bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2022–06–26
35 papers selected by
Catalina Vasilescu, University of Helsinki
  1. Case Report: Optic Atrophy and Nephropathy With m.13513G>A/MT-ND5 mtDNA Pathogenic Variant.
  2. Pathogenic variants of the mitochondrial aspartate/glutamate carrier causing citrin deficiency.
  3. Substrate binding in the mitochondrial ADP/ATP carrier is a step-wise process guiding the structural changes in the transport cycle.
  4. Disease causing mutation (P178L) in mitochondrial transcription factor A results in impaired mitochondrial transcription initiation.
  5. Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit.
  6. Gene Therapy for Mitochondrial Diseases: Current Status and Future Perspective.
  7. ncRNA regulation of mitochondrial transcription.
  8. Clinical and genetic spectrum of Mitochondrial DNA depletion syndromes: a report of 6 cases with 4 novel variants.
  9. Mitochondrial transport and metabolism of the major methyl donor and versatile cofactor S-adenosylmethionine, and related diseases: A review†.
  10. Protocol for engineering and validating a synthetic mitochondrial intermembrane bridge in mammalian cells.
  11. Identifying Somatic Mitochondrial DNA Mutations.
  12. Shaping fuel utilization by mitochondria.
  13. Chronic inhibition of the mitochondrial ATP synthase in skeletal muscle triggers sarcoplasmic reticulum distress and tubular aggregates.
  14. Use of Next-Generation Sequencing for Identifying Mitochondrial Disorders.
  15. TMEM63C mutations cause mitochondrial morphology defects and underlie hereditary spastic paraplegia.
  16. Variant Annotation and Functional Prediction: SnpEff.
  17. Mitochondrial-derived vesicles: Gatekeepers of mitochondrial response to oxidative stress.
  18. A novel homozygous missense mutation in the FASTKD2 gene leads to Lennox-Gastaut syndrome.
  19. Is Drp1 sufficient to catalyze membrane fission?
  20. Mitochondrial FAD shortage in SLC25A32 deficiency affects folate-mediated one-carbon metabolism.
  21. Coordination of metal center biogenesis in human cytochrome c oxidase.
  22. The regenerating skeletal muscle niche drives satellite cell return to quiescence.
  23. New Developments and Possibilities in Reanalysis and Reinterpretation of Whole Exome Sequencing Datasets for Unsolved Rare Diseases Using Machine Learning Approaches.
  24. Structural Variant Detection from Long-Read Sequencing Data with cuteSV.
  25. Data Processing and Germline Variant Calling with the Sentieon Pipeline.
  26. New Insights into the Neurodegeneration Mechanisms Underlying Riboflavin Transporter Deficiency (RTD): Involvement of Energy Dysmetabolism and Cytoskeletal Derangement.
  27. A randomized placebo-controlled clinical trial for pharmacological activation of BCAA catabolism in patients with type 2 diabetes.
  28. YAP/TAZ-TEAD link angiogenesis to nutrients.
  29. Targeted Deletion of Mitofusin 1 and Mitofusin 2 Causes Female Infertility and Loss of Follicular Reserve.
  30. mGWAS-Explorer: Linking SNPs, Genes, Metabolites, and Diseases for Functional Insights.
  31. eIF5B and eIF1A reorient initiator tRNA to allow ribosomal subunit joining.
  32. UMI-Varcal: A Low-Frequency Variant Caller for UMI-Tagged Paired-End Sequencing Data.
  33. RDscan: A New Method for Improving Germline and Somatic Variant Calling Based on Read Depth Distribution.
  34. ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2.
  35. Quantitative Comparison of Statistical Methods for Analyzing Human Metabolomics Data.
  1. Front Genet. 2022 ;13 887696
    Case Report: Optic Atrophy and Nephropathy With m.13513G>A/MT-ND5 mtDNA Pathogenic Variant.
    Valentina Barone, Chiara La Morgia, Leonardo Caporali, Claudio Fiorini, Michele Carbonelli, Laura Ludovica Gramegna, Fiorina Bartiromo, Caterina Tonon, Luca Morandi, Rocco Liguori, Aurelia Petrini, Rachele Brugnano, Rachele Del Sordo, Carla Covarelli, Manrico Morroni, Raffaele Lodi, Valerio Carelli.
      Isolated complex I deficiency represents the most common mitochondrial respiratory chain defect involved in mitochondrial disorders. Among these, the mitochondrial DNA (mtDNA) m.13513G>A pathogenic variant in the NADH dehydrogenase 5 subunit gene (MT-ND5) has been associated with heterogenous manifestations, including phenotypic overlaps of mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes, Leigh syndrome, and Leber's hereditary optic neuropathy (LHON). Interestingly, this specific mutation has been recently described in patients with adult-onset nephropathy. We, here, report the unique combination of LHON, nephropathy, sensorineural deafness, and subcortical and cerebellar atrophy in association with the m.13513G>A variant.
    Keywords:  LHON; MT-ND5; Mitochondrial nephropathy; cerebellum; m.13513G>A mutation
    DOI:  https://doi.org/10.3389/fgene.2022.887696
  2. Trends Endocrinol Metab. 2022 Jun 17. pii: S1043-2760(22)00099-6. [Epub ahead of print]
    Pathogenic variants of the mitochondrial aspartate/glutamate carrier causing citrin deficiency.
    Sotiria Tavoulari, Denis Lacabanne, Chancievan Thangaratnarajah, Edmund R S Kunji.
      Citrin deficiency is a pan-ethnic and highly prevalent mitochondrial disease with three different stages: neonatal intrahepatic cholestasis (NICCD), a relatively mild adaptation stage, and type II citrullinemia in adulthood (CTLN2). The cause is the absence or dysfunction of the calcium-regulated mitochondrial aspartate/glutamate carrier 2 (AGC2/SLC25A13), also called citrin, which imports glutamate into the mitochondrial matrix and exports aspartate to the cytosol. In citrin deficiency, these missing transport steps lead to impairment of the malate-aspartate shuttle, gluconeogenesis, amino acid homeostasis, and the urea cycle. In this review, we describe the geological spread and occurrence of citrin deficiency, the metabolic consequences and use our current knowledge of the structure to predict the impact of the known pathogenic mutations on the calcium-regulatory and transport mechanism of citrin.
    Keywords:  SLC25A12; SLC25A13; calcium regulation; mitochondrial carrier family; transport; urea cycle disorders
    DOI:  https://doi.org/10.1016/j.tem.2022.05.002
  3. Nat Commun. 2022 Jun 23. 13(1): 3585
    Substrate binding in the mitochondrial ADP/ATP carrier is a step-wise process guiding the structural changes in the transport cycle.
    Vasiliki Mavridou, Martin S King, Sotiria Tavoulari, Jonathan J Ruprecht, Shane M Palmer, Edmund R S Kunji.
