Exclusive Neuronal Expression of SUCLA2 in the Human Brain
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Two Transgenic Mouse Models for Β-Subunit Components of Succinate-Coa Ligase Yielding Pleiotropic Metabolic Alterations
Two transgenic mouse models for -subunit components of succinate-CoA ligase yielding pleiotropic metabolic alterations Kacso, Gergely; Ravasz, Dora; Doczi, Judit; Németh, Beáta; Madgar, Ory; Saada, Ann; Ilin, Polina; Miller, Chaya; Ostergaard, Elsebet; Iordanov, Iordan; Adams, Daniel; Vargedo, Zsuzsanna; Araki, Masatake; Araki, Kimi; Nakahara, Mai; Ito, Haruka; Gál, Aniko; Molnár, Mária J; Nagy, Zsolt; Patocs, Attila; Adam-Vizi, Vera; Chinopoulos, Christos Published in: Biochemical Journal DOI: 10.1042/BCJ20160594 Publication date: 2016 Document version Publisher's PDF, also known as Version of record Document license: CC BY Citation for published version (APA): Kacso, G., Ravasz, D., Doczi, J., Németh, B., Madgar, O., Saada, A., Ilin, P., Miller, C., Ostergaard, E., Iordanov, I., Adams, D., Vargedo, Z., Araki, M., Araki, K., Nakahara, M., Ito, H., Gál, A., Molnár, M. J., Nagy, Z., ... Chinopoulos, C. (2016). Two transgenic mouse models for -subunit components of succinate-CoA ligase yielding pleiotropic metabolic alterations. Biochemical Journal, 473(20), 3463-3485. https://doi.org/10.1042/BCJ20160594 Download date: 02. okt.. 2021 Biochemical Journal (2016) 473 3463–3485 DOI: 10.1042/BCJ20160594 Research Article Two transgenic mouse models for β-subunit components of succinate-CoA ligase yielding pleiotropic metabolic alterations Gergely Kacso1,2, Dora Ravasz1,2, Judit Doczi1,2, Beáta Németh1,2, Ory Madgar1,2, Ann Saada3, Polina Ilin3, Chaya Miller3, Elsebet Ostergaard4, Iordan Iordanov1,5, Daniel Adams1,2, Zsuzsanna Vargedo1,2, Masatake -
Whole-Genome Microarray Detects Deletions and Loss of Heterozygosity of Chromosome 3 Occurring Exclusively in Metastasizing Uveal Melanoma
Anatomy and Pathology Whole-Genome Microarray Detects Deletions and Loss of Heterozygosity of Chromosome 3 Occurring Exclusively in Metastasizing Uveal Melanoma Sarah L. Lake,1 Sarah E. Coupland,1 Azzam F. G. Taktak,2 and Bertil E. Damato3 PURPOSE. To detect deletions and loss of heterozygosity of disease is fatal in 92% of patients within 2 years of diagnosis. chromosome 3 in a rare subset of fatal, disomy 3 uveal mela- Clinical and histopathologic risk factors for UM metastasis noma (UM), undetectable by fluorescence in situ hybridization include large basal tumor diameter (LBD), ciliary body involve- (FISH). ment, epithelioid cytomorphology, extracellular matrix peri- ϩ ETHODS odic acid-Schiff-positive (PAS ) loops, and high mitotic M . Multiplex ligation-dependent probe amplification 3,4 5 (MLPA) with the P027 UM assay was performed on formalin- count. Prescher et al. showed that a nonrandom genetic fixed, paraffin-embedded (FFPE) whole tumor sections from 19 change, monosomy 3, correlates strongly with metastatic death, and the correlation has since been confirmed by several disomy 3 metastasizing UMs. Whole-genome microarray analy- 3,6–10 ses using a single-nucleotide polymorphism microarray (aSNP) groups. Consequently, fluorescence in situ hybridization were performed on frozen tissue samples from four fatal dis- (FISH) detection of chromosome 3 using a centromeric probe omy 3 metastasizing UMs and three disomy 3 tumors with Ͼ5 became routine practice for UM prognostication; however, 5% years’ metastasis-free survival. to 20% of disomy 3 UM patients unexpectedly develop metas- tases.11 Attempts have therefore been made to identify the RESULTS. Two metastasizing UMs that had been classified as minimal region(s) of deletion on chromosome 3.12–15 Despite disomy 3 by FISH analysis of a small tumor sample were found these studies, little progress has been made in defining the key on MLPA analysis to show monosomy 3. -
