mitochondria are transported to the perinuclear region prior to their removal via mitophagy. Our previous work has indicated that conjugation of SUMO2 (Small Ubiquitin-like Modifier 2) to mitofusins (Mfns) may be necessary for congression of mitochondria into SUMO2-/ubiquitin-/LC3-positive compact structures resembling mito-aggresomes at the perinuclear region in CCCP-treated HEK293 cells. Here, we demonstrate that Mfns are SUMOylated, and mitochondria are transported to the perinuclear region; however, mitochondria fail to congress into mito-aggresome-like structures in CCCP-treated A-T cells. Defect in mitochondrial congression is causally related to constitutively elevated ISG15 (Interferon-Stimulated Gene 15), an antagonist of the ubiquitin pathway, in A-T cells. Suppression of the ISG15 pathway restores mitochondrial congression, reduce oxidative stress, and level of unhealthy mitochondria, which is suggestive of restoration of mitophagy in A-T cells. ISG15 is also constitutively elevated and mitophagy is defective in Amytrophic Lateral Sclerosis (ALS). The constitutively elevated ISG15 pathway therefore appears to be a common unifying biochemical mechanism underlying defective mitophagy in neurodegenerative disorders thus, implying the broader significance of our findings, and suggest the potential role of ISG15 inhibitors in their treatment.
    Keywords:  26S proteasome; Ataxia Telangiectasia; Autophagy; Interferon-Stimulated Gene 15 (ISG15); Mitofusin; Mitophagy; Ubiquitin
  24. Ageing Res Rev. 2021 Feb 21. pii: S1568-1637(21)00056-8. [Epub ahead of print] 101309
      Mitochondria are highly dynamic organelles capable of adapting their network, morphology, and function, playing a role in oxidative phosphorylation and many cellular processes in most cell types. Skeletal muscle is a very plastic tissue, subjected to many morphological changes following diverse stimuli, such as during myogenic differentiation and regenerative myogenesis. For some time now, mitochondria have been reported to be involved in myogenesis by promoting a bioenergetic remodeling and assisting myoblasts in surviving the process. However, not much is known about the interplay between mitochondrial quality control and myogenic differentiation. Sestrin2 (SESN2) is a well described regulator of autophagy and antioxidant responses and has been gaining attention due to its role in aging-associated pathologies and redox signaling promoted by reactive oxygen species (ROS) in many tissues. Current evidence involving SESN2-associated pathways suggest that it can act as a potential regulator of mitochondrial quality control following induction by ROS under stress conditions, such as during myogenesis. Yet, there are no studies directly assessing SESN2 involvement in myogenic differentiation. This review provides novel insights pertaining the involvement of SESN2 in myogenic differentiation by analyzing the interactions between ROS and mitochondrial remodeling.
    Keywords:  SESN2; differentiation; mitochondria; mitohormesis; myogenesis
  25. FEBS Lett. 2021 Feb 22.
      Mitophagy is one of the selective autophagy pathways that catabolizes dysfunctional or superfluous mitochondria. Under mitophagy-inducing conditions, mitochondria are labeled with specific molecular landmarks that recruit the autophagy machinery to the surface of mitochondria, enclosed into autophagosomes, and delivered to lysosomes (vacuoles in yeast) for degradation. As damaged mitochondria are the major sources of reactive oxygen species, mitophagy is critical for mitochondrial quality control and cellular health. Moreover, appropriate control of mitochondrial quantity via mitophagy is vital for the energy supply-demand balance in cells and whole organisms, cell differentiation, and developmental programs. Thus, it seems conceivable that defects in mitophagy could elicit pleiotropic pathologies such as excess inflammation, tissue injury, neurodegeneration, and ageing. In this review, we will focus on the molecular basis and physiological relevance of mitophagy, and potential of mitophagy as a therapeutic target to overcome such disorders.
    Keywords:  adaptor; ageing; autophagy; inflammation; mitochondria; neurodegeneration; ubiquitin
  26. J Pediatr Endocrinol Metab. 2021 Feb 23.
      OBJECTIVES: Diagnostic process of mitochondrial disorders (MD) is challenging because of the clinical variability and genetic heterogeneity of these conditions. Next-Generation Sequencing (NGS) technology offers a high-throughput platform for nuclear MD.METHODS: We included 59 of 72 patients that undergone WES and targeted exome sequencing panel suspected to have potential PMDs. Patients who were included in the analysis considering the possible PMD were reviewed retrospectively and scored according to the Mitochondrial Disease Criteria Scale.