      Mitochondrial ADP/ATP carriers import ADP into the mitochondrial matrix and export ATP to the cytosol to fuel cellular processes. Structures of the inhibited cytoplasmic- and matrix-open states have confirmed an alternating access transport mechanism, but the molecular details of substrate binding remain unresolved. Here, we evaluate the role of the solvent-exposed residues of the translocation pathway in the process of substrate binding. We identify the main binding site, comprising three positively charged and a set of aliphatic and aromatic residues, which bind ADP and ATP in both states. Additionally, there are two pairs of asparagine/arginine residues on opposite sides of this site that are involved in substrate binding in a state-dependent manner. Thus, the substrates are directed through a series of binding poses, inducing the conformational changes of the carrier that lead to their translocation. The properties of this site explain the electrogenic and reversible nature of adenine nucleotide transport.
    DOI:  https://doi.org/10.1038/s41467-022-31366-5
  4. Biochim Biophys Acta Mol Basis Dis. 2022 Jun 15. pii: S0925-4439(22)00138-7. [Epub ahead of print] 166467
    Disease causing mutation (P178L) in mitochondrial transcription factor A results in impaired mitochondrial transcription initiation.
    Majda Mehmedović, Martial Martucci, Henrik Spåhr, Layal Ishak, Anup Mishra, Maria Eugenia Sanchez-Sandoval, Carlos Pardo-Hernández, Bradley Peter, Siet M van den Wildenberg, Maria Falkenberg, Geraldine Farge.
      Mitochondrial transcription factor A (TFAM) is essential for the maintenance, expression, and packaging of mitochondrial DNA (mtDNA). Recently, a pathogenic homozygous variant in TFAM (P178L) has been associated with a severe mtDNA depletion syndrome leading to neonatal liver failure and early death. We have performed a biochemical characterization of the TFAM variant P178L in order to understand the molecular basis for the pathogenicity of this mutation. We observe no effects on DNA binding, and compaction of DNA is only mildly affected by the P178L amino acid change. Instead, the mutation severely impairs mtDNA transcription initiation at the mitochondrial heavy and light strand promoters. Molecular modeling suggests that the P178L mutation affects promoter sequence recognition and the interaction between TFAM and the tether helix of POLRMT, thus explaining transcription initiation deficiency.
    Keywords:  Disease causing mutation; Mitochondria; TFAM; Transcription initiation; mtDNA depletion
    DOI:  https://doi.org/10.1016/j.bbadis.2022.166467
  5. Commun Biol. 2022 Jun 23. 5(1): 620
    Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit.
    David Molina-Granada, Emiliano González-Vioque, Marris G Dibley, Raquel Cabrera-Pérez, Antoni Vallbona-Garcia, Javier Torres-Torronteras, Leonid A Sazanov, Michael T Ryan, Yolanda Cámara, Ramon Martí.
      Imbalanced mitochondrial dNTP pools are known players in the pathogenesis of multiple human diseases. Here we show that, even under physiological conditions, dGTP is largely overrepresented among other dNTPs in mitochondria of mouse tissues and human cultured cells. In addition, a vast majority of mitochondrial dGTP is tightly bound to NDUFA10, an accessory subunit of complex I of the mitochondrial respiratory chain. NDUFA10 shares a deoxyribonucleoside kinase (dNK) domain with deoxyribonucleoside kinases in the nucleotide salvage pathway, though no specific function beyond stabilizing the complex I holoenzyme has been described for this subunit. We mutated the dNK domain of NDUFA10 in human HEK-293T cells while preserving complex I assembly and activity. The NDUFA10E160A/R161A shows reduced dGTP binding capacity in vitro and leads to a 50% reduction in mitochondrial dGTP content, proving that most dGTP is directly bound to the dNK domain of NDUFA10. This interaction may represent a hitherto unknown mechanism regulating mitochondrial dNTP availability and linking oxidative metabolism to DNA maintenance.
    DOI:  https://doi.org/10.1038/s42003-022-03568-6
  6. Pharmaceutics. 2022 Jun 17. pii: 1287. [Epub ahead of print]14(6):
    Gene Therapy for Mitochondrial Diseases: Current Status and Future Perspective.
    Alessia Di Donfrancesco, Giulia Massaro, Ivano Di Meo, Valeria Tiranti, Emanuela Bottani, Dario Brunetti.
      Mitochondrial diseases (MDs) are a group of severe genetic disorders caused by mutations in the nuclear or mitochondrial genome encoding proteins involved in the oxidative phosphorylation (OXPHOS) system. MDs have a wide range of symptoms, ranging from organ-specific to multisystemic dysfunctions, with different clinical outcomes. The lack of natural history information, the limits of currently available preclinical models, and the wide range of phenotypic presentations seen in MD patients have all hampered the development of effective therapies. The growing number of pre-clinical and clinical trials over the last decade has shown that gene therapy is a viable precision medicine option for treating MD. However, several obstacles must be overcome, including vector design, targeted tissue tropism and efficient delivery, transgene expression, and immunotoxicity. This manuscript offers a comprehensive overview of the state of the art of gene therapy in MD, addressing the main challenges, the most feasible solutions, and the future perspectives of the field.
    Keywords:  gene therapy; mitochondria; mitochondrial DNA; mitochondrial disease; precision medicine
    DOI:  https://doi.org/10.3390/pharmaceutics14061287
  7. Nat Rev Mol Cell Biol. 2022 Jun 21.
    ncRNA regulation of mitochondrial transcription.
    Eytan Zlotorynski.
      
    DOI:  https://doi.org/10.1038/s41580-022-00509-3
  8. Mitochondrion. 2022 Jun 21. pii: S1567-7249(22)00052-6. [Epub ahead of print]
    Clinical and genetic spectrum of Mitochondrial DNA depletion syndromes: a report of 6 cases with 4 novel variants.
    Nihal Al Menabawy, Hebatallah M Hassaan, Manal Ramadan, Iman Ehsan Abdel Meguid, Hala Ahmed El Gindy, Christian Beetz, Laila Selim.
      Mitochondrial DNA (mtDNA) depletion syndromes (MDS) are a heterogeneous group of rare autosomal recessive genetic disorders characterized by a decrease in the number of mtDNA copies inside the organ involved. There are three distinct forms of MDS including the hepatocerebral, the myopathic and the encephalomyopathic forms. The diversity in the clinical and genetic spectrum of these disorders makes the diagnosis challenging. Here, we describe the clinical phenotype and the genetic spectrum of 6 patients with MDS including 4 novel variants and compare them with previously reported cases. Subject and Methods Six patients from six unrelated families were included in this study. All the patients were subjected to a detailed history, thorough general and neurologic examination, basic laboratory investigations including lactic acid and ammonia, amino acids, acylcarnitine profiles and brain MRI. Whole-exome sequencing was performed for all of them to confirm the suspicion of mitochondrial disorder. RESULTS: In our series, four patients presented with the hepatocerebral form of MDS with the major presenting manifestation of progressive liver cell failure with severe hypotonia and global developmental delay. Four variants in the DGUOK gene and the MPV17 have been identified including 2 novel variants. One patient was identified in the myopathic form presenting with myopathy associated with two novel variants in the TK2 gene. One patient was diagnosed with encephalomyopathic form presenting with persistent lactic acidosis and global delay due to a homozygous variant in the FBXL4 gene. CONCLUSION: MDS has a wide spectrum of heterogeneous clinical presentations and about nine different genes involved. Whole exome sequencing (WES) has resulted in faster diagnosis of these challenging cases as the phenotype overlap with many other disorders. This should be considered the first-tier diagnostic test obviating the need for more invasive testing like muscle biopsies.