Identification and Characterization of TPRKB Dependency in TP53 Deficient Cancers
Identification and Characterization of TPRKB Dependency in TP53 Deficient Cancers. by Kelly Kennaley A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Molecular and Cellular Pathology) in the University of Michigan 2019 Doctoral Committee: Associate Professor Zaneta Nikolovska-Coleska, Co-Chair Adjunct Associate Professor Scott A. Tomlins, Co-Chair Associate Professor Eric R. Fearon Associate Professor Alexey I. Nesvizhskii Kelly R. Kennaley [email protected] ORCID iD: 0000-0003-2439-9020 © Kelly R. Kennaley 2019 Acknowledgements I have immeasurable gratitude for the unwavering support and guidance I received throughout my dissertation. First and foremost, I would like to thank my thesis advisor and mentor Dr. Scott Tomlins for entrusting me with a challenging, interesting, and impactful project. He taught me how to drive a project forward through set-backs, ask the important questions, and always consider the impact of my work. I’m truly appreciative for his commitment to ensuring that I would get the most from my graduate education. I am also grateful to the many members of the Tomlins lab that made it the supportive, collaborative, and educational environment that it was. I would like to give special thanks to those I’ve worked closely with on this project, particularly Dr. Moloy Goswami for his mentorship, Lei Lucy Wang, Dr. Sumin Han, and undergraduate students Bhavneet Singh, Travis Weiss, and Myles Barlow. I am also grateful for the support of my thesis committee, Dr. Eric Fearon, Dr. Alexey Nesvizhskii, and my co-mentor Dr. Zaneta Nikolovska-Coleska, who have offered guidance and critical evaluation since project inception. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Complex I Deficiency Due to Loss of Ndufs4 in the Brain Results
Complex I deficiency due to loss of Ndufs4 in the brain results in progressive encephalopathy resembling Leigh syndrome Albert Quintanaa,1, Shane E. Krusea,1, Raj P. Kapurb, Elisenda Sanzc, and Richard D. Palmitera,2 aHoward Hughes Medical Institute and Department of Biochemistry, University of Washington, Seattle, WA 98195; bDepartment of Laboratories, Seattle Children’s Hospital, Seattle, WA 98105; and cDepartment of Pharmacology, University of Washington, Seattle, WA 98195 Contributed by Richard D. Palmiter, May 5, 2010 (sent for review April 22, 2010) To explore the lethal, ataxic phenotype of complex I deficiency in least one intact Ndufs4 allele are indistinguishable from WT Ndufs4 knockout (KO) mice, we inactivated Ndufs4 selectively in mice, and they are sometimes used interchangeably with WT as neurons and glia (NesKO mice). NesKO mice manifested the same controls (CT). To examine the role of the CNS in pathology, we symptoms as KO mice including retarded growth, loss of motor restricted the inactivation of Ndufs4 gene to neurons and lox/lox ability, breathing abnormalities, and death by ∼7 wk. Progressive astroglial cells by crossing the Ndufs4 mice with mice neuronal deterioration and gliosis in specific brain areas corre- expressing Cre recombinase from the Nestin locus (19) to create sponded to behavioral changes as the disease advanced, with mice that we refer to as NesKO mice. We confirmed that Nestin- early involvement of the olfactory bulb, cerebellum, and vestibular Cre results in recombination primarily in the CNS by crossing the nuclei. Neurons, particularly in these brain regions, had aberrant mice with a Rosa26-reporter line and by PCR analysis of DNA mitochondrial morphology. -
SUCLG2 Identified As Both a Determinator of CSF Ab1– 42 Levels and an Attenuator of Cognitive Decline in Alzheimer's Disease