    RESULTS: Sixty-one percent of the patients were diagnosed with whole-exome sequencing (WES) (36/59) and 15% with targeted exome sequencing (TES) (9/59). Patients with MD-related gene defects were included in the mito group, patients without MD-related gene defects were included in the nonmito group, and patients in whom no etiological cause could be identified were included in the unknown etiology group. In 11 out of 36 patients diagnosed with WES, a TES panel was applied prior to WES. In 47 probands in 39 genes (SURF1, SDHAF1, MTO1, FBXL4, SLC25A12, GLRX5, C19oRF12, NDUFAF6, DARS2, BOLA3, SLC19A3, SCO1, HIBCH, PDHA1, PDHAX, PC, ETFA, TRMU, TUFM, NDUFS6, WWOX, UBCD TREX1, ATL1, VAC14, GFAP, PLA2G6, TPRKB, ATP8A2, PEX13, IGHMBP2, LAMB2, LPIN1, GFPT1, CLN5, DOLK) (20 mito group, 19 nonmito group) 59 variants (31 mito group, 18 nonmito group) were detected. Seven novel variants in the mito group (SLC25A12, GLRX5, DARS2, SCO1, PC, ETFA, NDUFS6), nine novel variants in the nonmito group (IVD, GCDH, COG4, VAC14, GFAP, PLA2G6, ATP8A2, PEX13, LPIN1) were detected.
    CONCLUSIONS: We explored the feasibility of identifying pathogenic alleles using WES and TES in MD. Our results show that WES is the primary method of choice in the diagnosis of MD until at least all genes responsible for PMD are found and are highly effective in facilitating the diagnosis process.
    Keywords:  Leigh syndrome; Mendelian mitochondrial disorder; next-generation sequencing; nuclear mitochondrial disorders; whole exome sequencing
  27. J Am Coll Cardiol. 2021 Mar 02. pii: S0735-1097(21)00067-X. [Epub ahead of print]77(8): 1073-1088
      BACKGROUND: Mitochondrial dysfunction results in an imbalance between energy supply and demand in a failing heart. An innovative therapy that targets the intracellular bioenergetics directly through mitochondria transfer may be necessary.OBJECTIVES: The purpose of this study was to establish a preclinical proof-of-concept that extracellular vesicle (EV)-mediated transfer of autologous mitochondria and their related energy source enhance cardiac function through restoration of myocardial bioenergetics.
    METHODS: Human-induced pluripotent stem cell-derived cardiomyocytes (iCMs) were employed. iCM-conditioned medium was ultracentrifuged to collect mitochondria-rich EVs (M-EVs). Therapeutic effects of M-EVs were investigated using in vivo murine myocardial infarction (MI) model.
    RESULTS: Electron microscopy revealed healthy-shaped mitochondria inside M-EVs. Confocal microscopy showed that M-EV-derived mitochondria were transferred into the recipient iCMs and fused with their endogenous mitochondrial networks. Treatment with 1.0 × 108/ml M-EVs significantly restored the intracellular adenosine triphosphate production and improved contractile profiles of hypoxia-injured iCMs as early as 3 h after treatment. In contrast, isolated mitochondria that contained 300× more mitochondrial proteins than 1.0 × 108/ml M-EVs showed no effect after 24 h. M-EVs contained mitochondrial biogenesis-related messenger ribonucleic acids, including proliferator-activated receptor γ coactivator-1α, which on transfer activated mitochondrial biogenesis in the recipient iCMs at 24 h after treatment. Finally, intramyocardial injection of 1.0 × 108 M-EVs demonstrated significantly improved post-MI cardiac function through restoration of bioenergetics and mitochondrial biogenesis.
    CONCLUSIONS: M-EVs facilitated immediate transfer of their mitochondrial and nonmitochondrial cargos, contributing to improved intracellular energetics in vitro. Intramyocardial injection of M-EVs enhanced post-MI cardiac function in vivo. This therapy can be developed as a novel, precision therapeutic for mitochondria-related diseases including heart failure.