    DOI:  https://doi.org/10.1016/j.mito.2022.06.004
  9. IUBMB Life. 2022 Jun 22.
    Mitochondrial transport and metabolism of the major methyl donor and versatile cofactor S-adenosylmethionine, and related diseases: A review†.
    Magnus Monné, Carlo M T Marobbio, Gennaro Agrimi, Luigi Palmieri, Ferdinando Palmieri.
      S-adenosyl-L-methionine (SAM) is a coenzyme and the most commonly used methyl-group donor for the modification of metabolites, DNA, RNA and proteins. SAM biosynthesis and SAM regeneration from the methylation reaction product S-adenosyl-L-homocysteine (SAH) take place in the cytoplasm. Therefore, the intramitochondrial SAM-dependent methyltransferases require the import of SAM and export of SAH for recycling. Orthologous mitochondrial transporters belonging to the mitochondrial carrier family have been identified to catalyze this antiport transport step: Sam5p in yeast, SLC25A26 (SAMC) in humans, and SAMC1-2 in plants. In mitochondria SAM is used by a vast number of enzymes implicated in the following processes: the regulation of replication, transcription, translation, and enzymatic activities; the maturation and assembly of mitochondrial tRNAs, ribosomes and protein complexes; and the biosynthesis of cofactors, such as ubiquinone, lipoate, and molybdopterin. Mutations in SLC25A26 and mitochondrial SAM-dependent enzymes have been found to cause human diseases, which emphasizes the physiological importance of these proteins.
    Keywords:  S-adenosyl-L-methionine; diseases; metabolism; methyltransferase; mitochondria; mitochondrial carrier; mitochondrial transport
    DOI:  https://doi.org/10.1002/iub.2658
  10. STAR Protoc. 2022 Sep 16. 3(3): 101454
    Protocol for engineering and validating a synthetic mitochondrial intermembrane bridge in mammalian cells.
    Gunjan Purohit, Martonio Ponte Viana, Oleh Khalimonchuk.
      Membrane contact sites are recognized as critical means of intercompartmental communication. Here, we describe a protocol for engineering and validating a synthetic bridge between the inner and outer mitochondrial membranes to support functioning of the endogenous mitochondrial contact site and cristae organizing system (MICOS). A chimeric protein, MitoT, is stably expressed in cultured mammalian cells to bridge the mitochondrial membranes. This approach can be a valuable tool to study the function of the MICOS complex and associated proteins. For complete details on the use and execution of this protocol, please refer to Viana et al. (2021).
    Keywords:  Biotechnology and bioengineering; Cell Biology; Cell Membrane; Cell culture; Cell isolation; Flow Cytometry/Mass Cytometry; Metabolism; Microscopy; Molecular Biology
    DOI:  https://doi.org/10.1016/j.xpro.2022.101454
  11. Methods Mol Biol. 2022 ;2493 153-165
    Identifying Somatic Mitochondrial DNA Mutations.
    Jisong An, Kyoung Il Min, Young Seok Ju.
      Mitochondria are cellular organelles that play an essential role in eukaryotes, producing the energy needed for a cell to survive. Beyond the ~3.2 Gb of nuclear genomic DNA, each human cell has hundreds of mitochondria which carry one or a few copies of the 16.5 kb circular mitochondria DNA (mtDNA). Despite its small size, the circular genome encodes 37 genes, including 13 proteins that generate respiratory chain complexes together with other proteins of nuclear origin. Similar to nuclear genome, mtDNA in cancer cells frequently harbor somatically acquired alterations. Whole-genome or whole-exome sequencing of the tumor and its matched normal tissues (frequently blood or adjacent non-tumor tissues) enables sensitive and efficient detection of somatic mtDNA mutations. Because each cancer cell commonly carries hundreds to thousands of mtDNA copies, detection of mtDNA mutations is dependent on the heteroplasmic level of each mutation. Here, we describe strategies to accurately identify somatic mtDNA mutations in cancer genome studies.
    Keywords:  Bioinformatics; Genome sequencing; Genomics; Heteroplasmy; Mitochondria; Next-generation sequencing; Somatic mutations
    DOI:  https://doi.org/10.1007/978-1-0716-2293-3_10
  12. Curr Biol. 2022 Jun 20. pii: S0960-9822(22)00765-5. [Epub ahead of print]32(12): R618-R623
    Shaping fuel utilization by mitochondria.
    Lukas Alan, Luca Scorrano.
      Mitochondria are central to cellular metabolism. They provide intermediate metabolites that are used in biosynthetic pathways and they process diet-derived nutrients into the energy-rich compound ATP. Mitochondrial ATP biosynthesis is a marvel of thermodynamic efficiency. Via the tricarboxylic acid cycle (TCA) and fatty acid β-oxidation, mitochondria extract electrons from dietary carbon compounds and pass them to nucleotides that ultimately deliver them to the respiratory chain complexes located in invaginations in the inner mitochondrial membrane (IMM) known as cristae. The respiratory chain complexes donate electrons in stepwise redox reactions to molecular oxygen and, with the exception of complex II, use the liberated energy to pump protons across the proton-impermeable IMM, generating a proton electrochemical gradient. This gradient is then utilized by the ATP synthase, which, in a rotary mechanism, catalyzes the formation of the high-energy γ-phosphate chemical bond between ADP and inorganic phosphate. The conversion of the chemical energy of carbon compounds into a physical, vectorial form of energy (the electrochemical gradient) maximizes the yield of the ATP biosynthetic process and is perhaps one of the foundations of life as we know it.
    DOI:  https://doi.org/10.1016/j.cub.2022.05.006
  13. Cell Death Dis. 2022 Jun 22. 13(6): 561
    Chronic inhibition of the mitochondrial ATP synthase in skeletal muscle triggers sarcoplasmic reticulum distress and tubular aggregates.
    Cristina Sánchez-González, Juan Cruz Herrero Martín, Beñat Salegi Ansa, Cristina Núñez de Arenas, Brina Stančič, Marta P Pereira, Laura Contreras, José M Cuezva, Laura Formentini.
