bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2022–06–05
twenty papers selected by
Catalina Vasilescu, University of Helsinki
  1. Mitochondrial matrix-localized Src kinase regulates mitochondrial morphology.
  2. Modelling autosomal dominant optic atrophy associated with OPA1 variants in iPSC-derived retinal ganglion cells.
  3. Leukocyte cytokine responses in adult patients with mitochondrial DNA defects.
  4. Reciprocal Regulation of Mitofusin 2-Mediated Mitophagy and Mitochondrial Fusion by Different PINK1 Phosphorylation Events.
  5. Use of Whole-Genome Sequencing for Mitochondrial Disease Diagnosis.
  6. CHCHD10 and SLP2 control the stability of the PHB complex: a key factor for motor neuron viability.
  7. ER-lysosome lipid transfer protein VPS13C/PARK23 prevents aberrant mtDNA-dependent STING signaling.
  8. The Mitochondrial Pyruvate Carrier at the Crossroads of Intermediary Metabolism.
  9. Heterozygous PRKN mutations are common but do not increase the risk of Parkinson's disease.
  10. 232nd ENMC international workshop: Recommendations for treatment of mitochondrial DNA maintenance disorders. 16 - 18 June 2017, Heemskerk, The Netherlands.
  11. Mitochondrial Transplantation: A Unique Treatment Strategy.
  12. High-intensity interval training remodels the proteome and acetylome of human skeletal muscle.
  13. Boosting mitochondrial health to counteract neurodegeneration.
  14. Data-driven discovery of cardiolipin-selective small molecules by computational active learning.
  15. NAXE deficiency: A neurometabolic disorder of NAD(P)HX repair amenable for metabolic correction.
  16. NAD+ and Vascular Dysfunction: From Mechanisms to Therapeutic Opportunities.
  17. Guidelines for clinical interpretation of variant pathogenicity using RNA phenotypes.
  18. New views of old proteins: clarifying the enigmatic proteome.
  19. Computationally designed hyperactive Cas9 enzymes.
  20. Mitochondrial E3 ubiquitin ligase 1 (MUL1) as a novel therapeutic target for diseases associated with mitochondrial dysfunction.
  1. Cell Mol Life Sci. 2022 May 30. 79(6): 327
    Mitochondrial matrix-localized Src kinase regulates mitochondrial morphology.
    Olivier Lurette, Hala Guedouari, Jordan L Morris, Rebeca Martín-Jiménez, Julie-Pier Robichaud, Geneviève Hamel-Côté, Mehtab Khan, Nicholas Dauphinee, Nicolas Pichaud, Julien Prudent, Etienne Hebert-Chatelain.
      The architecture of mitochondria adapts to physiological contexts: while mitochondrial fragmentation is usually associated to quality control and cell death, mitochondrial elongation often enhances cell survival during stress. Understanding how these events are regulated is important to elucidate how mitochondrial dynamics control cell fate. Here, we show that the tyrosine kinase Src regulates mitochondrial morphology. Deletion of Src increased mitochondrial size and reduced cellular respiration independently of mitochondrial mass, mitochondrial membrane potential or ATP levels. Re-expression of Src targeted to the mitochondrial matrix, but not of Src targeted to the plasma membrane, rescued mitochondrial morphology in a kinase activity-dependent manner. These findings highlight a novel function for Src in the control of mitochondrial dynamics.
    Keywords:  Cellular respiration; Mitochondria-shaping protein; Mitochondrial dynamics; Oxidative phosphorylation
    DOI:  https://doi.org/10.1007/s00018-022-04325-y
  2. Hum Mol Genet. 2022 Jun 02. pii: ddac128. [Epub ahead of print]
    Modelling autosomal dominant optic atrophy associated with OPA1 variants in iPSC-derived retinal ganglion cells.
    Paul E Sladen, Katarina Jovanovic, Rosellina Guarascio, Daniele Ottaviani, Grace Salsbury, Tatiana Novoselova, J Paul Chapple, Patrick Yu-Wai-Man, Michael E Cheetham.