    Keywords:  bioenergetics; heart failure; human stem cells; mitochondria; myocardial infarction
  28. Genome Med. 2021 Feb 22. 13(1): 31
      BACKGROUND: Splicing of genomic exons into mRNAs is a critical prerequisite for the accurate synthesis of human proteins. Genetic variants impacting splicing underlie a substantial proportion of genetic disease, but are challenging to identify beyond those occurring at donor and acceptor dinucleotides. To address this, various methods aim to predict variant effects on splicing. Recently, deep neural networks (DNNs) have been shown to achieve better results in predicting splice variants than other strategies.METHODS: It has been unclear how best to integrate such process-specific scores into genome-wide variant effect predictors. Here, we use a recently published experimental data set to compare several machine learning methods that score variant effects on splicing. We integrate the best of those approaches into general variant effect prediction models and observe the effect on classification of known pathogenic variants.
    RESULTS: We integrate two specialized splicing scores into CADD (Combined Annotation Dependent Depletion; ), a widely used tool for genome-wide variant effect prediction that we previously developed to weight and integrate diverse collections of genomic annotations. With this new model, CADD-Splice, we show that inclusion of splicing DNN effect scores substantially improves predictions across multiple variant categories, without compromising overall performance.
    CONCLUSIONS: While splice effect scores show superior performance on splice variants, specialized predictors cannot compete with other variant scores in general variant interpretation, as the latter account for nonsense and missense effects that do not alter splicing. Although only shown here for splice scores, we believe that the applied approach will generalize to other specific molecular processes, providing a path for the further improvement of genome-wide variant effect prediction.
  29. Nat Protoc. 2021 Feb 24.
      Quantification of cellular proliferation in humans is important for understanding biology and responses to injury and disease. However, existing methods require administration of tracers that cannot be ethically administered in humans. We present a protocol for the direct quantification of cellular proliferation in human hearts. The protocol involves administration of non-radioactive, non-toxic stable isotope 15Nitrogen-enriched thymidine (15N-thymidine), which is incorporated into DNA during S-phase, in infants with tetralogy of Fallot, a common form of congenital heart disease. Infants with tetralogy of Fallot undergo surgical repair, which requires the removal of pieces of myocardium that would otherwise be discarded. This protocol allows for the quantification of cardiomyocyte proliferation in this discarded tissue. We quantitatively analyzed the incorporation of 15N-thymidine with multi-isotope imaging spectrometry (MIMS) at a sub-nuclear resolution, which we combined with correlative confocal microscopy to quantify formation of binucleated cardiomyocytes and cardiomyocytes with polyploid nuclei. The entire protocol spans 3-8 months, which is dependent on the timing of surgical repair, and 3-4.5 researcher days. This protocol could be adapted to study cellular proliferation in a variety of human tissues.
  30. BMC Bioinformatics. 2021 Feb 24. 22(1): 85
      BACKGROUND: Benchmarking the performance of complex analytical pipelines is an essential part of developing Lab Developed Tests (LDT). Reference samples and benchmark calls published by Genome in a Bottle (GIAB) consortium have enabled the evaluation of analytical methods. The performance of such methods is not uniform across the different genomic regions of interest and variant types. Several benchmarking methods such as, vcfeval, and vcflib are available to assess the analytical performance characteristics of variant calling algorithms. However, assessing the performance characteristics of an overall LDT assay still requires stringing together several such methods and experienced bioinformaticians to interpret the results. In addition, these methods are dependent on the hardware, operating system and other software libraries, making it impossible to reliably repeat the analytical assessment, when any of the underlying dependencies change in the assay. Here we present a scalable and reproducible, cloud-based benchmarking workflow that is independent of the laboratory and the technician executing the workflow, or the underlying compute hardware used to rapidly and continually assess the performance of LDT assays, across their regions of interest and reportable range, using a broad set of benchmarking samples.RESULTS: The benchmarking workflow was used to evaluate the performance characteristics for secondary analysis pipelines commonly used by Clinical Genomics laboratories in their LDT assays such as the GATK HaplotypeCaller v3.7 and the SpeedSeq workflow based on FreeBayes v0.9.10. Five reference sample truth sets generated by Genome in a Bottle (GIAB) consortium, six samples from the Personal Genome Project (PGP) and several samples with validated clinically relevant variants from the Centers for Disease Control were used in this work. The performance characteristics were evaluated and compared for multiple reportable ranges, such as whole exome and the clinical exome.