      Tubular aggregates (TA) are honeycomb-like arrays of sarcoplasmic-reticulum (SR) tubules affecting aged glycolytic fibers of male individuals and inducing severe sarcomere disorganization and muscular pain. TA develop in skeletal muscle from Tubular Aggregate Myopathy (TAM) patients as well as in other disorders including endocrine syndromes, diabetes, and ageing, being their primary cause unknown. Nowadays, there is no cure for TA. Intriguingly, both hypoxia and calcium dyshomeostasis prompt TA formation, pointing to a possible role for mitochondria in their setting. However, a functional link between mitochondrial dysfunctions and TA remains unknown. Herein, we investigate the alteration in muscle-proteome of TAM patients, the molecular mechanism of TA onset and a potential therapy in a preclinical mouse model of the disease. We show that in vivo chronic inhibition of the mitochondrial ATP synthase in muscle causes TA. Upon long-term restrained oxidative phosphorylation (OXPHOS), oxidative soleus experiments a metabolic and structural switch towards glycolytic fibers, increases mitochondrial fission, and activates mitophagy to recycle damaged mitochondria. TA result from the overresponse of the fission controller DRP1, that upregulates the Store-Operate-Calcium-Entry and increases the mitochondria-SR interaction in a futile attempt to buffer calcium overloads upon prolonged OXPHOS inhibition. Accordingly, hypoxic muscles cultured ex vivo show an increase in mitochondria/SR contact sites and autophagic/mitophagic zones, where TA clusters grow around defective mitochondria. Moreover, hypoxia triggered a stronger TA formation upon ATP synthase inhibition, and this effect was reduced by the DRP1 inhibitor mDIVI. Remarkably, the muscle proteome of TAM patients displays similar alterations in mitochondrial dynamics and in ATP synthase contents. In vivo edaravone treatment in mice with restrained OXPHOS restored a healthy phenotype by prompting mitogenesis and mitochondrial fusion. Altogether, our data provide a functional link between the ATP synthase/DRP1 axis and the setting of TA, and repurpose edaravone as a possible treatment for TA-associated disorders.
    DOI:  https://doi.org/10.1038/s41419-022-05016-z
  14. Curr Issues Mol Biol. 2022 Feb 27. 44(3): 1127-1148
    Use of Next-Generation Sequencing for Identifying Mitochondrial Disorders.
    Shafi Mahmud, Suvro Biswas, Shamima Afrose, Mohasana Akter Mita, Md Robiul Hasan, Mst Sharmin Sultana Shimu, Gobindo Kumar Paul, Sanghyun Chung, Md Abu Saleh, Sultan Alshehri, Momammed M Ghoneim, Maha Alruwaily, Bonglee Kim.
      Mitochondria are major contributors to ATP synthesis, generating more than 90% of the total cellular energy production through oxidative phosphorylation (OXPHOS): metabolite oxidation, such as the β-oxidation of fatty acids, and the Krebs's cycle. OXPHOS inadequacy due to large genetic lesions in mitochondrial as well as nuclear genes and homo- or heteroplasmic point mutations in mitochondrially encoded genes is a characteristic of heterogeneous, maternally inherited genetic disorders known as mitochondrial disorders that affect multisystemic tissues and organs with high energy requirements, resulting in various signs and symptoms. Several traditional diagnostic approaches, including magnetic resonance imaging of the brain, cardiac testing, biochemical screening, variable heteroplasmy genetic testing, identifying clinical features, and skeletal muscle biopsies, are associated with increased risks, high costs, a high degree of false-positive or false-negative results, or a lack of precision, which limits their diagnostic abilities for mitochondrial disorders. Variable heteroplasmy levels, mtDNA depletion, and the identification of pathogenic variants can be detected through genetic sequencing, including the gold standard Sanger sequencing. However, sequencing can be time consuming, and Sanger sequencing can result in the missed recognition of larger structural variations such as CNVs or copy-number variations. Although each sequencing method has its own limitations, genetic sequencing can be an alternative to traditional diagnostic methods. The ever-growing roster of possible mutations has led to the development of next-generation sequencing (NGS). The enhancement of NGS methods can offer a precise diagnosis of the mitochondrial disorder within a short period at a reasonable expense for both research and clinical applications.
    Keywords:  NGS; OXPHOS; mitochondrial disorder; mtDNA; nDNA
    DOI:  https://doi.org/10.3390/cimb44030074
  15. Brain. 2022 Jun 20. pii: awac123. [Epub ahead of print]
    TMEM63C mutations cause mitochondrial morphology defects and underlie hereditary spastic paraplegia.
    Luis Carlos Tábara, Fatema Al-Salmi, Reza Maroofian, Amna Mohammed Al-Futaisi, Fathiya Al-Murshedi, Joanna Kennedy, Jacob O Day, Thomas Courtin, Aisha Al-Khayat, Hamid Galedari, Neda Mazaheri, Margherita Protasoni, Mark Johnson, Joseph S Leslie, Claire G Salter, Lettie E Rawlins, James Fasham, Almundher Al-Maawali, Nikol Voutsina, Perrine Charles, Laura Harrold, Boris Keren, Edmund R S Kunji, Barbara Vona, Gholamreza Jelodar, Alireza Sedaghat, Gholamreza Shariati, Henry Houlden, Andrew H Crosby, Julien Prudent, Emma L Baple.
      The hereditary spastic paraplegias (HSP) are among the most genetically diverse of all Mendelian disorders. They comprise a large group of neurodegenerative diseases that may be divided into 'pure HSP' in forms of the disease primarily entailing progressive lower-limb weakness and spasticity, and 'complex HSP' when these features are accompanied by other neurological (or non-neurological) clinical signs. Here, we identified biallelic variants in the transmembrane protein 63C (TMEM63C) gene, encoding a predicted osmosensitive calcium-permeable cation channel, in individuals with hereditary spastic paraplegias associated with mild intellectual disability in some, but not all cases. Biochemical and microscopy analyses revealed that TMEM63C is an endoplasmic reticulum-localized protein, which is particularly enriched at mitochondria-endoplasmic reticulum contact sites. Functional in cellula studies indicate a role for TMEM63C in regulating both endoplasmic reticulum and mitochondrial morphologies. Together, these findings identify autosomal recessive TMEM63C variants as a cause of pure and complex HSP and add to the growing evidence of a fundamental pathomolecular role of perturbed mitochondrial-endoplasmic reticulum dynamics in motor neurone degenerative diseases.
    Keywords:  TMEM63C; endoplasmic reticulum/ER; hereditary spastic paraplegia/HSP; mitochondria; mitochondria-ER contact sites/MERCs
    DOI:  https://doi.org/10.1093/brain/awac123
  16. Methods Mol Biol. 2022 ;2493 289-314
    Variant Annotation and Functional Prediction: SnpEff.
    Pablo Cingolani.
      Variant annotations, in general, refer to the process of information enrichment of genomic variants from a sequencing experiment. Typically these annotations include functional predictions, such as predicting the amino acid sequence changes from the DNA variant, predicting whether the variant will induce a splice anomaly, or predicting nonsense mediated decay. But other annotations also include combining with genomic databases, adding conservation scores, or comparing to allele frequencies from large population databases. Finally, all these annotations are combined to prioritize and filter variants into a reduced set of highly relevant variants for the study or clinical assay.