      Autosomal dominant optic atrophy (DOA) is the most common inherited optic neuropathy, characterised by the preferential loss of retinal ganglion cells (RGCs), resulting in optic nerve degeneration and progressive bilateral central vision loss. Over 60% of genetically confirmed DOA patients carry variants in the nuclear OPA1 gene, which encodes for a ubiquitously expressed, mitochondrial GTPase protein. OPA1 has diverse functions within the mitochondrial network, facilitating inner membrane fusion and cristae modelling, regulating mitochondrial DNA maintenance and coordinating mitochondrial bioenergetics. There are currently no licensed disease-modifying therapies for DOA and the disease mechanisms driving RGC degeneration are poorly understood. Here, we describe the generation of isogenic, heterozygous OPA1 null iPSC (OPA1+/-) through CRISPR/Cas9 gene editing of a control cell line, in conjunction with the generation of DOA patient-derived iPSC carrying OPA1 variants, namely, the c.2708_2711delTTAG variant (DOA iPSC), and previously reported missense variant iPSC line (c.1334G>A, DOA+ iPSC) and CRISPR/Cas9 corrected controls. A two-dimensional (2D) differentiation protocol was used to study the effect of OPA1 variants on iPSC-RGC differentiation and mitochondrial function. OPA1+/-, DOA and DOA+ iPSC showed no differentiation deficit compared to control iPSC lines, exhibiting comparable expression of all relevant markers at each stage of differentiation. OPA1+/- and OPA1 variant iPSC-RGCs exhibited impaired mitochondrial homeostasis, with reduced bioenergetic output and compromised mitochondrial DNA maintenance. These data highlight mitochondrial deficits associated with OPA1 dysfunction in human iPSC-RGCs, and establish a platform to study disease mechanisms that contribute to RGC loss in DOA, as well as potential therapeutic interventions.
    DOI:  https://doi.org/10.1093/hmg/ddac128
  3. J Mol Med (Berl). 2022 Jun;100(6): 963-971
    Leukocyte cytokine responses in adult patients with mitochondrial DNA defects.
    Kalpita R Karan, Caroline Trumpff, Marissa Cross, Kristin M Engelstad, Anna L Marsland, Peter J McGuire, Michio Hirano, Martin Picard.
      Patients with oxidative phosphorylation (OxPhos) defects causing mitochondrial diseases appear particularly vulnerable to infections. Although OxPhos defects modulate cytokine production in vitro and in animal models, little is known about how circulating leukocytes of patients with inherited mitochondrial DNA (mtDNA) defects respond to acute immune challenges. In a small cohort of healthy controls (n = 21) and patients (n = 12) with either the m.3243A > G mutation or single, large-scale mtDNA deletions, we examined (i) cytokine responses (IL-6, TNF-α, IL-1β) in response to acute lipopolysaccharide (LPS) exposure and (ii) sensitivity to the immunosuppressive effects of glucocorticoid signaling (dexamethasone) on cytokine production. In dose-response experiments to determine the half-maximal effective LPS concentration (EC50), relative to controls, leukocytes from patients with mtDNA deletions showed 74-79% lower responses for IL-6 and IL-1β (pIL-6 = 0.031, pIL-1β = 0.009). Moreover, whole blood from patients with mtDNA deletions (pIL-6 = 0.006), but not patients with the m.3243A > G mutation, showed greater sensitivity to the immunosuppressive effects of dexamethasone. Together, these ex vivo data provide preliminary evidence that some systemic OxPhos defects may compromise immune cytokine responses and increase the sensitivity to immune cytokine suppression by glucocorticoids. Further work in larger cohorts is needed to define the nature of immune dysregulation in patients with mitochondrial disease, and their potential implications for disease phenotypes. KEY MESSAGES: Little is known about leukocyte cytokine responses in patients with mitochondrial diseases. Leukocytes of patients with mtDNA deletions show blunted LPS sensitivity and cytokine responses. Leukocytes of patients with mtDNA deletions are more sensitive to glucocorticoid-mediated IL-6 suppression. Work in larger cohorts is needed to delineate potential immune alterations in mitochondrial diseases.
    Keywords:  3243A > G; Cytokine; Glucocorticoid; Inflammation; Inflammation Suppression; Interleukin; Mitochondrial disease; mtDNA deletion
    DOI:  https://doi.org/10.1007/s00109-022-02206-2
  4. Front Cell Dev Biol. 2022 ;10 868465
    Reciprocal Regulation of Mitofusin 2-Mediated Mitophagy and Mitochondrial Fusion by Different PINK1 Phosphorylation Events.
    Jiajia Li, Xiawei Dang, Antonietta Franco, Gerald W Dorn.
