bims-mitdis 2024-09-22 papers

bims-mitdis

Biomed News

on Mitochondrial disorders

Issue of 2024–09–22
twenty-one papers selected by
Catalina Vasilescu, Helmholz Munich

Biallelic PTPMT1 variants disrupt cardiolipin metabolism and lead to a neurodevelopmental syndrome.
Quantitative proteomics of patient fibroblasts reveal biomarkers and diagnostic signatures of mitochondrial disease.
Overactive mitochondrial DNA replication disrupts perinatal cardiac maturation.
Streamlined process for effective and strand-selective mitochondrial base editing using mitoBEs.
Characterization of Shy1, the Schizosaccharomyces pombe homolog of human SURF1.
Multiple distinct evolutionary mechanisms govern the dynamics of selfish mitochondrial genomes in Caenorhabditis elegans.
Alternative splicing of Mff regulates AMPK-mediated phosphorylation, mitochondrial fission and antiviral response.
Sensory-motor neuropathy in Mfn2 T105M knock-in mice and its reversal by a novel piperine-derived mitofusin activator.
Discovery of novel SS-31 (d-Arg-dimethylTyr-Lys-Phe-NH2) derivatives as potent agents to ameliorate inflammation and increase mitochondrial ATP synthesis.
Activation of parkin by a molecular glue.
Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures.
Manipulating mitochondrial reactive oxygen species alters survival in unexpected ways in a Drosophila Cdk5 model of neurodegeneration.
CoA synthase plays a critical role in neurodevelopment and neurodegeneration.
Atomic vacancies of molybdenum disulfide nanoparticles stimulate mitochondrial biogenesis.
Glial swip-10 controls systemic mitochondrial function, oxidative stress, and neuronal viability via copper ion homeostasis.
Complex trait associations in rare diseases and impacts on Mendelian variant interpretation.
TBK1 adaptor AZI2/NAP1 regulates NDP52-driven mitochondrial autophagy.
Lys716 in the transmembrane domain of yeast mitofusin Fzo1 modulates anchoring and fusion.
Tissue-aware interpretation of genetic variants advances the etiology of rare diseases.
Genome-scale models in human metabologenomics.
Invariance of Mitochondria and Synapses in the Primary Visual Cortex of Mammals Provides Insight Into Energetics and Function.

Brain. 2024 Aug 30. pii: awae268. [Epub ahead of print]

Biallelic PTPMT1 variants disrupt cardiolipin metabolism and lead to a neurodevelopmental syndrome.

Micol Falabella, Chiara Pizzamiglio, Luis Carlos Tabara, Benjamin Munro, Mohamed S Abdel-Hamid, Ece Sonmezler, William L Macken, Shanti Lu, Lisa Tilokani, Padraig J Flannery, Nina Patel, Simon A S Pope, Simon J R Heales, Dania B H Hammadi, Charlotte L Alston, Robert W Taylor, Hanns Lochmuller, Cathy E Woodward, Robyn Labrum, Jana Vandrovcova, Henry Houlden, Efstathia Chronopoulou, Germaine Pierre, Reza Maroofian, Michael G Hanna, Jan-Willem Taanman, Semra Hiz, Yavuz Oktay, Maha S Zaki, Rita Horvath, Julien Prudent, Robert D S Pitceathly.

  Primary mitochondrial diseases (PMDs) are among the most common inherited neurological disorders. They are caused by pathogenic variants in mitochondrial or nuclear DNA that disrupt mitochondrial structure and/or function, leading to impaired oxidative phosphorylation (OXPHOS). One emerging subcategory of PMDs involves defective phospholipid (PL) metabolism. Cardiolipin (CL), the signature PL of mitochondria, resides primarily in the inner mitochondrial membrane, where it is biosynthesised and remodelled via multiple enzymes and is fundamental to several aspects of mitochondrial biology. Genes that contribute to CL biosynthesis have recently been linked with PMD. However, the pathophysiological mechanisms that underpin human CL-related PMDs are not fully characterised. Here, we report six individuals, from three independent families, harbouring biallelic variants in PTPMT1, a mitochondrial tyrosine phosphatase required for de novo CL biosynthesis. All patients presented with a complex, neonatal/infantile onset neurological and neurodevelopmental syndrome comprising developmental delay, microcephaly, facial dysmorphism, epilepsy, spasticity, cerebellar ataxia and nystagmus, sensorineural hearing loss, optic atrophy, and bulbar dysfunction. Brain MRI revealed a variable combination of corpus callosum thinning, cerebellar atrophy, and white matter changes. Using patient-derived fibroblasts and skeletal muscle tissue, combined with cellular rescue experiments, we characterise the molecular defects associated with mutant PTPMT1 and confirm the downstream pathogenic effects that loss of PTPMT1 has on mitochondrial structure and function. To further characterise the functional role of PTPMT1 in CL homeostasis, we established a zebrafish ptpmt1 knockout model associated with abnormalities in body size, developmental alterations, decreased total CL levels, and OXPHOS deficiency. Together, these data indicate that loss of PTPMT1 function is associated with a new autosomal recessive PMD caused by impaired CL metabolism, highlight the contribution of aberrant CL metabolism towards human disease, and emphasise the importance of normal CL homeostasis during neurodevelopment.