    Keywords:  Functional annotations; Genomic variant prioritization; SnpEff; SnpSift; Variant annotation
    DOI:  https://doi.org/10.1007/978-1-0716-2293-3_19
  17. Free Radic Biol Med. 2022 Jun 21. pii: S0891-5849(22)00460-9. [Epub ahead of print]
    Mitochondrial-derived vesicles: Gatekeepers of mitochondrial response to oxidative stress.
    Tingting Peng, Yinyin Xie, Hanqing Sheng, Cui Wang, Yajun Lian, Nanchang Xie.
      Mitochondrial quality control (MQC) mechanisms are a series of adaptive responses that ensure the relative stability of mitochondrial morphology, quantity, and quality to preserve cellular survival and function. While MQC mechanisms range from mitochondrial biogenesis and fusion/fission to mitophagy, mitochondrial-derived vesicles (MDVs) may represent an essential component of MQC. MDVs precede mitochondrial autophagy and serve as the first line of defense against oxidative stress by selectively transferring damaged mitochondrial substances to the lysosome for degradation. In fact, the function of MDVs is dependent on the cargo, the shuttle route, and the ultimate destination. Abnormal MDVs disrupt metabolite clearance and the immune response, predisposing to pathological conditions, including neurodegeneration, cardiovascular diseases, and cancers. Therefore, MDV regulation may be a potential therapeutic for the therapy of these diseases. In this review, we highlight recent advances in the study of MDVs and their misregulation in various diseases from the perspectives of formation, cargo selection, regulation, and transportation.
    Keywords:  Aging; Diseases; Mitochondria; Mitochondrial quality control; Mitochondrial-derived vesicle; Therapeutics
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2022.06.233
  18. J Hum Genet. 2022 Jun 21.
    A novel homozygous missense mutation in the FASTKD2 gene leads to Lennox-Gastaut syndrome.
    Tenghui Wu, Leilei Mao, Chen Chen, Fei Yin, Jing Peng.
      FASTKD2 encodes an RNA-binding protein, which is a key post-transcriptional regulator of mitochondrial gene expression. Mutations in FASTKD2 have recently been found in mitochondrial encephalomyopathy, which is characterized by a deficiency in mitochondrial function. To date, seven patients have been reported. Six patients were identified with nonsense or frameshift mutations in the FASTKD2 gene, and only one patient harbored a missense mutation and a nonsense mutation. Here, we identified a novel FASTKD2 homozygous mutation, c.911 T > C, in a patient diagnosed with Lennox-Gastaut syndrome. We observed that the expression of FASTKD2 and the levels of mitochondrial 16 S rRNA were lower in the patient than in the unaffected controls. In conclusion, the missense mutation c.911 T > C caused loss of function in FASTKD2, which was associated with a new phenotype, Lennox-Gastaut syndrome.
    DOI:  https://doi.org/10.1038/s10038-022-01056-7
  19. Proc Natl Acad Sci U S A. 2022 Jul 05. 119(27): e2201709119
    Is Drp1 sufficient to catalyze membrane fission?
    Krishnendu Roy, Thomas J Pucadyil.
      
    DOI:  https://doi.org/10.1073/pnas.2201709119
  20. Cell Mol Life Sci. 2022 Jun 21. 79(7): 375
    Mitochondrial FAD shortage in SLC25A32 deficiency affects folate-mediated one-carbon metabolism.
    Min-Zhi Peng, Yong-Xian Shao, Xiu-Zhen Li, Kang-Di Zhang, Yan-Na Cai, Yun-Ting Lin, Min-Yan Jiang, Zong-Cai Liu, Xue-Ying Su, Wen Zhang, Xiao-Ling Jiang, Li Liu.
      The SLC25A32 dysfunction is associated with neural tube defects (NTDs) and exercise intolerance, but very little is known about disease-specific mechanisms due to a paucity of animal models. Here, we generated homozygous (Slc25a32Y174C/Y174C and Slc25a32K235R/K235R) and compound heterozygous (Slc25a32Y174C/K235R) knock-in mice by mimicking the missense mutations identified from our patient. A homozygous knock-out (Slc25a32-/-) mouse was also generated. The Slc25a32K235R/K235R and Slc25a32Y174C/K235R mice presented with mild motor impairment and recapitulated the biochemical disturbances of the patient. While Slc25a32-/- mice die in utero with NTDs. None of the Slc25a32 mutations hindered the mitochondrial uptake of folate. Instead, the mitochondrial uptake of flavin adenine dinucleotide (FAD) was specifically blocked by Slc25a32Y174C/K235R, Slc25a32K235R/K235R, and Slc25a32-/- mutations. A positive correlation between SLC25A32 dysfunction and flavoenzyme deficiency was observed. Besides the flavoenzymes involved in fatty acid β-oxidation and amino acid metabolism being impaired, Slc25a32-/- embryos also had a subunit of glycine cleavage system-dihydrolipoamide dehydrogenase damaged, resulting in glycine accumulation and glycine derived-formate reduction, which further disturbed folate-mediated one-carbon metabolism, leading to 5-methyltetrahydrofolate shortage and other folate intermediates accumulation. Maternal formate supplementation increased the 5-methyltetrahydrofolate levels and ameliorated the NTDs in Slc25a32-/- embryos. The Slc25a32K235R/K235R and Slc25a32Y174C/K235R mice had no glycine accumulation, but had another formate donor-dimethylglycine accumulated and formate deficiency. Meanwhile, they suffered from the absence of all folate intermediates in mitochondria. Formate supplementation increased the folate amounts, but this effect was not restricted to the Slc25a32 mutant mice only. In summary, we established novel animal models, which enabled us to understand the function of SLC25A32 better and to elucidate the role of SLC25A32 dysfunction in human disease development and progression.
    Keywords:  Clubfoot; Dimethylglycine dehydrogenase; Hypoplasia of fibulae; Multiple acyl-coenzyme A dehydrogenation deficiency; Riboflavin-responsive exercise intolerance; Serine metabolism
    DOI:  https://doi.org/10.1007/s00018-022-04404-0
  21. Nat Commun. 2022 Jun 24. 13(1): 3615
    Coordination of metal center biogenesis in human cytochrome c oxidase.
    Eva Nývltová, Jonathan V Dietz, Javier Seravalli, Oleh Khalimonchuk, Antoni Barrientos.