Human Molecular Genetics, 2014, Vol. 23, No. 24 6644–6658 doi:10.1093/hmg/ddu372 Advance Access published on July 15, 2014 SUCLG2 identified as both a determinator of CSF Ab1– 42 levels and an attenuator of cognitive decline in Alzheimer’s disease Alfredo Ramirez1,2,{,∗, Wiesje M. van der Flier6,7,{, Christine Herold8,{, David Ramonet3,{, Stefanie Heilmann2,4, Piotr Lewczuk9, Julius Popp1, Andre´ Lacour8, Dmitriy Drichel8, Eva Louwersheimer6,7, Markus P. Kummer3,8, Carlos Cruchaga10,11, Per Hoffmann2,4,13, Charlotte 6,7 6,7 9 14 15 Teunissen , Henne Holstege , Johannes Kornhuber , Oliver Peters , Adam C. Naj , Vincent Downloaded from Chouraki16,17,Ce´line Bellenguez18,19,20, Amy Gerrish21, International Genomics of Alzheimer’s Project (IGAP){, Alzheimer’s Disease Neuroimaging Initiative (ADNI)}, Reiner Heun1, Lutz Fro¨ lich22, Michael Hu¨ ll23, Lara Buscemi24, Stefan Herms2,4,13, Heike Ko¨ lsch1, Philip Scheltens6,7, Monique M. Breteler8, Eckart Ru¨ ther25, Jens Wiltfang25, Alison Goate10,12, Frank Jessen1,8, http://hmg.oxfordjournals.org/ Wolfgang Maier1,8, Michael T. Heneka3,8,§, Tim Becker5,8,§ and Markus M. No¨ then2,4,§ 1Department of Psychiatry and Psychotherapy, 2Institute of Human Genetics, 3Clinical Neuroscience Unit, Department of Neurology, 4Department of Genomics, Life & Brain Center, 5Institute for Medical Biometry, Informatics, and Epidemiology, University of Bonn, 53127, Bonn, Germany, 6Department of Neurology and Alzheimer Center, Neuroscience Campus Amsterdam, VU University Medical Center, 1081 HZ, Amsterdam, The Netherlands, -
Mitochondrial Genetics
Mitochondrial genetics Patrick Francis Chinnery and Gavin Hudson* Institute of Genetic Medicine, International Centre for Life, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK Introduction: In the last 10 years the field of mitochondrial genetics has widened, shifting the focus from rare sporadic, metabolic disease to the effects of mitochondrial DNA (mtDNA) variation in a growing spectrum of human disease. The aim of this review is to guide the reader through some key concepts regarding mitochondria before introducing both classic and emerging mitochondrial disorders. Sources of data: In this article, a review of the current mitochondrial genetics literature was conducted using PubMed (http://www.ncbi.nlm.nih.gov/pubmed/). In addition, this review makes use of a growing number of publically available databases including MITOMAP, a human mitochondrial genome database (www.mitomap.org), the Human DNA polymerase Gamma Mutation Database (http://tools.niehs.nih.gov/polg/) and PhyloTree.org (www.phylotree.org), a repository of global mtDNA variation. Areas of agreement: The disruption in cellular energy, resulting from defects in mtDNA or defects in the nuclear-encoded genes responsible for mitochondrial maintenance, manifests in a growing number of human diseases. Areas of controversy: The exact mechanisms which govern the inheritance of mtDNA are hotly debated. Growing points: Although still in the early stages, the development of in vitro genetic manipulation could see an end to the inheritance of the most severe mtDNA disease. Keywords: mitochondria/genetics/mitochondrial DNA/mitochondrial disease/ mtDNA Accepted: April 16, 2013 Mitochondria *Correspondence address. The mitochondrion is a highly specialized organelle, present in almost all Institute of Genetic Medicine, International eukaryotic cells and principally charged with the production of cellular Centre for Life, Newcastle energy through oxidative phosphorylation (OXPHOS). -
OXPHOS Remodeling in High-Grade Prostate Cancer Involves Mtdna Mutations and Increased Succinate Oxidation