Keywords:  cardiolipin; mitochondria; mitochondrial dynamics; neurodevelopmental syndrome; primary mitochondrial disease

DOI:  https://doi.org/10.1093/brain/awae268
JCI Insight. 2024 Sep 17. pii: e178645. [Epub ahead of print]

Quantitative proteomics of patient fibroblasts reveal biomarkers and diagnostic signatures of mitochondrial disease.

Sandrina P Correia, Marco F Moedas, Lucie S Taylor, Karin Naess, Albert Z Lim, Robert McFarland, Zuzanna Kazior, Anastasia Rumyantseva, Rolf Wibom, Martin Engvall, Helene Bruhn, Nicole Lesko, Ákos Végvári, Lukas Käll, Matthias Trost, Charlotte L Alston, Christoph Freyer, Robert W Taylor, Anna Wedell, Anna Wredenberg.

   BACKGROUND: Mitochondrial diseases belong to the group of inborn errors of metabolism (IEM), with a prevalence of 1:2,000-1:5,000. They are the most common form of IEM, but despite advances in next-generation sequencing technologies, almost half of the patients are left genetically undiagnosed.
METHODS: We investigated a cohort of 61 patients with defined mitochondrial disease to improve diagnostics, identify biomarkers, and correlate metabolic pathways to specific disease groups. Clinical presentations were structured using human phenotype ontology terms, and mass spectrometry-based proteomics was performed on primary fibroblasts. Additionally, we integrated six patients carrying variants of uncertain significance (VUS) to test proteomics as a diagnostic expansion.
RESULTS: Proteomic profiles from patient samples could be classified according to their biochemical and genetic characteristics, with the expression of five proteins (GPX4, MORF4L1, MOXD1, MSRA and TMED9) correlating with the disease cohort, and thus, acting as putative biomarkers. Pathway analysis showed a deregulation of inflammatory and mitochondrial stress responses. This included the upregulation of glycosphingolipid metabolism and mitochondrial protein import, as well as the downregulation of arachidonic acid metabolism. Furthermore, we could assign pathogenicity to a VUS in MRPS23 by demonstrating the loss of associated mitochondrial ribosome subunits.
CONCLUSION: We established mass spectrometry-based proteomics on patient fibroblasts as a viable and versatile tool for diagnosing patients with mitochondrial disease.
FUNDING: The NovoNordisk Foundation, Knut and Alice Wallenberg Foundation, Wellcome Centre for Mitochondrial Research, UK Medical Research Council, and the UK NHS Highly Specialised Service for Rare Mitochondrial Disorders of Adults and Children.

Keywords:  Metabolism; Mitochondria; Molecular diagnosis; Proteomics

DOI:  https://doi.org/10.1172/jci.insight.178645
Nat Commun. 2024 Sep 14. 15(1): 8066

Overactive mitochondrial DNA replication disrupts perinatal cardiac maturation.

Juan C Landoni, Semin Erkul, Tuomas Laalo, Steffi Goffart, Riikka Kivelä, Karlo Skube, Anni I Nieminen, Sara A Wickström, James Stewart, Anu Suomalainen.

High mitochondrial DNA (mtDNA) amount has been reported to be beneficial for resistance and recovery of metabolic stress, while increased mtDNA synthesis activity can drive aging signs. The intriguing contrast of these two mtDNA boosting outcomes prompted us to jointly elevate mtDNA amount and frequency of replication in mice. We report that high activity of mtDNA synthesis inhibits perinatal metabolic maturation of the heart. The offspring of the asymptomatic parental lines are born healthy but manifest dilated cardiomyopathy and cardiac collapse during the first days of life. The pathogenesis, further enhanced by mtDNA mutagenesis, involves prenatal upregulation of mitochondrial integrated stress response and the ferroptosis-inducer MESH1, leading to cardiac fibrosis and cardiomyocyte death after birth. Our evidence indicates that the tight control of mtDNA replication is critical for early cardiac homeostasis. Importantly, ferroptosis sensitivity is a potential targetable mechanism for infantile-onset cardiomyopathy, a common manifestation of mitochondrial diseases.

DOI: https://doi.org/10.1038/s41467-024-52164-1
Biophys Rep. 2024 Aug 31. 10(4): 191-200

Streamlined process for effective and strand-selective mitochondrial base editing using mitoBEs.

Xiaoxue Zhang, Zongyi Yi, Wei Tang, Wensheng Wei.

  Mitochondrial base editing tools hold great promise for the investigation and treatment of mitochondrial diseases. Mitochondrial DNA base editors (mitoBEs) integrate a programmable transcription-activator-like effector (TALE) protein with single-stranded DNA deaminase (TadA8e-V106W, APOBEC1, etc.) and nickase (MutH, Nt.BspD6I(C), etc.) to achieve heightened precision and efficiency in mitochondrial base editing. This innovative mitochondrial base editing tool exhibits a number of advantages, including strand-selectivity for editing, high efficiency, and the capacity to perform diverse types of base editing on the mitochondrial genome by employing various deaminases. In this context, we provide a detailed experimental protocol for mitoBEs to assist others in achieving proficient mitochondrial base editing.