      Mitochondrial cytochrome c oxidase (CcO) or respiratory chain complex IV is a heme aa3-copper oxygen reductase containing metal centers essential for holo-complex biogenesis and enzymatic function that are assembled by subunit-specific metallochaperones. The enzyme has two copper sites located in the catalytic core subunits. The COX1 subunit harbors the CuB site that tightly associates with heme a3 while the COX2 subunit contains the binuclear CuA site. Here, we report that in human cells the CcO copper chaperones form macromolecular assemblies and cooperate with several twin CX9C proteins to control heme a biosynthesis and coordinate copper transfer sequentially to the CuA and CuB sites. These data on CcO illustrate a mechanism that regulates the biogenesis of macromolecular enzymatic assemblies with several catalytic metal redox centers and prevents the accumulation of cytotoxic reactive assembly intermediates.
    DOI:  https://doi.org/10.1038/s41467-022-31413-1
  22. iScience. 2022 Jun 17. 25(6): 104444
    The regenerating skeletal muscle niche drives satellite cell return to quiescence.
    Alicia A Cutler, Bradley Pawlikowski, Joshua R Wheeler, Nicole Dalla Betta, Tiffany Elston, Rebecca O'Rourke, Kenneth Jones, Bradley B Olwin.
      Skeletal muscle stem cells, or satellite cells (SCs), are essential to regenerate and maintain muscle. Quiescent SCs reside in an asymmetric niche between the basal lamina and myofiber membrane. To repair muscle, SCs activate, proliferate, and differentiate, fusing to repair myofibers or reacquiring quiescence to replenish the SC niche. Little is known about when SCs reacquire quiescence during regeneration or the cellular processes that direct SC fate decisions. We find that most SCs reacquire quiescence 5-10 days after muscle injury, following differentiation and fusion of most cells to regenerate myofibers. Single-cell sequencing of myogenic cells in regenerating muscle identifies SCs reacquiring quiescence and reveals that noncell autonomous signaling networks influence SC fate decisions during regeneration. SC transplantation experiments confirm that the regenerating environment influences SC fate. We define a window for SC repopulation of the niche, emphasizing the temporal contribution of the regenerative muscle environment on SC fate.
    Keywords:  Cell biology; Omics; Stem cells research; Transcriptomics
    DOI:  https://doi.org/10.1016/j.isci.2022.104444
  23. Int J Mol Sci. 2022 Jun 18. pii: 6792. [Epub ahead of print]23(12):
    New Developments and Possibilities in Reanalysis and Reinterpretation of Whole Exome Sequencing Datasets for Unsolved Rare Diseases Using Machine Learning Approaches.
    Samarth Thonta Setty, Marie-Pier Scott-Boyer, Tania Cuppens, Arnaud Droit.
      Rare diseases impact the lives of 300 million people in the world. Rapid advances in bioinformatics and genomic technologies have enabled the discovery of causes of 20-30% of rare diseases. However, most rare diseases have remained as unsolved enigmas to date. Newer tools and availability of high throughput sequencing data have enabled the reanalysis of previously undiagnosed patients. In this review, we have systematically compiled the latest developments in the discovery of the genetic causes of rare diseases using machine learning methods. Importantly, we have detailed methods available to reanalyze existing whole exome sequencing data of unsolved rare diseases. We have identified different reanalysis methodologies to solve problems associated with sequence alterations/mutations, variation re-annotation, protein stability, splice isoform malfunctions and oligogenic analysis. In addition, we give an overview of new developments in the field of rare disease research using whole genome sequencing data and other omics.
    Keywords:  machine learning; rare diseases; reanalysis
    DOI:  https://doi.org/10.3390/ijms23126792
  24. Methods Mol Biol. 2022 ;2493 137-151
    Structural Variant Detection from Long-Read Sequencing Data with cuteSV.
    Tao Jiang, Shiqi Liu, Shuqi Cao, Yadong Wang.
      Structural Variation (SV) represents genomic rearrangements and is strongly associated with human health and disease. Recently, long-read sequencing technologies provide the opportunity to more comprehensive identification of SVs at an ever-high resolution. However, under the circumstance of high sequencing errors and the complexity of SVs, there remains lots of technical issues to be settled. Hence, we propose cuteSV, a sensitive, fast, and scalable alignment-based SV detection approach to complete comprehensive discovery of diverse SVs. The benchmarking results indicate cuteSV is suitable for large-scale genome project since its excellent SV yields and ultra-fast speed. Here, we explain the overall framework for providing a detailed outline for users to apply cuteSV correctly and comprehensively. More details are available at https://github.com/tjiangHIT/cuteSV .
    Keywords:  Alignment-based calling; Bioinformatics; Germline mutation calling; Long-read sequencing; Population-based calling; Scaling performance; Structural variants detection
    DOI:  https://doi.org/10.1007/978-1-0716-2293-3_9
  25. Methods Mol Biol. 2022 ;2493 1-19
    Data Processing and Germline Variant Calling with the Sentieon Pipeline.
    Rafael Aldana, Donald Freed.
      Public and private genomic sequencing initiatives generate ever-increasing amounts of genomic data creating a need for improved solutions for genomics data processing (Stephens et al.PLoS Biol 13:e1002195, 2015). The Sentieon® Genomics software enables rapid and accurate analysis of next-generation sequence data. In this work, we present a typical use of the Sentieon Genomics software for germline variant calling. The Sentieon germline variant calling pipeline produces more accurate results than other tools on third-party benchmarks (Katherine et al. Front Genet 10:736, 2019; Shen et al. bioRxiv, 885517, 2019) in one tenth the time of comparable pipelines. Parts of this guide come from the official Sentieon Genomics software manual in https://support.sentieon.com/manual (Sentieon. Sentieon Genomics software manual, n.d.) and from the official Sentieon Genomics software application notes in https://support.sentieon.com/appnotes  (Sentieon. Sentieon Genomics software application notes, n.d.) and are republished with permission. For additional details and advanced usage instructions of the Sentieon tools, refer to the software manual.
    Keywords:  Bioinformatics; DNA sequencing; Genomics; Machine learning; Variant calling
    DOI:  https://doi.org/10.1007/978-1-0716-2293-3_1
  26. Biomedicines. 2022 Jun 06. pii: 1329. [Epub ahead of print]10(6):
    New Insights into the Neurodegeneration Mechanisms Underlying Riboflavin Transporter Deficiency (RTD): Involvement of Energy Dysmetabolism and Cytoskeletal Derangement.
    Fiorella Colasuonno, Chiara Marioli, Marco Tartaglia, Enrico Bertini, Claudia Compagnucci, Sandra Moreno.
      Riboflavin transporter deficiency (RTD) is a rare genetic disorder characterized by motor, sensory and cranial neuropathy. This childhood-onset neurodegenerative disease is caused by biallelic pathogenic variants in either SLC52A2 or SLC52A3 genes, resulting in insufficient supply of riboflavin (vitamin B2) and consequent impairment of flavoprotein-dependent metabolic pathways. Current therapy, empirically based high-dose riboflavin supplementation, ameliorates the progression of the disease, even though response to treatment is variable and partial. Recent studies have highlighted concurrent pathogenic contribution of cellular energy dysmetabolism and cytoskeletal derangement. In this context, patient specific RTD models, based on induced pluripotent stem cell (iPSC) technology, have provided evidence of redox imbalance, involving mitochondrial and peroxisomal dysfunction. Such oxidative stress condition likely causes cytoskeletal perturbation, associated with impaired differentiation of RTD motor neurons. In this review, we discuss the most recent findings obtained using different RTD models. Relevantly, the integration of data from innovative iPSC-derived in vitro models and invertebrate in vivo models may provide essential information on RTD pathophysiology. Such novel insights are expected to suggest custom therapeutic strategies, especially for those patients unresponsive to high-dose riboflavin treatments.