      Mitochondrial repair is essential to metabolic homeostasis. Outer mitochondrial membrane mitofusin (MFN) proteins orchestrate mitochondrial fusion that opposes mitochondrial degeneration caused by senescence. Depending upon physiological context, MFN2 can either mediate mitochondrial fusion or recruit cytosolic Parkin to initiate mitophagic elimination. Because it is not clear how these events are counter-regulated we engineered and expressed MFN2 mutants that mimic phosphorylated or non-phosphorylatable MFN2 at its PINK1 phosphorylation sites: T111, S378, and S442. By interrogating mitochondrial fusion, polarization status, and Parkin binding/mitophagy as a function of inferred MFN2 phosphorylation, we discovered that individual MFN2 phosphorylation events act as a biological "bar-code", directing mitochondrial fate based on phosphorylation site state. Experiments in Pink1 deficient cells supported a central role for PINK1 kinase as the pivotal regulator of MFN2 functionality. Contrary to popular wisdom that Parkin-mediated ubiquitination regulates MFN-mediated mitochondrial fusion, results in Prkn null cells demonstrated the dispensability of Parkin for MFN2 inactivation. These data demonstrate that PINK1-mediated phosphorylation is necessary and sufficient, and that Parkin is expendable, to switch MFN2 from fusion protein to mitophagy effector.
    Keywords:  MFN2; PINK1 kinase; Parkin; fusion; mitochondrial quality control; mitofusin regulation; phosphorylation
    DOI:  https://doi.org/10.3389/fcell.2022.868465
  5. Neurology. 2022 May 31. pii: 10.1212/WNL.0000000000200745. [Epub ahead of print]
    Use of Whole-Genome Sequencing for Mitochondrial Disease Diagnosis.
    Ryan L Davis, Kishore Raj R Kumar, Clare Puttick, Christina Liang, Kate E Ahmad, Fabienne Edema-Hildebrand, Jin-Sung Park, Andre E Minoche, Velimir Gayevskiy, Amali C Mallawaarachchi, John Christodoulou, Deborah Schofield, Marcel E Dinger, Mark J Cowley, Carolyn M Sue.
       OBJECTIVES: Mitochondrial diseases are the commonest group of heritable metabolic disorders. Phenotypic diversity can make molecular diagnosis challenging and causative genetic mutations may reside in either mitochondrial or nuclear DNA. A single comprehensive genetic diagnostic test would be highly useful and transform the field. We applied whole genome sequencing to evaluate the variant detection rate and diagnostic capacity of this technology with a view to simplifying and improving the mitochondrial disease diagnostic pathway.
    METHODS: Adult patients presenting to a specialist mitochondrial disease clinic in Sydney, Australia were recruited to the study if they satisfied clinical mitochondrial disease (Nijmegen) criteria. Whole genome sequencing was performed on blood DNA, followed by clinical genetic analysis for known pathogenic mitochondrial disease-associated variants and mitochondrial mimics.
    RESULTS: Of the 242 consecutive patients recruited, 62 subjects had 'definite', 108 had 'probable' and 72 had 'possible' mitochondrial disease classification by the Nijmegen criteria. Disease causing variants were identified for 130 subjects, regardless of the location of the causative genetic mutations, giving an overall diagnostic rate of 53.7% (130/242). Identification of causative genetic mutations informed precise treatment, restored reproductive confidence and optimised patient management.
    CONCLUSION: Comprehensive bigenomic sequencing accurately detects causative gene mutations in affected patients and simplifies mitochondrial disease diagnosis, enables early treatment and informs the risk of genetic transmission.
    DOI:  https://doi.org/10.1212/WNL.0000000000200745
  6. Brain. 2022 Jun 03. pii: awac197. [Epub ahead of print]
    CHCHD10 and SLP2 control the stability of the PHB complex: a key factor for motor neuron viability.
    Emmanuelle C Genin, Sylvie Bannwarth, Baptiste Ropert, Françoise Lespinasse, Alessandra Mauri-Crouzet, Gaelle Augé, Konstantina Fragaki, Charlotte Cochaud, Erminia Donnarumma, Sandra Lacas-Gervais, Timothy Wai, Véronique Paquis-Flucklinger.
      CHCHD10 is an amyotrophic lateral sclerosis/frontotemporal dementia (ALS/FTD) gene that encodes a mitochondrial protein whose precise function is unclear. Here we show that CHCHD10 interacts with the Stomatin-Like Protein 2 (SLP2) and participates to the stability of the Prohibitin (PHB) complex in the inner mitochondrial membrane. By using patient fibroblasts and mouse models expressing the same CHCHD10 variant (p.Ser59Leu), we show that SLP2 forms aggregates with prohibitins, found in vivo in the hippocampus and as aggresome-like inclusions in spinal motor neurons of Chchd10S59L/+ mice. Affected cells and tissues display instability of the PHB complex which participates at least in part to the activation of the OMA1 cascade with OPA1 processing leading to mitochondrial fragmentation, abnormal mitochondrial cristae morphogenesis and neuronal death found in spinal cord and the hippocampus of Chchd10S59L/+ animals. Destabilization of the PHB complex leads to the instability of the mitochondrial contact site and cristae organizing system (MICOS) complex, likely via the disruption of OPA1/Mitofilin interaction. Thus, SLP2/PHB aggregates and destabilization of the PHB complex are critical in the sequence of events leading to motor neuron death in CHCHD10S59L-related disease.