Keywords:  Deaminase; Mitochondrial DNA base editors (mitoBEs); Nickase; Transcription-activator-like effector (TALE)

DOI:  https://doi.org/10.52601/bpr.2024.240010
Sci Rep. 2024 09 17. 14(1): 21678

Characterization of Shy1, the Schizosaccharomyces pombe homolog of human SURF1.

Ying Luo, Yuanqi Xu, Fawad Ahmad, Gang Feng, Ying Huang.

  Cytochrome c oxidase (complex IV) is the terminal enzyme in the mitochondrial respiratory chain. As a rare neurometabolic disorder caused by mutations in the human complex IV assembly factor SURF1, Leigh Syndrome (LS) is associated with complex IV deficiency. In this study, we comprehensively characterized Schizosaccharomyces pombe Shy1, the homolog of human SURF1. Bioinformatics analysis revealed that Shy1 contains a conserved SURF1 domain that links to the biogenesis of complex IV and shares high structural similarity with its homologs in Saccharomyces cerevisiae and humans. Our study showed that Shy1 is required for the expression of mtDNA-encoded genes and physically interacts with structural subunits and assembly factors of complex IV. Interestingly, Rip1, the subunit of ubiquinone-cytochrome c oxidoreductase or cytochrome bc1 complex (complex III), can also co-immunoprecipitate with Shy1, suggesting Shy1 may be involved in the assembly of the mitochondrial respiratory chain supercomplexes. This conclusion is further corroborated by our BN-PAGE analysis. Unlike its homologs, deletion of shy1 does not critically disrupt respiratory chain assembly, indicating the presence of the compensatory mechanism(s) within S. pombe that ensure mitochondrial functionality. Collectively, our investigation elucidates that Shy1 plays a pivotal role in the sustainability of the regular function of mitochondria by participating in the assembly of complex IV in S. pombe.

Keywords:   Schizosaccharomyces pombe ; SURF1; Shy1; cytochrome c oxidase; mitochondria

DOI:  https://doi.org/10.1038/s41598-024-72681-9
Nat Commun. 2024 Sep 19. 15(1): 8237

Multiple distinct evolutionary mechanisms govern the dynamics of selfish mitochondrial genomes in Caenorhabditis elegans.

Bryan L Gitschlag, Claudia V Pereira, James P Held, David M McCandlish, Maulik R Patel.

Cells possess multiple mitochondrial DNA (mtDNA) copies, which undergo semi-autonomous replication and stochastic inheritance. This enables mutant mtDNA variants to arise and selfishly compete with cooperative (wildtype) mtDNA. Selfish mitochondrial genomes are subject to selection at different levels: they compete against wildtype mtDNA directly within hosts and indirectly through organism-level selection. However, determining the relative contributions of selection at different levels has proven challenging. We overcome this challenge by combining mathematical modeling with experiments designed to isolate the levels of selection. Applying this approach to many selfish mitochondrial genotypes in Caenorhabditis elegans reveals an unexpected diversity of evolutionary mechanisms. Some mutant genomes persist at high frequency for many generations, despite a host fitness cost, by aggressively outcompeting cooperative genomes within hosts. Conversely, some mutant genomes persist by evading inter-organismal selection. Strikingly, the mutant genomes vary dramatically in their susceptibility to genetic drift. Although different mechanisms can cause high frequency of selfish mtDNA, we show how they give rise to characteristically different distributions of mutant frequency among individuals. Given that heteroplasmic frequency represents a key determinant of phenotypic severity, this work outlines an evolutionary theoretic framework for predicting the distribution of phenotypic consequences among individuals carrying a selfish mitochondrial genome.

DOI: https://doi.org/10.1038/s41467-024-52596-9
Pharmacol Res. 2024 Sep 16. pii: S1043-6618(24)00359-1. [Epub ahead of print] 107414

Alternative splicing of Mff regulates AMPK-mediated phosphorylation, mitochondrial fission and antiviral response.

Yuki Hanada, Risa Maeda, Takaya Ishihara, Masaki Nakahashi, Yuichi Matsushima, Emi Ogasawara, Toshihiko Oka, Naotada Ishihara.