    Keywords:  cytoskeleton; energy metabolism; fatty acid oxidation; induced pluripotent stem cells; mitochondria; motor neuron disease; oxidative stress; peroxisome; riboflavin; riboflavin transporter deficiency
    DOI:  https://doi.org/10.3390/biomedicines10061329
  27. Nat Commun. 2022 Jun 18. 13(1): 3508
    A randomized placebo-controlled clinical trial for pharmacological activation of BCAA catabolism in patients with type 2 diabetes.
    Froukje Vanweert, Michael Neinast, Edmundo Erazo Tapia, Tineke van de Weijer, Joris Hoeks, Vera B Schrauwen-Hinderling, Megan C Blair, Marc R Bornstein, Matthijs K C Hesselink, Patrick Schrauwen, Zoltan Arany, Esther Phielix.
      Elevations in plasma branched-chain amino acid (BCAA) levels associate with insulin resistance and type 2 diabetes (T2D). Pre-clinical models suggest that lowering BCAA levels improve glucose tolerance, but data in humans are lacking. Here, we used sodium phenylbutyrate (NaPB), an accelerator of BCAA catabolism, as tool to lower plasma BCAA levels in patients with T2D, and evaluate its effect on metabolic health. This trial (NetherlandsTrialRegister: NTR7426) had a randomized, placebo-controlled, double-blind cross-over design and was performed in the Maastricht University Medical Center (MUMC+), the Netherlands, between February 2019 and February 2020. Patients were eligible for the trial if they were 40-75years, BMI of 25-38 kg/m², relatively well-controlled T2D (HbA1C < 8.5%) and treated with oral glucose-lowering medication. Eighteen participants were randomly assigned to receive either NaPB 4.8 g/m²/day and placebo for 2 weeks via controlled randomization and sixteen participants completed the study. The primary outcome was peripheral insulin sensitivity. Secondary outcomes were ex vivo muscle mitochondrial oxidative capacity, substrate oxidation and ectopic fat accumulation. Fasting blood samples were collected to determine levels of BCAA, their catabolic intermediates, insulin, triglycerides, free fatty acids (FFA) and glucose. NaPB led to a robust 27% improvement in peripheral insulin sensitivity compared to placebo (ΔRd:13.2 ± 1.8 vs. 9.6 ± 1.8 µmol/kg/min, p = 0.02). This was paralleled by an improvement in pyruvate-driven muscle mitochondrial oxidative capacity and whole-body insulin-stimulated carbohydrate oxidation, and a reduction in plasma BCAA and glucose levels. No effects were observed on levels of insulin, triglycerides and FFA, neither did fat accumulation in muscle and liver change. No adverse events were reported. These data establish the proof-of-concept in humans that modulating the BCAA oxidative pathway may represent a potential treatment strategy for patients with T2D.
    DOI:  https://doi.org/10.1038/s41467-022-31249-9
  28. Nat Metab. 2022 Jun 20.
    YAP/TAZ-TEAD link angiogenesis to nutrients.
    Roxana E Oberkersch, Massimo M Santoro.
      
    DOI:  https://doi.org/10.1038/s42255-022-00579-9
  29. Reprod Sci. 2022 Jun 23.
    Targeted Deletion of Mitofusin 1 and Mitofusin 2 Causes Female Infertility and Loss of Follicular Reserve.
    Mauro Cozzolino, Yagmur Ergun, Emre Seli.
      Mitochondria are dynamic organelles that regulate their size, shape, and morphology through mechanisms called fusion and fission, to continually adapt themselves to their bioenergetic environment. These mechanisms play a critical role to maintain the mitochondrial function under metabolic and environmental stress. Mitofusin 1 (MFN1) and mitofusin 2 (MFN2) are transmembrane GTPases that regulate mitochondrial fusion mechanism and are required for the maintenance of cellular homeostasis. In this study, we aimed to determine the role of mitofusins in female reproductive competence and senescence using a mouse model with oocyte-specific double deletion of Mfn1 and Mfn2, eliminating the potential functional redundancy of these two proteins. Oocyte-specific targeted double deletion of Mfn1 and Mfn2 in mice resulted in female infertility associated with impaired follicular development and oocyte maturation. It also resulted in altered mitochondrial dynamics and mitochondrial dysfunction. Lack of Mfn1 and Mfn2 in oocytes resulted in accelerated follicular depletion and impaired oocyte quality which are consistent with phenotype of reproductive aging.
    Keywords:  Female fertility; Follicular depletion; Mitochondrial dysfunction; Mitochondrial fusion; Mitofusin
    DOI:  https://doi.org/10.1007/s43032-022-01014-w
  30. Metabolites. 2022 Jun 07. pii: 526. [Epub ahead of print]12(6):
    mGWAS-Explorer: Linking SNPs, Genes, Metabolites, and Diseases for Functional Insights.
    Le Chang, Guangyan Zhou, Huiting Ou, Jianguo Xia.
      Tens of thousands of single-nucleotide polymorphisms (SNPs) have been identified to be significantly associated with metabolite abundance in over 65 genome-wide association studies with metabolomics (mGWAS) to date. Obtaining mechanistic or functional insights from these associations for translational applications has become a key research area in the mGWAS community. Here, we introduce mGWAS-Explorer, a user-friendly web-based platform to help connect SNPs, metabolites, genes, and their known disease associations via powerful network visual analytics. The application of the mGWAS-Explorer was demonstrated using a COVID-19 and a type 2 diabetes case studies.
    Keywords:  SNP; cross-phenotype association analysis; mGWAS; mQTL; metabolomics; network; pleiotropy
    DOI:  https://doi.org/10.3390/metabo12060526
  31. Nature. 2022 Jun 22.
    eIF5B and eIF1A reorient initiator tRNA to allow ribosomal subunit joining.
    Christopher P Lapointe, Rosslyn Grosely, Masaaki Sokabe, Carlos Alvarado, Jinfan Wang, Elizabeth Montabana, Nancy Villa, Byung-Sik Shin, Thomas E Dever, Christopher S Fraser, Israel S Fernández, Joseph D Puglisi.