    Keywords:   CHCHD10 ; amyotrophic lateral sclerosis; frontotemporal dementia; mitochondrion; motor neuron disease
    DOI:  https://doi.org/10.1093/brain/awac197
  7. J Cell Biol. 2022 Jul 04. pii: e202106046. [Epub ahead of print]221(7):
    ER-lysosome lipid transfer protein VPS13C/PARK23 prevents aberrant mtDNA-dependent STING signaling.
    William Hancock-Cerutti, Zheng Wu, Peng Xu, Narayana Yadavalli, Marianna Leonzino, Arun Kumar Tharkeshwar, Shawn M Ferguson, Gerald S Shadel, Pietro De Camilli.
      Mutations in VPS13C cause early-onset, autosomal recessive Parkinson's disease (PD). We have established that VPS13C encodes a lipid transfer protein localized to contact sites between the ER and late endosomes/lysosomes. In the current study, we demonstrate that depleting VPS13C in HeLa cells causes an accumulation of lysosomes with an altered lipid profile, including an accumulation of di-22:6-BMP, a biomarker of the PD-associated leucine-rich repeat kinase 2 (LRRK2) G2019S mutation. In addition, the DNA-sensing cGAS-STING pathway, which was recently implicated in PD pathogenesis, is activated in these cells. This activation results from a combination of elevated mitochondrial DNA in the cytosol and a defect in the degradation of activated STING, a lysosome-dependent process. These results suggest a link between ER-lysosome lipid transfer and innate immune activation in a model human cell line and place VPS13C in pathways relevant to PD pathogenesis.
    DOI:  https://doi.org/10.1083/jcb.202106046
  8. Am J Physiol Endocrinol Metab. 2022 May 30.
    The Mitochondrial Pyruvate Carrier at the Crossroads of Intermediary Metabolism.
    Nicole K H Yiew, Brian N Finck.
      Pyruvate metabolism, a central nexus of carbon homeostasis, is an evolutionarily-conserved process and aberrant pyruvate metabolism is associated with and contributes to numerous human metabolic disorders including diabetes, cancer, and heart disease. As a product of glycolysis, pyruvate is primarily generated in the cytosol before being transported into the mitochondrion for further metabolism. Pyruvate entry into the mitochondrial matrix is a critical step for efficient generation of reducing equivalents and ATP and for the biosynthesis of glucose, fatty acids, and amino acids from pyruvate. However, for many years the identity of the carrier protein(s) that transported pyruvate into the mitochondrial matrix remained a mystery. In 2012, the molecular-genetic identification of the mitochondrial pyruvate carrier (MPC), a heterodimeric complex composed of protein subunits MPC1 and MPC2, enabled studies that shed light on the many metabolic and physiologic processes regulated by pyruvate metabolism. A better understanding of the mechanisms regulating pyruvate transport and the processes affected by pyruvate metabolism may enable novel therapeutics to modulate mitochondrial pyruvate flux to treat a variety disorders. Herein, we review our current knowledge of the MPC, discuss recent advances in the understanding of mitochondrial pyruvate metabolism in various tissue and cell types, and address some of the outstanding questions relevant to this field.
    Keywords:  adipose tissue; heart; liver; mitochondrion; pyruvate
    DOI:  https://doi.org/10.1152/ajpendo.00074.2022
  9. Brain. 2022 May 31. pii: awab456. [Epub ahead of print]
    Heterozygous PRKN mutations are common but do not increase the risk of Parkinson's disease.
    William Zhu, Xiaoping Huang, Esther Yoon, Sara Bandres-Ciga, Cornelis Blauwendraat, Kimberly J Billingsley, Joshua H Cade, Beverly P Wu, Victoria H Williams, Alice B Schindler, Janet Brooks, J Raphael Gibbs, Dena G Hernandez, Debra Ehrlich, Andrew B Singleton, Derek P Narendra.