  Mitochondrial morphology and function change dynamically in response to intracellular signaling and the surrounding environment. The mitochondrial fission factor Mff, which localizes to the outer mitochondrial membrane, mediates not only mitochondrial fission by recruiting the dynamin-related GTPase Drp1 to mitochondrial fission sites but also the double-stranded RNA-induced antiviral response on mitochondria through mitochondrial antiviral signaling (MAVS). Mff is reported to be regulated by AMP-activated protein kinase (AMPK)-mediated protein phosphorylation and alternative pre-mRNA splicing; however, the relationships among RNA splicing, phosphorylation, and multiple functions of Mff have not been fully understood. Here, we showed that mouse Mff has a tissue-specific splicing pattern, and at least eight Mff splice isoforms were expressed in mouse embryonic fibroblasts (MEFs). We introduced single Mff isoforms into Mff knockout MEFs and found that insertion of exon 6 just after the phosphorylation site, by the alternative splicing, reduced its phosphorylation by AMPK and its functions in mitochondrial fission and the antiviral response. In addition, the underlying mechanism repressing these functions was independent of phosphorylation. These results indicate that multiple functions of Mff on mitochondria are regulated by AMPK-mediated phosphorylation and alternative splicing, under the control of energy metabolism and cellular differentiation.

Keywords:  Alternative splicing; Antiviral innate immune response; Energy, metabolism; Mitochondrial fission; mitochondria

DOI:  https://doi.org/10.1016/j.phrs.2024.107414
J Pharmacol Exp Ther. 2024 Sep 16. pii: JPET-AR-2024-002258. [Epub ahead of print]

Sensory-motor neuropathy in Mfn2 T105M knock-in mice and its reversal by a novel piperine-derived mitofusin activator.

Jochen Weigele, Lihong Zhang, Antonietta Franco, Etienne Cartier, Gerald W Dorn.

  Mitochondrial dysfunction is a hallmark of many genetic neurodegenerative diseases, but therapeutic options to reverse mitochondrial dysfunction are limited. While recent studies support the possibility of improving mitochondrial fusion/fission dynamics and motility to correct mitochondrial dysfunction and resulting neurodegeneration in Charcot-Marie-Tooth disease (CMT) and other neuropathies, the clinical utility of reported compounds and relevance of pre-clinical models are uncertain. Here, we describe motor and sensory neuron dysfunction characteristic of clinical CMT type 2A in a CRISPR/Casp-engineered Mfn2 Thr105Met (T105M) mutant knock-in mouse. We further demonstrate that daily oral treatment with a novel mitofusin activator derived from the natural product piperine can reverse these neurological phenotypes. Piperine derivative 8015 promoted mitochondrial fusion and motility in Mfn2-deficient cells in a mitofusin-dependent manner, and reversed mitochondrial dysfunction in cultured fibroblasts and reprogrammed motor neurons from a human CMT2A patient carrying the MFN2 T105M mutation. Like previous mitofusin activators, 8015 exhibited stereospecific functionality, but the more active stereoisomer, 8015-P2, is unique in that it has sub-nanomolar potency and undergoes entero-hepatic recirculation which extends its in vivo half-life. Daily administration of 8015-P2 to Mfn2 T105M knock-in mice for 6 weeks normalized neuromuscular and sensory dysfunction and corrected histological/ultrastructural neurodegeneration and neurogenic myoatrophy. These studies describe a more clinically relevant mouse model of CMT2A and an improved mitofusin activator derived from piperine. We posit that 8015-P2 and other piperine derivatives may benefit CMT2A or other neurodegenerative conditions wherein mitochondrial dysdynamism plays a contributory role. Significance Statement Mitochondrial dysfunction is widespread and broadly contributory in neurodegeneration, but difficult to target therapeutically. Here, we describe 8015-P2, a new small molecule mitofusin activator with ~10-fold greater potency and improved in vivo pharmacokinetics vs comparators, and demonstrate its rapid reversal of sensory and motor neuron dysfunction in an Mfn2 T105M knock-in mouse model of Charcot-Marie-Tooth disease type 2A. These findings further support the therapeutic approach of targeting mitochondrial dysdynamism in neurodegeneration.

Keywords:  Drug development; Neuroprotection; mitochondria

DOI:  https://doi.org/10.1124/jpet.124.002258
RSC Adv. 2024 Sep 18. 14(41): 29789-29799

Discovery of novel SS-31 (d-Arg-dimethylTyr-Lys-Phe-NH2) derivatives as potent agents to ameliorate inflammation and increase mitochondrial ATP synthesis.

Mei Li, Deyuan Kong, Liying Meng, Zheyi Wang, Zetai Bai, Guanzhao Wu.

Neuroinflammation and mitochondrial function are crucial for neuronal function and survival. SS-31 is a novel mitochondria-targeted peptide antioxidant that reduces mitochondrial reactive oxygen species production, increases ATP generation, protects the integrity of mitochondrial cristae and the mitochondrial respiratory chain, and reduces inflammatory responses. Exploring novel SS-31 derivatives is important for the treatment of neurodegenerative diseases. In this study, nineteen SS-31 derived peptides (5a-5s) were synthesized. Through cellular activity screening, we discovered that 5f and 5g exhibited significantly greater anti-inflammatory activity compared to SS-31, reducing LPS-induced TNF-α levels by 43% and 45%, respectively, at a concentration of 10 μM. Furthermore, treatment with 50 nM of 5f and 5g increased ATP synthesis by 42% and 41% in rotenone-induced HT22 cells and attenuated mitochondrial ROS production by preserving mitochondrial integrity. These findings demonstrate their direct protective effects on neuronal mitochondria. This work highlights the potential of 5f and 5g in the treatment of neurodegenerative diseases associated with inflammation and mitochondrial damage, offering a promising therapeutic avenue for mitochondrial-related conditions such as Alzheimer's disease.