    CONCLUSIONS: We have implemented a benchmarking workflow for clinical diagnostic laboratories that generates metrics such as specificity, precision and sensitivity for germline SNPs and InDels within a reportable range using whole exome or genome sequencing data. Combining these benchmarking results with validation using known variants of clinical significance in publicly available cell lines, we were able to establish the performance of variant calling pipelines in a clinical setting.
    Keywords:  Benchmarking; Docker; GIAB reference genomes; Germline variants; Lab developed tests; Precision; Recall; Truth set; Workflow
  31. Front Immunol. 2020 ;11 628576
      Mitochondria participate in immune regulation through various mechanisms, such as changes in the mitochondrial dynamics, as metabolic mediators of the tricarboxylic acid cycle, by the production of reactive oxygen species, and mitochondrial DNA damage, among others. In recent years, studies have shown that extracellular vesicles are widely involved in intercellular communication and exert important effects on immune regulation. Recently, the immunoregulatory effects of mitochondria from extracellular vesicles have gained increasing attention. In this article, we review the mechanisms by which mitochondria participate in immune regulation and exert immunoregulatory effects upon delivery by extracellular vesicles. We also focus on the influence of the immunoregulatory effects of mitochondria from extracellular vesicles to further shed light on the underlying mechanisms.
    Keywords:  extracellular vesicles; immune cell; immunoregulation; mesenchymal stem cells; mitochondria
  32. Pediatr Res. 2021 Feb 24.
      BACKGROUND: The aim of this study was to identify factors predicting outcome in patients with mitochondrial disease admitted to pediatric intensive care units (PICU).METHODS: Retrospective study of 2434 patients (age <21 years) admitted to a PICU from 1 January 2006 through 31 March 2016 and captured in the Virtual Pediatric Systems database with ICD9 diagnosis 277.87, disorders of mitochondrial metabolism. Factors influencing mortality and prolonged length of stay (≥14 days) were analyzed using logistic regression.
    RESULTS: Predictors independently affecting mortality (adjusted odds ratios and 95% confidence intervals, p < 0.05): age 1-23 months 3.4 (1.7-6.6) and mechanical ventilation 4.7 (2.6-8.6) were risk factors; post-operative 0.2 (0.1-0.6), readmission 0.5 (0.3-0.9), and neurologic reason for admittance 0.3 (0.1-0.9) were factors reducing risk. Predictors affecting prolonged length of stay: mechanical ventilation 7.4 (5.2-10.3) and infectious reason for admittance 2.0 (1.3-3.2) were risk factors, post-operative patients 0.3 (0.2-0.5) had lower risk. The utility of PRISM and PIM2 scores in this patient group was evaluated.
    CONCLUSIONS: The single most predictive factor for both mortality and prolonged length of stay is the presence of mechanical ventilation. Age 1-23 months is a risk factor for mortality, and infectious reason for admittance indicates risk for prolonged length of stay.
    IMPACT: Presence of mechanical ventilation is the factor most strongly associated with negative outcome in patients with mitochondrial disease in pediatric intensive care. Age 1-23 months is a risk factor for mortality, and infectious reason for admittance indicates risk for prolonged length of stay PRISM3 and PIM2 are not as accurate in patients with mitochondrial disease as in a mixed patient population.
  33. Analyst. 2021 Feb 26.
      Proteome stability constitutes an essential aspect of protein homeostasis (proteostasis). Proteostasis networks maintain proteins and their interactors in a defined conformation for their activity, localisation, and function. However, endogenous or exogenous stressors can perturb proteostasis integrity and deplete folding capacity, generating destabilized folding intermediates and deleterious aggregated species. Over the years, protein unfolding, misfolding and aggregation have been reported to be associated with aging and many diseases such as neurodegenerative diseases, diabetes, cardiac disease and toxicity, and cancers. Therefore, monitoring proteome stability is central to understanding underlying biological processes and mechanisms of disease progression. Herein, we review the recent bioanalytical methods to measure protein stability in cells on a proteome-wide scale.