      PRKN mutations are the most common recessive cause of Parkinson's disease and are a promising target for gene and cell replacement therapies. Identification of biallelic PRKN patients at the population scale, however, remains a challenge, as roughly half are copy number variants and many single nucleotide polymorphisms are of unclear significance. Additionally, the true prevalence and disease risk associated with heterozygous PRKN mutations is unclear, as a comprehensive assessment of PRKN mutations has not been performed at a population scale. To address these challenges, we evaluated PRKN mutations in two cohorts with near complete genotyping of both single nucleotide polymorphisms and copy number variants: the NIH-PD + AMP-PD cohort, the largest Parkinson's disease case-control cohort with whole genome sequencing data from 4094 participants, and the UK Biobank, the largest cohort study with whole exome sequencing and genotyping array data from 200 606 participants. Using the NIH-PD participants, who were genotyped using whole genome sequencing, genotyping array, and multi-plex ligation-dependent probe amplification, we validated genotyping array for the detection of copy number variants. Additionally, in the NIH-PD cohort, functional assays of patient fibroblasts resolved variants of unclear significance in biallelic carriers and suggested that cryptic loss of function variants in monoallelic carriers are not a substantial confounder for association studies. In the UK Biobank, we identified 2692 PRKN copy number variants from genotyping array data from nearly half a million participants (the largest collection to date). Deletions or duplications involving exon 2 accounted for roughly half of all copy number variants and the vast majority (88%) involved exons 2, 3, or 4. In the UK Biobank, we found a pathogenic PRKN mutation in 1.8% of participants and two mutations in ∼1/7800 participants. Those with one PRKN pathogenic variant were as likely as non-carriers to have Parkinson's disease [odds ratio = 0.91 (0.58-1.38), P-value 0.76] or a parent with Parkinson's disease [odds ratio = 1.12 (0.94-1.31), P-value = 0.19]. Similarly, those in the NIH-PD + AMP + PD cohort with one PRKN pathogenic variant were as likely as non-carriers to have Parkinson's disease [odds ratio = 1.29 (0.74-2.38), P-value = 0.43]. Together our results demonstrate that heterozygous pathogenic PRKN mutations are common in the population but do not increase the risk of Parkinson's disease.
    Keywords:  PARK2; early onset Parkinson’s disease; mitophagy; parkin; young onset Parkinson’s disease
    DOI:  https://doi.org/10.1093/brain/awab456
  10. Neuromuscul Disord. 2022 May 14. pii: S0960-8966(22)00145-6. [Epub ahead of print]
    232nd ENMC international workshop: Recommendations for treatment of mitochondrial DNA maintenance disorders. 16 - 18 June 2017, Heemskerk, The Netherlands.
    232nd ENMC Workshop Participants
      
    DOI:  https://doi.org/10.1016/j.nmd.2022.05.008
  11. J Cardiovasc Pharmacol. 2022 Feb 18.
    Mitochondrial Transplantation: A Unique Treatment Strategy.
    Manli Zhou, Yunfeng Yu, Ying Luo, Xiaoxin Luo, Yifan Zhang, Xiahui Zhou, Yilei Hu, Weixiong Jian.
      Mitochondrial transplantation refers to the process of introducing isolated mitochondria into a damaged area of the heart or other organs. In the past decade, this technique has been continuously updated as the fundamental research on the repair of damaged cells or tissues. Particularly, in the field of heart protection from ischemia-reperfusion injury, the MT therapy has been developed to the clinical trial stage. Generally speaking, the goal of therapeutic intervention is to replace damaged mitochondria or increase the transfer of mitochondria between cells so as to improve mitochondrial dysfunction. In this review, we summarized the studies on mitochondrial transplantation conducted at different time nodes and outlined a range of different methods for delivering mitochondria into the target site. Finally, we described the applications of mitochondrial transplantation in different diseases, and discussed the clinical studies of human mitochondrial transplantation currently in progress as well as the problems that need to be overcome. We hope to provide new ideas for the treatment of mitochondrial defects related diseases.
    DOI:  https://doi.org/10.1097/FJC.0000000000001247
  12. Elife. 2022 May 31. pii: e69802. [Epub ahead of print]11
    High-intensity interval training remodels the proteome and acetylome of human skeletal muscle.
    Morten Hostrup, Anders Krogh Lemminger, Ben Stocks, Alba Gonzalez-Franquesa, Jeppe Kjærgaard Larsen, Julia Prats Quesada, Martin Thomassen, Brian Tate Weinert, Jens Bangsbo, Atul Shahaji Deshmukh.
      Exercise is an effective strategy in the prevention and treatment of metabolic diseases. Alterations in the skeletal muscle proteome, including post-translational modifications, regulate its metabolic adaptations to exercise. Here, we examined the effect of high-intensity interval training (HIIT) on the proteome and acetylome of human skeletal muscle, revealing the response of 3168 proteins and 1263 lysine acetyl-sites on 464 acetylated proteins. We identified global protein adaptations to exercise training involved in metabolism, excitation-contraction coupling, and myofibrillar calcium sensitivity. Furthermore, HIIT increased the acetylation of mitochondrial proteins, particularly those of complex V. We also highlight the regulation of exercise-responsive histone acetyl-sites. These data demonstrate the plasticity of the skeletal muscle proteome and acetylome, providing insight into the regulation of contractile, metabolic and transcriptional processes within skeletal muscle. Herein, we provide a substantial hypothesis-generating resource to stimulate further mechanistic research investigating how exercise improves metabolic health.