DOI: https://doi.org/10.1039/d4ra05517a
Nat Commun. 2024 Sep 19. 15(1): 7707

Activation of parkin by a molecular glue.

Véronique Sauvé, Eric Stefan, Nathalie Croteau, Thomas Goiran, Rayan Fakih, Nupur Bansal, Adelajda Hadzipasic, Jing Fang, Paramasivam Murugan, Shimin Chen, Edward A Fon, Warren D Hirst, Laura F Silvian, Jean-François Trempe, Kalle Gehring.

Mutations in parkin and PINK1 cause early-onset Parkinson's disease (EOPD). The ubiquitin ligase parkin is recruited to damaged mitochondria and activated by PINK1, a kinase that phosphorylates ubiquitin and the ubiquitin-like domain of parkin. Activated phospho-parkin then ubiquitinates mitochondrial proteins to target the damaged organelle for degradation. Here, we present the mechanism of activation of a new class of small molecule allosteric modulators that enhance parkin activity. The compounds act as molecular glues to enhance the ability of phospho-ubiquitin (pUb) to activate parkin. Ubiquitination assays and isothermal titration calorimetry with the most active compound (BIO-2007817) identify the mechanism of action. We present the crystal structure of a closely related compound (BIO-1975900) bound to a complex of parkin and two pUb molecules. The compound binds next to pUb on RING0 and contacts both proteins. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) experiments confirm that activation occurs through release of the catalytic Rcat domain. In organello and mitophagy assays demonstrate that BIO-2007817 partially rescues the activity of parkin EOPD mutants, R42P and V56E, offering a basis for the design of activators as therapeutics for Parkinson's disease.

DOI: https://doi.org/10.1038/s41467-024-51889-3
Nat Methods. 2024 Sep 18.

Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures.

Seulki Kwon, Jordan Safer, Duyen T Nguyen, David Hoksza, Patrick May, Jeremy A Arbesfeld, Alan F Rubin, Arthur J Campbell, Alex Burgin, Sumaiya Iqbal.

Recent advances in AI-based methods have revolutionized the field of structural biology. Concomitantly, high-throughput sequencing and functional genomics have generated genetic variants at an unprecedented scale. However, efficient tools and resources are needed to link disparate data types-to 'map' variants onto protein structures, to better understand how the variation causes disease, and thereby design therapeutics. Here we present the Genomics 2 Proteins portal ( https://g2p.broadinstitute.org/ ): a human proteome-wide resource that maps 20,076,998 genetic variants onto 42,413 protein sequences and 77,923 structures, with a comprehensive set of structural and functional features. Additionally, the Genomics 2 Proteins portal allows users to interactively upload protein residue-wise annotations (for example, variants and scores) as well as the protein structure beyond databases to establish the connection between genomics to proteins. The portal serves as an easy-to-use discovery tool for researchers and scientists to hypothesize the structure-function relationship between natural or synthetic variations and their molecular phenotypes.

DOI: https://doi.org/10.1038/s41592-024-02409-0
Biol Open. 2024 Sep 18. pii: bio.060515. [Epub ahead of print]

Manipulating mitochondrial reactive oxygen species alters survival in unexpected ways in a Drosophila Cdk5 model of neurodegeneration.

Andrew P K Wodrich, Brent T Harris, Edward Giniger.

  Reactive oxygen species (ROS) are associated with aging and neurodegeneration, but the significance of this association remains obscure. Here, using a Drosophila Cdk5 model of age-related neurodegeneration, we probe this relationship in the pathologically relevant tissue, the brain, by quantifying three specific mitochondrial ROS and manipulating these redox species pharmacologically. Our goal is to ask whether pathology-associated changes in redox state are detrimental for survival, whether they may be beneficial responses to pathology, or whether they are covariates of pathology that do not alter viability. We find, surprisingly, that increasing mitochondrial H2O2 correlates with improved survival. We also find evidence that drugs that alter the mitochondrial glutathione redox potential modulate survival primarily through the compensatory effects they induce rather than through their direct effects on the final mitochondrial glutathione redox potential. We also find that the response to treatment with a redox-altering drug varies depending on the age and genotype of the individual receiving the drug as well as the duration of the treatment. These data have important implications for the design and interpretation of studies investigating the effect of redox state on health and disease as well as on efforts to modify the redox state to achieve therapeutic goals.

Keywords:  Cdk5; Mitochondria; Neurodegeneration; Reactive oxygen species (ROS)

DOI:  https://doi.org/10.1242/bio.060515
Front Cell Neurosci. 2024 ;18 1458475

CoA synthase plays a critical role in neurodevelopment and neurodegeneration.

Chiara Cavestro, Marco D'Amato, Maria Nicol Colombo, Floriana Cascone, Andrea Stefano Moro, Sonia Levi, Valeria Tiranti, Ivano Di Meo.