ARTICLE https://doi.org/10.1038/s41467-020-15237-5 OPEN OXPHOS remodeling in high-grade prostate cancer involves mtDNA mutations and increased succinate oxidation Bernd Schöpf 1, Hansi Weissensteiner 1, Georg Schäfer2, Federica Fazzini1, Pornpimol Charoentong3, Andreas Naschberger1, Bernhard Rupp1, Liane Fendt1, Valesca Bukur4, Irina Giese4, Patrick Sorn4, Ana Carolina Sant’Anna-Silva 5, Javier Iglesias-Gonzalez6, Ugur Sahin4, Florian Kronenberg 1, ✉ Erich Gnaiger 5,6 & Helmut Klocker 7 1234567890():,; Rewiring of energy metabolism and adaptation of mitochondria are considered to impact on prostate cancer development and progression. Here, we report on mitochondrial respiration, DNA mutations and gene expression in paired benign/malignant human prostate tissue samples. Results reveal reduced respiratory capacities with NADH-pathway substrates glu- tamate and malate in malignant tissue and a significant metabolic shift towards higher succinate oxidation, particularly in high-grade tumors. The load of potentially deleterious mitochondrial-DNA mutations is higher in tumors and associated with unfavorable risk factors. High levels of potentially deleterious mutations in mitochondrial Complex I-encoding genes are associated with a 70% reduction in NADH-pathway capacity and compensation by increased succinate-pathway capacity. Structural analyses of these mutations reveal amino acid alterations leading to potentially deleterious effects on Complex I, supporting a causal relationship. A metagene signature extracted from the transcriptome of tumor samples exhibiting a severe mitochondrial phenotype enables identification of tumors with shorter survival times. 1 Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University Innsbruck, Schöpfstraße 41, A-6020 Innsbruck, Austria. 2 Institute of Pathology, Neuropathology and Molecular Pathology, Medical University Innsbruck, Müllerstraße 44, A-6020 Innsbruck, Austria. -
A High-Throughput Approach to Uncover Novel Roles of APOBEC2, a Functional Orphan of the AID/APOBEC Family
Rockefeller University Digital Commons @ RU Student Theses and Dissertations 2018 A High-Throughput Approach to Uncover Novel Roles of APOBEC2, a Functional Orphan of the AID/APOBEC Family Linda Molla Follow this and additional works at: https://digitalcommons.rockefeller.edu/ student_theses_and_dissertations Part of the Life Sciences Commons A HIGH-THROUGHPUT APPROACH TO UNCOVER NOVEL ROLES OF APOBEC2, A FUNCTIONAL ORPHAN OF THE AID/APOBEC FAMILY A Thesis Presented to the Faculty of The Rockefeller University in Partial Fulfillment of the Requirements for the degree of Doctor of Philosophy by Linda Molla June 2018 © Copyright by Linda Molla 2018 A HIGH-THROUGHPUT APPROACH TO UNCOVER NOVEL ROLES OF APOBEC2, A FUNCTIONAL ORPHAN OF THE AID/APOBEC FAMILY Linda Molla, Ph.D. The Rockefeller University 2018 APOBEC2 is a member of the AID/APOBEC cytidine deaminase family of proteins. Unlike most of AID/APOBEC, however, APOBEC2’s function remains elusive. Previous research has implicated APOBEC2 in diverse organisms and cellular processes such as muscle biology (in Mus musculus), regeneration (in Danio rerio), and development (in Xenopus laevis). APOBEC2 has also been implicated in cancer. However the enzymatic activity, substrate or physiological target(s) of APOBEC2 are unknown. For this thesis, I have combined Next Generation Sequencing (NGS) techniques with state-of-the-art molecular biology to determine the physiological targets of APOBEC2. Using a cell culture muscle differentiation system, and RNA sequencing (RNA-Seq) by polyA capture, I demonstrated that unlike the AID/APOBEC family member APOBEC1, APOBEC2 is not an RNA editor. Using the same system combined with enhanced Reduced Representation Bisulfite Sequencing (eRRBS) analyses I showed that, unlike the AID/APOBEC family member AID, APOBEC2 does not act as a 5-methyl-C deaminase. -
SUCLA2 Mutations Cause Global Protein Succinylation Contributing To