    Keywords:  acetylation; biochemistry; calcium sensitivity; chemical biology; computational biology; exercise; human; mitochondria; proteomics; skeletal muscle; systems biology
    DOI:  https://doi.org/10.7554/eLife.69802
  13. Prog Neurobiol. 2022 May 27. pii: S0301-0082(22)00075-2. [Epub ahead of print] 102289
    Boosting mitochondrial health to counteract neurodegeneration.
    Johannes Burtscher, Mario Romani, Greta Bernardo, Traian Popa, Elena Ziviani, Friedhelm C Hummel, Vincenzo Sorrentino, Grégoire P Millet.
      Mitochondrial health is based on a delicate balance of specific mitochondrial functions (e.g. metabolism, signaling, dynamics) that are impaired in neurodegenerative diseases. Rescuing mitochondrial function by selectively targeting mitochondrial stressors, such as reactive oxygen species, inflammation or proteotoxic insults ("bottom-up" approaches) thus is a widely investigated therapeutic strategy. While successful in preclinical studies, these approaches have largely failed to show clear clinical benefits. Promoting the capacity of mitochondria - and other cellular components - to restore a healthy cellular environment is a promising complementary or alternative approach. Herein, we provide a non-technical overview for neurologists and scientists interested in brain metabolism on neuroprotective strategies targeting mitochondria and focus on top-down interventions such as metabolic modulators, exercise, dietary restriction, brain stimulation and conditioning. We highlight general conceptual differences to bottom-up approaches and provide hypotheses on how these mechanistically comparatively poorly characterized top-down therapies may work, discussing notably mitochondrial stress responses and mitohormesis.
    Keywords:  ageing; conditioning; exercise; hormesis; mitochondria; neurodegeneration
    DOI:  https://doi.org/10.1016/j.pneurobio.2022.102289
  14. Chem Sci. 2022 Apr 20. 13(16): 4498-4511
    Data-driven discovery of cardiolipin-selective small molecules by computational active learning.
    Bernadette Mohr, Kirill Shmilovich, Isabel S Kleinwächter, Dirk Schneider, Andrew L Ferguson, Tristan Bereau.
      Subtle variations in the lipid composition of mitochondrial membranes can have a profound impact on mitochondrial function. The inner mitochondrial membrane contains the phospholipid cardiolipin, which has been demonstrated to act as a biomarker for a number of diverse pathologies. Small molecule dyes capable of selectively partitioning into cardiolipin membranes enable visualization and quantification of the cardiolipin content. Here we present a data-driven approach that combines a deep learning-enabled active learning workflow with coarse-grained molecular dynamics simulations and alchemical free energy calculations to discover small organic compounds able to selectively permeate cardiolipin-containing membranes. By employing transferable coarse-grained models we efficiently navigate the all-atom design space corresponding to small organic molecules with molecular weight less than ≈500 Da. After direct simulation of only 0.42% of our coarse-grained search space we identify molecules with considerably increased levels of cardiolipin selectivity compared to a widely used cardiolipin probe 10-N-nonyl acridine orange. Our accumulated simulation data enables us to derive interpretable design rules linking coarse-grained structure to cardiolipin selectivity. The findings are corroborated by fluorescence anisotropy measurements of two compounds conforming to our defined design rules. Our findings highlight the potential of coarse-grained representations and multiscale modelling for materials discovery and design.
    DOI:  https://doi.org/10.1039/d2sc00116k
  15. Mol Genet Metab. 2022 Apr 18. pii: S1096-7192(22)00299-2. [Epub ahead of print]
    NAXE deficiency: A neurometabolic disorder of NAD(P)HX repair amenable for metabolic correction.
    Joshua Manor, Daniel Calame, Charul Gijavanekar, Kristen Fisher, Jill Hunter, Elizabeth Mizerik, Carlos Bacino, Fernando Scaglia, Sarah H Elsea.