  34. Arch Biochem Biophys. 2021 Feb 18. pii: S0003-9861(21)00065-5. [Epub ahead of print]701 108815
      Glaucoma is a neurodegenerative disease that affects eye structures and brain areas related to the visual system. Oxidative stress plays a key role in the development and progression of the disease. The aims of the present study were to evaluate the mitochondrial function and its participation in the brain redox metabolism in an experimental glaucoma model. 3-month-old female Wistar rats were subjected to cauterization of two episcleral veins of the left eye to elevate the intraocular pressure. Seven days after surgery, animals were sacrificed, the brain was carefully removed and the primary visual cortex was dissected. Mitochondrial bioenergetics and ROS production, and the antioxidant enzyme defenses from both mitochondrial and cytosolic fractions were evaluated. When compared to control, glaucoma decreased mitochondrial ATP production (23%, p < 0.05), with an increase in superoxide and hydrogen peroxide production (30%, p < 0.01 and 28%, p < 0.05, respectively), whereas no changes were observed in membrane potential and oxygen consumption rate. In addition, the glaucoma group displayed a decrease in complex II activity (34%, p < 0.01). Moreover, NOX4 expression was increased in glaucoma compared to the control group (27%, p < 0.05). Regarding the activity of enzymes associated with the regulation of the redox status, glaucoma showed an increase in mitochondrial SOD activity (34%, p < 0.05), mostly due to an increase in Mn-SOD (50%, p < 0.05). A decrease in mitochondrial GST activity was observed (11%, p < 0.05). GR and TrxR activity were decreased in both mitochondrial (16%, p < 0.05 and 20%, p < 0.05 respectively) and cytosolic (21%, p < 0.01 and 50%, p < 0.01 respectively) fractions in the glaucoma group. Additionally, glaucoma showed an increase in cytoplasmatic GPx (50%, p < 0.01). In this scenario, redox imbalance took place resulting in damage to mitochondrial lipids (39%, p < 0.01) and proteins (70%, p < 0.05). These results suggest that glaucoma leads to mitochondrial function impairment in brain visual targets, that is accompanied by an alteration in both mitochondrial and cytoplasmatic enzymatic defenses. As a consequence of redox imbalance, oxidative damage to macromolecules takes place and can further affect vital cellular functions. Understanding the role of the mitochondria in the development and progression of the disease could bring up new neuroprotective therapies.
    Keywords:  Glaucoma; Mitochondria; Neurodegeneration; Oxidative stress; Primary visual cortex
  35. J Cell Sci. 2021 Feb 23. pii: jcs.249276. [Epub ahead of print]
      A genome-wide screen recently identified SEC24A as a novel mediator of thapsigargin-induced cell death in HAP1 cells. Here, we determined the cellular mechanism and specificity of SEC24A-mediated cytotoxicity. Measurement of calcium levels using organelle-specific fluorescent indicator dyes showed that calcium efflux from endoplasmic reticulum (ER) and influx into mitochondria were significantly impaired in SEC24A knockout cells. Furthermore, SEC24A knockout cells also showed ∼44% less colocalization of mitochondria and peripheral tubular ER. Knockout of SEC24A, but not its paralogs SEC24B, SEC24C, or SEC24D, rescued HAP1 cells from cell death induced by three different inhibitors of Sarcoplasmic/Endoplasmic Reticulum Ca2+ ATPase (SERCA) but not from cell death induced by a topoisomerase inhibitor. Thapsigargin-treated SEC24A knockout cells showed a ∼2.5-fold increase in autophagic flux and ∼10-fold reduction in apoptosis compared to wild-type cells. Taken together, our findings indicate that SEC24A plays a previously unrecognized role in regulating association and calcium flux between the ER and mitochondria, thereby impacting processes dependent on mitochondrial calcium levels, including autophagy and apoptosis.
    Keywords:  Apoptosis; Autophagy; Calcium; ER stress; Mitochondrial-associated membranes; SEC24A; SERCA; Thapsigargin
  36. Trends Biochem Sci. 2021 Feb 19. pii: S0968-0004(21)00029-3. [Epub ahead of print]
      Recently, three groups, Girardi et al., Kory et al., and Luongo et al., independently identified solute carrier (SLC) 25A51 as the long-sought, major mitochondrial NAD+ transporter in mammalian cells. These studies not only deorphan an uncharacterized transporter of the SLC25A family, but also shed light on other aspects of NAD+ biology.