  Coenzyme A (CoA), which is widely distributed and vital for cellular metabolism, is a critical molecule essential in both synthesizing and breaking down key energy sources in the body. Inborn errors of metabolism in the cellular de novo biosynthetic pathway of CoA have been linked to human genetic disorders, emphasizing the importance of this pathway. The COASY gene encodes the bifunctional enzyme CoA synthase, which catalyzes the last two reactions of the CoA biosynthetic pathway and serves as one of the rate-limiting components of the pathway. Recessive variants of this gene cause an exceptionally rare and devastating disease called COASY protein-associated neurodegeneration (CoPAN) while complete loss-of-function variants in COASY have been identified in fetuses/neonates with Pontocerebellar Hypoplasia type 12 (PCH 12). Understanding why the different symptoms emerge in these disorders and what determines the development of one syndrome over the other is still not achieved. To shed light on the pathogenesis, we generated a new conditional animal model in which Coasy was deleted under the control of the human GFAP promoter. We used this mouse model to investigate how defects in the CoA biosynthetic pathway affect brain development. This model showed a broad spectrum of severity of the in vivo phenotype, ranging from very short survival (less than 2 weeks) to normal life expectancy in some animals. Surviving mice displayed a behavioral phenotype with sensorimotor defects. Ex vivo histological analysis revealed variable but consistent cerebral and cerebellar cortical hypoplasia, in parallel with a broad astrocytic hyper-proliferation in the cerebral cortex. In addition, primary astrocytes derived from this model exhibited lipid peroxidation, iron dyshomeostasis, and impaired mitochondrial respiration. Notably, Coasy ablation in radial glia and astrocytic lineage triggers abnormal neuronal development and chronic neuroinflammation, offering new insights into disease mechanisms.

Keywords:  COASY protein-associated neurodegeneration; CoA synthase; animal models; neurodegeneration; neurodevelopment; pontocerebellar hypoplasia type 12

DOI:  https://doi.org/10.3389/fncel.2024.1458475
Nat Commun. 2024 Sep 17. 15(1): 8136

Atomic vacancies of molybdenum disulfide nanoparticles stimulate mitochondrial biogenesis.

Kanwar Abhay Singh, John Soukar, Mohammad Zulkifli, Anna Kersey, Giriraj Lokhande, Sagnika Ghosh, Aparna Murali, Natalie M Garza, Harman Kaur, Justin N Keeney, Ramu Banavath, Hatice Ceylan Koydemir, Raquel Sitcheran, Irtisha Singh, Vishal M Gohil, Akhilesh K Gaharwar.

Diminished mitochondrial function underlies many rare inborn errors of energy metabolism and contributes to more common age-associated metabolic and neurodegenerative disorders. Thus, boosting mitochondrial biogenesis has been proposed as a potential therapeutic approach for these diseases; however, currently we have a limited arsenal of compounds that can stimulate mitochondrial function. In this study, we designed molybdenum disulfide (MoS2) nanoflowers with predefined atomic vacancies that are fabricated by self-assembly of individual two-dimensional MoS2 nanosheets. Treatment of mammalian cells with MoS2 nanoflowers increased mitochondrial biogenesis by induction of PGC-1α and TFAM, which resulted in increased mitochondrial DNA copy number, enhanced expression of nuclear and mitochondrial-DNA encoded genes, and increased levels of mitochondrial respiratory chain proteins. Consistent with increased mitochondrial biogenesis, treatment with MoS2 nanoflowers enhanced mitochondrial respiratory capacity and adenosine triphosphate production in multiple mammalian cell types. Taken together, this study reveals that predefined atomic vacancies in MoS2 nanoflowers stimulate mitochondrial function by upregulating the expression of genes required for mitochondrial biogenesis.

DOI: https://doi.org/10.1038/s41467-024-52276-8
Proc Natl Acad Sci U S A. 2024 Sep 24. 121(39): e2320611121

Glial swip-10 controls systemic mitochondrial function, oxidative stress, and neuronal viability via copper ion homeostasis.

Peter Rodriguez, Vrinda Kalia, Cristina Fenollar-Ferrer, Chelsea L Gibson, Zayna Gichi, Andre Rajoo, Carson D Matier, Aidan T Pezacki, Tong Xiao, Lucia Carvelli, Christopher J Chang, Gary W Miller, Andy V Khamoui, Jana Boerner, Randy D Blakely.