      The NAD(P)HX repair system is a metabolite damage repair mechanism responsible for restoration of NADH and NADPH after their inactivation by hydration. Deficiency in either of its two enzymes, NAD(P)HX dehydratase (NAXD) or NAD(P)HX epimerase (NAXE), causes a fatal neurometabolic disorder characterized by decompensations precipitated by inflammatory stress. Clinical findings include rapidly progressive muscle weakness, ataxia, ophthalmoplegia, and motor and cognitive regression, while neuroimaging abnormalities are subtle or nonspecific, making a clinical diagnosis challenging. During stress, nonenzymatic conversion of NAD(P)H to NAD(P)HX increases, and in the absence of repair, NAD(P)H is depleted, and NAD(P)HX accumulates, leading to decompensation; however, the contribution of each to the metabolic derangement is not established. Herein, we summarize the clinical knowledge of NAXE deficiency from 30 cases and lessons learned about disease pathogenesis from cell cultures and model organisms and describe a metabolomics signature obtained by untargeted metabolomics analysis in one case at the time of crisis and after initiation of treatment. Overall, biochemical findings support a model of acute depletion of NAD+, signs of mitochondrial dysfunction, and altered lipidomics. These findings are further substantiated by untargeted metabolomics six months post-crisis showing that niacin supplementation reverses primary metabolomic abnormalities concurrent with improved clinical status.
    Keywords:  Fever induced encephalopathy; Mitochondrial dysfunction; NAD(+); NAD(P)HX epimerase; NAXE; Neurometabolic disorders; PEBEL1; Pellagra
    DOI:  https://doi.org/10.1016/j.ymgme.2022.04.003
  16. J Lipid Atheroscler. 2022 May;11(2): 111-132
    NAD+ and Vascular Dysfunction: From Mechanisms to Therapeutic Opportunities.
    Mahmoud Abdellatif, Heiko Bugger, Guido Kroemer, Simon Sedej.
      Nicotinamide adenine dinucleotide (NAD+) is an essential and pleiotropic coenzyme involved not only in cellular energy metabolism, but also in cell signaling, epigenetic regulation, and post-translational protein modifications. Vascular disease risk factors are associated with aberrant NAD+ metabolism. Conversely, the therapeutic increase of NAD+ levels through the administration of NAD+ precursors or inhibitors of NAD+-consuming enzymes reduces chronic low-grade inflammation, reactivates autophagy and mitochondrial biogenesis, and enhances oxidative metabolism in vascular cells of humans and rodents with vascular pathologies. As such, NAD+ has emerged as a potential target for combatting age-related cardiovascular and cerebrovascular disorders. This review discusses NAD+-regulated mechanisms critical for vascular health and summarizes new advances in NAD+ research directly related to vascular aging and disease, including hypertension, atherosclerosis, coronary artery disease, and aortic aneurysms. Finally, we enumerate challenges and opportunities for NAD+ repletion therapy while anticipating the future of this exciting research field, which will have a major impact on vascular medicine.
    Keywords:  Aging; Autophagy; Hypertension; Inflammation; Mitochondria; Nicotinamide adenine dinucleotide; Vascular disease
    DOI:  https://doi.org/10.12997/jla.2022.11.2.111
  17. Hum Mutat. 2022 May 29.
    Guidelines for clinical interpretation of variant pathogenicity using RNA phenotypes.
    Dmitrii Smirnov, Lea D Schlieben, Fatemeh Peymani, Riccardo Berutti, Holger Prokisch.
      Over the last five years, RNA sequencing (RNA-seq) has been established and is increasingly applied as an effective approach complementary to DNA sequencing in molecular diagnostics. Currently, three RNA phenotypes, aberrant expression, aberrant splicing, and allelic imbalance, are considered to provide information about pathogenic variants. By providing a high-throughput, transcriptome-wide functional readout on variants causing aberrant RNA phenotypes, RNA-seq has increased diagnostic rates by about 15% over whole-exome sequencing. This breakthrough encouraged the development of computational tools and pipelines aiming to streamline RNA-seq analysis for implementation in clinical diagnostics. Although a number of studies showed the added value of RNA-seq for the molecular diagnosis of individuals with Mendelian disorders, there is no formal consensus on assessing variant pathogenicity strength based on RNA phenotypes. Taking RNA-seq as a functional assay for genetic variants, we evaluated the value of statistical significance and effect size of RNA phenotypes as evidence for the strength of variant pathogenicity. This was determined by the analysis of 394 pathogenic variants, of which 198 were associated with aberrant RNA phenotypes and 723 benign variants. Overall, this study seeks to establish recommendations for integrating functional RNA-seq data into the ACMG/AMP guidelines classification system. This article is protected by copyright. All rights reserved.
    Keywords:  RNA sequencing; guidelines; rare disorders; variant interpretation
    DOI:  https://doi.org/10.1002/humu.24416
  18. Mol Cell Proteomics. 2022 May 30. pii: S1535-9476(22)00062-7. [Epub ahead of print] 100254
    New views of old proteins: clarifying the enigmatic proteome.
    Kristin E Burnum-Johnson, Thomas P Conrads, Richard R Drake, Amy E Herr, Ravi Iyengar, Ryan T Kelly, Emma Lundberg, Michael J MacCoss, Alexandra Naba, Garry P Nolan, Pavel A Pevzner, Karin D Rodland, Salvatore Sechi, Nikolai Slavov, Jeffrey M Spraggins, Jennifer E Van Eyk, Marc Vidal, Christine Vogel, David R Walt, Neil L Kelleher.