    Keywords:  NAD; SLC25A family; mitochondrial transporter; redox; respiration
  37. Cell Mol Life Sci. 2021 Feb 23.
      Preservation of mitochondrial quality is paramount for cellular homeostasis. The integrity of mitochondria is guarded by the balanced interplay between anabolic and catabolic mechanisms. The removal of bio-energetically flawed mitochondria is mediated by the process of mitophagy; the impairment of which leads to the accumulation of defective mitochondria which signal the activation of compensatory mechanisms to the nucleus. This process is known as the mitochondrial retrograde response (MRR) and is enacted by Reactive Oxygen Species (ROS), Calcium (Ca2+), ATP, as well as imbalanced lipid and proteostasis. Central to this mitochondria-to-nucleus signalling are the transcription factors (e.g. the nuclear factor kappa-light-chain-enhancer of activated B cells, NF-κB) which drive the expression of genes to adapt the cell to the compromised homeostasis. An increased degree of cellular proliferation is among the consequences of the MRR and as such, engagement of mitochondrial-nuclear communication is frequently observed in cancer. Mitophagy and the MRR are therefore interlinked processes framed to, respectively, prevent or compensate for mitochondrial defects.In this review, we discuss the available knowledge on the interdependency of these processes and their contribution to cell signalling in cancer.
    Keywords:  Cell signalling and Cancer; Mitochondrial retrograde response; Mitophagy
  38. Nucleic Acids Res. 2021 Feb 22. pii: gkab104. [Epub ahead of print]
      GTPBP3 and MTO1 cooperatively catalyze 5-taurinomethyluridine (τm5U) biosynthesis at the 34th wobble position of mitochondrial tRNAs. Mutations in tRNAs, GTPBP3 or MTO1, causing τm5U hypomodification, lead to various diseases. However, efficient in vitro reconstitution and mechanistic study of τm5U modification have been challenging, in part due to the lack of pure and active enzymes. A previous study reported that purified human GTPBP3 (hGTPBP3) is inactive in GTP hydrolysis. Here, we identified the mature form of hGTPBP3 and showed that hGTPBP3 is an active GTPase in vitro that is critical for tRNA modification in vivo. Unexpectedly, the isolated G domain and a mutant with the N-terminal domain truncated catalyzed GTP hydrolysis to only a limited extent, exhibiting high Km values compared with that of the mature enzyme. We further described several important pathogenic mutations of hGTPBP3, associated with alterations in hGTPBP3 localization, structure and/or function in vitro and in vivo. Moreover, we discovered a novel cytoplasm-localized isoform of hGTPBP3, indicating an unknown potential noncanonical function of hGTPBP3. Together, our findings established, for the first time, the GTP hydrolysis mechanism of hGTPBP3 and laid a solid foundation for clarifying the τm5U modification mechanism and etiology of τm5U deficiency-related diseases.
  39. Clin Transl Med. 2021 Feb;11(2): e336
      BACKGROUND: Upper motor neurons (UMNs) are a key component of motor neuron circuitry. Their degeneration is a hallmark for diseases, such as hereditary spastic paraplegia (HSP), primary lateral sclerosis (PLS), and amyotrophic lateral sclerosis (ALS). Currently there are no preclinical assays investigating cellular responses of UMNs to compound treatment, even for diseases of the UMNs. The basis of UMN vulnerability is not fully understood, and no compound has yet been identified to improve the health of diseased UMNs: two major roadblocks for building effective treatment strategies.METHODS: Novel UMN reporter models, in which UMNs that are diseased because of misfolded superoxide dismutase protein (mSOD1) toxicity and TDP-43 pathology are labeled with eGFP expression, allow direct assessment of UMN response to compound treatment. Electron microscopy reveals very precise aspects of endoplasmic reticulum (ER) and mitochondrial damage. Administration of NU-9, a compound initially identified based on its ability to reduce mSOD1 toxicity, has profound impact on improving the health and stability of UMNs, as identified by detailed cellular and ultrastructural analyses.