      Translation initiation defines the identity and quantity of a synthesized protein. The process is dysregulated in many human diseases1,2. A key commitment step is when the ribosomal subunits join at a translation start site on a messenger RNA to form a functional ribosome. Here, we combined single-molecule spectroscopy and structural methods using an in vitro reconstituted system to examine how the human ribosomal subunits join. Single-molecule fluorescence revealed when the universally conserved eukaryotic initiation factors eIF1A and eIF5B associate with and depart from initiation complexes. Guided by single-molecule dynamics, we visualized initiation complexes that contained both eIF1A and eIF5B using single-particle cryo-electron microscopy. The resulting structure revealed how eukaryote-specific contacts between the two proteins remodel the initiation complex to orient the initiator aminoacyl-tRNA in a conformation compatible with ribosomal subunit joining. Collectively, our findings provide a quantitative and architectural framework for the molecular choreography orchestrated by eIF1A and eIF5B during translation initiation in humans.
    DOI:  https://doi.org/10.1038/s41586-022-04858-z
  32. Methods Mol Biol. 2022 ;2493 235-245
    UMI-Varcal: A Low-Frequency Variant Caller for UMI-Tagged Paired-End Sequencing Data.
    Vincent Sater, Pierre-Julien Viailly, Thierry Lecroq, Élise Prieur-Gaston, Élodie Bohers, Mathieu Viennot, Philippe Ruminy, Hélène Dauchel, Pierre Vera, Fabrice Jardin.
      The rapid transition from traditional sequencing methods to Next-Generation Sequencing (NGS) has allowed for a faster and more accurate detection of somatic variants (Single-Nucleotide Variant (SNV) and Copy Number Variation (CNV)) in tumor cells. NGS technologies require a succession of steps during which false variants can be silently added at low frequencies. Filtering these artifacts can be a rather difficult task especially when the experiments are designed to look for very low frequency variants. Recently, adding unique molecular barcodes called UMI (Unique Molecular Identifier) to the DNA fragments appears to be a very effective strategy to specifically filter out false variants from the variant calling results (Kukita et al. DNA Res 22(4):269-277, 2015; Newman et al. Nat Biotechnol 34(5):547-555, 2016; Schmitt et al. Proc Natl Acad Sci U S A 109(36):14508-14513). Here, we describe UMI-VarCal (Sater et al. Bioinformatics 36:2718-2724, 2020), which can use the UMI information from UMI-tagged reads to offer a faster and more accurate variant calling analysis.
    Keywords:  Bioinformatics; NGS; Sequencing; UMI; Variant calling
    DOI:  https://doi.org/10.1007/978-1-0716-2293-3_14
  33. J Comput Biol. 2022 Jun 24.
    RDscan: A New Method for Improving Germline and Somatic Variant Calling Based on Read Depth Distribution.
    Sunho Lee, Seokchol Hong, Jonathan Woo, Jae-Hak Lee, Kyunghee Kim, Lucia Kim, Kunsoo Park, Jongsun Jung.
      Several tools have been developed for calling variants from next-generation sequencing (NGS) data. Although they are generally accurate and reliable, most of them have room for improvement, especially regarding calling variants in datasets with low read depth. In addition, the somatic variants predicted by several somatic variant callers tend to have very low concordance rates. In this study, we developed a new method (RDscan) for improving germline and somatic variant calling in NGS data. RDscan removes misaligned reads, repositions reads, and calculates RDscore based on the read depth distribution. With RDscore, RDscan improves the precision of variant callers by removing false-positive variant calls. When we tested our new tool using the latest variant calling algorithms and data from the 1000 Genomes Project and Illumina's public datasets, accuracy was improved for most of the algorithms. After screening variants with RDscan, calling accuracies increased for germline variants in 11 of 12 cases and for somatic variants in 21 of 24 cases. RDscan is simple to use and can effectively remove false-positive variants while maintaining a low computation load. Therefore, RDscan, along with existing variant callers, should contribute to improvements in genome analysis.
    Keywords:  germline variant; next-generation sequencing; read depth distribution; somatic variant; variant calling; variant filtering
    DOI:  https://doi.org/10.1089/cmb.2021.0269
  34. Bioinformatics. 2022 Jun 25. pii: btac409. [Epub ahead of print]
    ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2.
    Emil K Gustavsson, David Zhang, Regina H Reynolds, Sonia Garcia-Ruiz, Mina Ryten.
       MOTIVATION: The advent of long-read sequencing technologies has increased demand for the visualisation and interpretation of transcripts. However, tools that perform such visualizations remain inflexible and lack the ability to easily identify differences between transcript structures. Here, we introduce ggtranscript, an R package that provides a fast and flexible method to visualize and compare transcripts. As a ggplot2 extension, ggtranscript inherits the functionality and familiarity of ggplot2 making it easy to use.
    AVAILABILITY: ggtranscript is an R package available at https://github.com/dzhang32/ggtranscript (DOI: https://doi.org/10.5281/zenodo.6374061) via an open-source MIT license. Further is available at https://dzhang32.github.io/ggtranscript/.
    SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
    DOI:  https://doi.org/10.1093/bioinformatics/btac409
  35. Metabolites. 2022 Jun 04. pii: 519. [Epub ahead of print]12(6):
    Quantitative Comparison of Statistical Methods for Analyzing Human Metabolomics Data.
    Mir Henglin, Brian L Claggett, Joseph Antonelli, Mona Alotaibi, Gino Alberto Magalang, Jeramie D Watrous, Kim A Lagerborg, Gavin Ovsak, Gabriel Musso, Olga V Demler, Ramachandran S Vasan, Martin G Larson, Mohit Jain, Susan Cheng.
      Emerging technologies now allow for mass spectrometry-based profiling of thousands of small molecule metabolites ('metabolomics') in an increasing number of biosamples. While offering great promise for insight into the pathogenesis of human disease, standard approaches have not yet been established for statistically analyzing increasingly complex, high-dimensional human metabolomics data in relation to clinical phenotypes, including disease outcomes. To determine optimal approaches for analysis, we formally compare traditional and newer statistical learning methods across a range of metabolomics dataset types. In simulated and experimental metabolomics data derived from large population-based human cohorts, we observe that with an increasing number of study subjects, univariate compared to multivariate methods result in an apparently higher false discovery rate as represented by substantial correlation between metabolites directly associated with the outcome and metabolites not associated with the outcome. Although the higher frequency of such associations would not be considered false in the strict statistical sense, it may be considered biologically less informative. In scenarios wherein the number of assayed metabolites increases, as in measures of nontargeted versus targeted metabolomics, multivariate methods performed especially favorably across a range of statistical operating characteristics. In nontargeted metabolomics datasets that included thousands of metabolite measures, sparse multivariate models demonstrated greater selectivity and lower potential for spurious relationships. When the number of metabolites was similar to or exceeded the number of study subjects, as is common with nontargeted metabolomics analysis of relatively small cohorts, sparse multivariate models exhibited the most-robust statistical power with more consistent results. These findings have important implications for metabolomics analysis in human disease.
    Keywords:  metabolomics; multivariate; statistical methods; univariate
    DOI:  https://doi.org/10.3390/metabo12060519
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