      All human diseases involve proteins, yet our current tools to characterize and quantify them are limited. To better elucidate proteins across space, time, and molecular composition, we provide a >10 year projection for technologies to meet the challenges that protein biology presents. With a broad perspective, we discuss grand opportunities to transition the science of proteomics into a more propulsive enterprise. Extrapolating recent trends, we describe a next generation of approaches to define, quantify and visualize the multiple dimensions of the proteome, thereby transforming our understanding and interactions with human disease in the coming decade.
    Keywords:  biotechnology; proteins; proteomics; single molecule sequencing; single-cell biology
    DOI:  https://doi.org/10.1016/j.mcpro.2022.100254
  19. Nat Commun. 2022 May 31. 13(1): 3023
    Computationally designed hyperactive Cas9 enzymes.
    Pascal D Vos, Giulia Rossetti, Jessica L Mantegna, Stefan J Siira, Andrianto P Gandadireja, Mitchell Bruce, Samuel A Raven, Olga Khersonsky, Sarel J Fleishman, Aleksandra Filipovska, Oliver Rackham.
      The ability to alter the genomes of living cells is key to understanding how genes influence the functions of organisms and will be critical to modify living systems for useful purposes. However, this promise has long been limited by the technical challenges involved in genetic engineering. Recent advances in gene editing have bypassed some of these challenges but they are still far from ideal. Here we use FuncLib to computationally design Cas9 enzymes with substantially higher donor-independent editing activities. We use genetic circuits linked to cell survival in yeast to quantify Cas9 activity and discover synergistic interactions between engineered regions. These hyperactive Cas9 variants function efficiently in mammalian cells and introduce larger and more diverse pools of insertions and deletions into targeted genomic regions, providing tools to enhance and expand the possible applications of CRISPR-based gene editing.
    DOI:  https://doi.org/10.1038/s41467-022-30598-9
  20. IUBMB Life. 2022 May 30.
    Mitochondrial E3 ubiquitin ligase 1 (MUL1) as a novel therapeutic target for diseases associated with mitochondrial dysfunction.
    Ximena Calle, Valeria Garrido-Moreno, Erik Lopez, Ignacio Norambuena-Soto, Daniela Martínez, Allan Peñaloza-Otárola, Angelo Troncossi, Alejandra Guerrero-Moncayo, Angélica Ortega, Vinicius Maracaja-Coutinho, Valentina Parra, Mario Chiong, Sergio Lavandero.
      Mitochondrial E3 ubiquitin ligase (MUL1) is a mitochondrial outer membrane-anchored protein-containing transmembrane domains in both its N- and C-terminal regions, where both are exposed to the cytosol. Interestingly the C-terminal region has a RING finger domain responsible for its E3 ligase activity, as ubiquitin or in SUMOylation, interacting with proteins related to mitochondrial fusion and fission, cell survival, and tumor suppressor proteins, such as Akt. Therefore, MUL1 is involved in various cellular processes, such as mitochondrial dynamics, inter-organelle communication, proliferation, mitophagy, immune response, inflammation and cell apoptosis. MUL1 is expressed at a higher basal level in the heart, immune system organs, and blood. Here, we discuss the role of MUL1 in mitochondrial dynamics and its function in various pathological models, both in vitro and in vivo. In this context, we describe the role of MUL1 in: (1) the inflammatory response, by regulating NF-κB activity, (2) cancer, by promoting cell death and regulating exonuclear function of proteins, such as p53 (3) neurological diseases, by maintaining communication with other organelles and interacting with proteins to eliminate damaged organelles and (4) cardiovascular diseases, by maintaining mitochondrial fusion/fission homeostasis. In this review, we summarize the latest advances in the physiological and pathological functions of MUL1. We also describe the different substrates of MUL1, acting as a positive or negative regulator in various pathologies associated with mitochondrial dysfunction. In conclusion, MUL1 could be a potential key target for the development of therapies that focus on ensuring the functionality of the mitochondrial network and, furthermore, the quality control of intracellular components by synchronously modulating the activity of different cellular mechanisms involved in the aforementioned pathologies. This, in turn, will guide the development of targeted therapies. This article is protected by copyright. All rights reserved.
    Keywords:  Akt; C1orf166; FLJ12875; GIDE; MAPL; MULAN; Mitochondrial E3 ubiquitin ligase 1; RNF218; cell death; inflammation; mitochondria morphology
    DOI:  https://doi.org/10.1002/iub.2657
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