    RESULTS: Problems with mitochondria and ER are conserved in diseased UMNs among different species. NU-9 has drug-like pharmacokinetic properties. It lacks toxicity and crosses the blood brain barrier. NU-9 improves the structural integrity of mitochondria and ER, reduces levels of mSOD1, stabilizes degenerating UMN apical dendrites, improves motor behavior measured by the hanging wire test, and eliminates ongoing degeneration of UMNs that become diseased both because of mSOD1 toxicity and TDP-43 pathology, two distinct and important overarching causes of motor neuron degeneration.
    CONCLUSIONS: Mechanism-focused and cell-based drug discovery approaches not only addressed key cellular defects responsible for UMN loss, but also identified NU-9, the first compound to improve the health of diseased UMNs, neurons that degenerate in ALS, HSP, PLS, and ALS/FTLD patients.
    Keywords:  ALS; HSP; NU-9; PLS; TDP-43 pathology; mSOD1; upper motor neurons
  40. Nucleic Acids Res. 2021 Feb 23. pii: gkab098. [Epub ahead of print]
      Precise identification of correct exon-intron boundaries is a prerequisite to analyze the location and structure of genes. The existing framework for genomic signals, delineating exon and introns in a genomic segment, seems insufficient, predominantly due to poor sequence consensus as well as limitations of training on available experimental data sets. We present here a novel concept for characterizing exon-intron boundaries in genomic segments on the basis of structural and energetic properties. We analyzed boundary junctions on both sides of all the exons (3 28 368) of protein coding genes from human genome (GENCODE database) using 28 structural and three energy parameters. Study of sequence conservation at these sites shows very poor consensus. It is observed that DNA adopts a unique structural and energy state at the boundary junctions. Also, signals are somewhat different for housekeeping and tissue specific genes. Clustering of 31 parameters into four derived vectors gives some additional insights into the physical mechanisms involved in this biological process. Sites of structural and energy signals correlate well to the positions playing important roles in pre-mRNA splicing.
  41. Nat Metab. 2021 Feb;3(2): 274-286
      The gut microbiome has important effects on human health, yet its importance in human ageing remains unclear. In the present study, we demonstrate that, starting in mid-to-late adulthood, gut microbiomes become increasingly unique to individuals with age. We leverage three independent cohorts comprising over 9,000 individuals and find that compositional uniqueness is strongly associated with microbially produced amino acid derivatives circulating in the bloodstream. In older age (over ~80 years), healthy individuals show continued microbial drift towards a unique compositional state, whereas this drift is absent in less healthy individuals. The identified microbiome pattern of healthy ageing is characterized by a depletion of core genera found across most humans, primarily Bacteroides. Retaining a high Bacteroides dominance into older age, or having a low gut microbiome uniqueness measure, predicts decreased survival in a 4-year follow-up. Our analysis identifies increasing compositional uniqueness of the gut microbiome as a component of healthy ageing, which is characterized by distinct microbial metabolic outputs in the blood.
  42. Am J Physiol Renal Physiol. 2021 Feb 22.
      Stimulator of interferon genes (STING) is an important adaptor in the cytosolic DNA sensing pathways. Recent study found that the deletion of STING ameliorated cisplatin-induced acute kidney injury (AKI), suggesting that STING could serve as a potential target for AKI therapy. Up to now, a series of small-molecule STING inhibitors/antagonists have been identified. However, none of research was performed to explore the role of human STING inhibitors in AKI. Here we investigated the effect of a newly generated covalent antagonist H151 targeting both human and murine STING, in cisplatin-induced AKI. We found that H151 treatment significantly ameliorated cisplatin-induced kidney injury as shown by the improvement of renal function, kidney morphology and renal inflammation. Besides, tubular cell apoptosis and the increased renal tubular injury marker NGAL induced by cisplatin were also effectively attenuated in H151-treated mice. Moreover, the mitochondrial injury caused by cisplatin was also reversed as evidenced by the improved mitochondrial morphology, restored mitochondrial DNA (mtDNA) content, and reversed mitochondrial genes expression. Finally, we observed enhanced mtDNA levels in the plasma of patients receiving platinum-based chemotherapy compared to the healthy controls, which could potentially activate STING signaling. Taken together, these findings suggested that H151 could be a potential therapeutic agent for treating AKI possibly through inhibiting STING-mediated inflammation and mitochondrial injury.
    Keywords:  Acute kidney injury; Cisplatin; H151; Mitochondrial dysfunction; STING