  Cuprous copper [Cu(I)] is an essential cofactor for enzymes that support many fundamental cellular functions including mitochondrial respiration and suppression of oxidative stress. Neurons are particularly reliant on mitochondrial production of ATP, with many neurodegenerative diseases, including Parkinson's disease, associated with diminished mitochondrial function. The gene MBLAC1 encodes a ribonuclease that targets pre-mRNA of replication-dependent histones, proteins recently found in yeast to reduce Cu(II) to Cu(I), and when mutated disrupt ATP production, elevates oxidative stress, and severely impacts cell growth. Whether this process supports neuronal and/or systemic physiology in higher eukaryotes is unknown. Previously, we identified swip-10, the putative Caenorhabditis elegans ortholog of MBLAC1, establishing a role for glial swip-10 in limiting dopamine (DA) neuron excitability and sustaining DA neuron viability. Here, we provide evidence from computational modeling that SWIP-10 protein structure mirrors that of MBLAC1 and locates a loss of function coding mutation at a site expected to disrupt histone RNA hydrolysis. Moreover, we find through genetic, biochemical, and pharmacological studies that deletion of swip-10 in worms negatively impacts systemic Cu(I) levels, leading to deficits in mitochondrial respiration and ATP production, increased oxidative stress, and neurodegeneration. These phenotypes can be offset in swip-10 mutants by the Cu(I) enhancing molecule elesclomol and through glial expression of wildtype swip-10. Together, these studies reveal a glial-expressed pathway that supports systemic mitochondrial function and neuronal health via regulation of Cu(I) homeostasis, a mechanism that may lend itself to therapeutic strategies to treat devastating neurodegenerative diseases.

Keywords:  C. elegans; copper; glia; neurodegeneration; swip-10

DOI:  https://doi.org/10.1073/pnas.2320611121
Nat Commun. 2024 Sep 18. 15(1): 8196

Complex trait associations in rare diseases and impacts on Mendelian variant interpretation.

Genomic Answers for Kids Consortium

Emerging evidence implicates common genetic variation - aggregated into polygenic scores (PGS) - in the onset and phenotypic presentation of rare diseases. Here, we comprehensively map individual polygenic liability for 1102 open-source PGS in a cohort of 3059 probands enrolled in the Genomic Answers for Kids (GA4K) rare disease study, revealing widespread associations between rare disease phenotypes and PGSs for common complex diseases and traits, blood protein levels, and brain and other organ morphological measurements. Using this resource, we demonstrate increased polygenic liability in probands with an inherited candidate disease variant (VUS) compared to unaffected carrier parents. Further, we show an enrichment for large-effect rare variants in putative core PGS genes for associated complex traits. Overall, our study supports and expands on previous findings of complex trait associations in rare diseases, implicates polygenic liability as a potential mechanism underlying variable penetrance of candidate causal variants, and provides a framework for identifying novel candidate rare disease genes.

DOI: https://doi.org/10.1038/s41467-024-52407-1
J Biol Chem. 2024 Sep 12. pii: S0021-9258(24)02276-2. [Epub ahead of print] 107775

TBK1 adaptor AZI2/NAP1 regulates NDP52-driven mitochondrial autophagy.

Ryu Endo, Hiroki Kinefuchi, Momoha Sawada, Reika Kikuchi, Waka Kojima, Noriyuki Matsuda, Koji Yamano.

  Damaged mitochondria are selectively eliminated in a process called mitophagy. PINK1 and Parkin amplify ubiquitin signals on damaged mitochondria, which are then recognized by autophagy adaptors to induce local autophagosome formation. NDP52 and OPTN, two essential mitophagy adaptors, facilitate de novo synthesis of pre-autophagosomal membranes near damaged mitochondria by linking ubiquitinated mitochondria and ATG8 family proteins and by recruiting core autophagy initiation components. The multifunctional serine/threonine kinase TBK1 also plays important roles in mitophagy. OPTN directly binds TBK1 to form a positive feedback loop for isolation membrane expansion. TBK1 is also thought to indirectly interact with NDP52; however, its role in NDP52-driven mitophagy remains largely unknown. Here, we focused on two TBK1 adaptors, AZI2/NAP1 and TBKBP1/SINTBAD, that are thought to mediate the TBK1-NDP52 interaction. We found that both AZI2 and TBKBP1 are recruited to damaged mitochondria during Parkin-mediated mitophagy. Further, a series of AZI2 and TBKBP1 knockout constructs combined with an OPTN knockout showed that AZI2, but not TBKBP1, impacts NDP52-driven mitophagy. In addition, we found that AZI2 at S318 is phosphorylated during mitophagy, the impairment of which slightly inhibits mitochondrial degradation. These results suggest that AZI2, in concert with TBK1, plays an important role in NDP52-driven mitophagy.

Keywords:  autophagy; mitochondria; mitophagy; polyubiquitin chain; serine/threonine protein kinase

DOI:  https://doi.org/10.1016/j.jbc.2024.107775
Structure. 2024 Sep 12. pii: S0969-2126(24)00334-4. [Epub ahead of print]

Lys716 in the transmembrane domain of yeast mitofusin Fzo1 modulates anchoring and fusion.

Raphaëlle Versini, Marc Baaden, Laetitia Cavellini, Mickaël M Cohen, Antoine Taly, Patrick F J Fuchs.

  Outer mitochondrial membrane fusion, a vital cellular process, is mediated by mitofusins. However, the underlying molecular mechanism remains elusive. We have performed extensive multiscale molecular dynamics simulations to predict a model of the transmembrane (TM) domain of the yeast mitofusin Fzo1. Coarse-grained simulations of the two TM domain helices, TM1 and TM2, reveal a stable interface, which is controlled by the charge status of residue Lys716. Atomistic replica-exchange simulations further tune our model, which is confirmed by a remarkable agreement with an independent AlphaFold2 (AF2) prediction of Fzo1 in complex with its fusion partner Ugo1. Furthermore, the presence of the TM domain destabilizes the membrane, even more if Lys716 is charged, which can be an asset for initiating fusion. The functional role of Lys716 was confirmed with yeast experiments, which show that mutating Lys716 to a hydrophobic residue prevents mitochondrial fusion.

Keywords:  Fzo1; Lys716; mitofusin; molecular modeling; outer mitochondrial membrane fusion; transmembrane domain

DOI:  https://doi.org/10.1016/j.str.2024.08.017
Mol Syst Biol. 2024 Sep 16.

Tissue-aware interpretation of genetic variants advances the etiology of rare diseases.

Chanan M Argov, Ariel Shneyour, Juman Jubran, Eric Sabag, Avigdor Mansbach, Yair Sepunaru, Emmi Filtzer, Gil Gruber, Miri Volozhinsky, Yuval Yogev, Ohad Birk, Vered Chalifa-Caspi, Lior Rokach, Esti Yeger-Lotem.

  Pathogenic variants underlying Mendelian diseases often disrupt the normal physiology of a few tissues and organs. However, variant effect prediction tools that aim to identify pathogenic variants are typically oblivious to tissue contexts. Here we report a machine-learning framework, denoted "Tissue Risk Assessment of Causality by Expression for variants" (TRACEvar, https://netbio.bgu.ac.il/TRACEvar/ ), that offers two advancements. First, TRACEvar predicts pathogenic variants that disrupt the normal physiology of specific tissues. This was achieved by creating 14 tissue-specific models that were trained on over 14,000 variants and combined 84 attributes of genetic variants with 495 attributes derived from tissue omics. TRACEvar outperformed 10 well-established and tissue-oblivious variant effect prediction tools. Second, the resulting models are interpretable, thereby illuminating variants' mode of action. Application of TRACEvar to variants of 52 rare-disease patients highlighted pathogenicity mechanisms and relevant disease processes. Lastly, the interpretation of all tissue models revealed that top-ranking determinants of pathogenicity included attributes of disease-affected tissues, particularly cellular process activities. Collectively, these results show that tissue contexts and interpretable machine-learning models can greatly enhance the etiology of rare diseases.

Keywords:  Genomic Medicine; Machine Learning; Tissue-selectivity; Variant Effect Prediction; Variant Interpretation

DOI:  https://doi.org/10.1038/s44320-024-00061-6
Nat Rev Genet. 2024 Sep 19.

Genome-scale models in human metabologenomics.

Adil Mardinoglu, Bernhard Ø Palsson.

Metabologenomics integrates metabolomics with other omics data types to comprehensively study the genetic and environmental factors that influence metabolism. These multi-omics data can be incorporated into genome-scale metabolic models (GEMs), which are highly curated knowledge bases that explicitly account for genes, transcripts, proteins and metabolites. By including all known biochemical reactions catalysed by enzymes and transporters encoded in the human genome, GEMs analyse and predict the behaviour of complex metabolic networks. Continued advancements to the scale and scope of GEMs - from cells and tissues to microbiomes and the whole body - have helped to design effective treatments and develop better diagnostic tools for metabolic diseases. Furthermore, increasing amounts of multi-omics data are incorporated into GEMs to better identify the underlying mechanisms, biomarkers and potential drug targets of metabolic diseases.

DOI: https://doi.org/10.1038/s41576-024-00768-0
J Comp Neurol. 2024 Sep;532(9): e25669

Invariance of Mitochondria and Synapses in the Primary Visual Cortex of Mammals Provides Insight Into Energetics and Function.

Molly T Karl, Young Do Kim, Kavita Rajendran, Paul R Manger, Chet C Sherwood.

  The cerebral cortex accounts for substantial energy expenditure, primarily driven by the metabolic demands of synaptic signaling. Mitochondria, the organelles responsible for generating cellular energy, play a crucial role in this process. We investigated ultrastructural characteristics of the primary visual cortex in 18 phylogenetically diverse mammals, spanning a broad range of brain sizes from mouse to elephant. Our findings reveal remarkable uniformity in synapse density, postsynaptic density (PSD) length, and mitochondria density, indicating functional and metabolic constraints that maintain these fundamental features. Notably, we observed an average of 1.9 mitochondria per synapse across mammalian species. When considered together with the trend of decreasing neuron density with larger brain size, we find that brain enlargement in mammals is characterized by increasing proportions of synapses and mitochondria per cortical neuron. These results shed light on the adaptive mechanisms and metabolic dynamics that govern cortical ultrastructure across mammals.

Keywords:  RRID:SCR_008515; RRID:SCR_021162; brain evolution; energy; mammals; mitochondria; neocortex; synapse

DOI:  https://doi.org/10.1002/cne.25669