ARTICLE https://doi.org/10.1038/s41467-020-19743-4 OPEN SUCLA2 mutations cause global protein succinylation contributing to the pathomechanism of a hereditary mitochondrial disease ✉ Philipp Gut 1,2,17 , Sanna Matilainen3,17, Jesse G. Meyer4,14,17, Pieti Pällijeff3, Joy Richard2, Christopher J. Carroll5, Liliya Euro 3, Christopher B. Jackson 3, Pirjo Isohanni3,6, Berge A. Minassian7,8, Reem A. Alkhater9, Elsebet Østergaard10, Gabriele Civiletto2, Alice Parisi2, Jonathan Thevenet2, Matthew J. Rardin4,15, Wenjuan He1, Yuya Nishida1, John C. Newman 1, Xiaojing Liu11,16, Stefan Christen2, ✉ ✉ Sofia Moco 2, Jason W. Locasale 11, Birgit Schilling 4,18 , Anu Suomalainen 3,12,13,18 & 1234567890():,; ✉ Eric Verdin 1,4,18 Mitochondrial acyl-coenzyme A species are emerging as important sources of protein modification and damage. Succinyl-CoA ligase (SCL) deficiency causes a mitochondrial encephalomyopathy of unknown pathomechanism. Here, we show that succinyl-CoA accumulates in cells derived from patients with recessive mutations in the tricarboxylic acid cycle (TCA) gene succinyl-CoA ligase subunit-β (SUCLA2), causing global protein hyper- succinylation. Using mass spectrometry, we quantify nearly 1,000 protein succinylation sites on 366 proteins from patient-derived fibroblasts and myotubes. Interestingly, hyper- succinylated proteins are distributed across cellular compartments, and many are known targets of the (NAD+)-dependent desuccinylase SIRT5. To test the contribution of hyper- succinylation to disease progression, we develop a zebrafish model of the SCL deficiency and find that SIRT5 gain-of-function reduces global protein succinylation and improves survival. Thus, increased succinyl-CoA levels contribute to the pathology of SCL deficiency through post-translational modifications. -
Screen for Abnormal Mitochondrial Phenotypes in Mouse Embryonic Stem Cells Identifies a Model for Succinyl-Coa Ligase Deficiency and Mtdna Depletion Taraka R
© 2014. Published by The Company of Biologists Ltd | Disease Models & Mechanisms (2014) 7, 271-280 doi:10.1242/dmm.013466 RESOURCE ARTICLE Screen for abnormal mitochondrial phenotypes in mouse embryonic stem cells identifies a model for succinyl-CoA ligase deficiency and mtDNA depletion Taraka R. Donti1,‡, Carmen Stromberger1,*,‡, Ming Ge1, Karen W. Eldin2, William J. Craigen1,3 and Brett H. Graham1,§ ABSTRACT prevalence of mitochondrial disorders might be as high as 1 in 5000, Mutations in subunits of succinyl-CoA synthetase/ligase (SCS), a making mitochondrial disease one of the more common genetic component of the citric acid cycle, are associated with mitochondrial causes of encephalomyopathies and multisystem disease (Schaefer et encephalomyopathy, elevation of methylmalonic acid (MMA), and al., 2004; Elliott et al., 2008; Schaefer et al., 2008). Despite important mitochondrial DNA (mtDNA) depletion. A FACS-based retroviral- insights into clinical, biochemical and molecular features of these mediated gene trap mutagenesis screen in mouse embryonic stem disorders, the underlying molecular pathogenesis remains poorly (ES) cells for abnormal mitochondrial phenotypes identified a gene understood and no clearly effective therapies exist. Mitochondria trap allele of Sucla2 (Sucla2SAβgeo), which was used to generate contain their own genome that consists of a multicopy, ~16.4-kilobase transgenic mice. Sucla2 encodes the ADP-specific β-subunit isoform circular chromosome. This mitochondrial DNA (mtDNA) encodes 13 of SCS. Sucla2SAβgeo homozygotes exhibited recessive lethality, with polypeptides that are subunits of various respiratory chain complexes most mutants dying late in gestation (e18.5). Mutant placenta and as well as 22 tRNAs and two rRNAs required for mitochondrial embryonic (e17.5) brain, heart and muscle showed varying degrees protein translation. -
Succinyl-Coa Synthetase Deficiency in Siblings with Impaired Pyruvate Dehydrogenase Complex (PDC) and Other Oxidative
Harvard Medical School Succinyl-CoA synthetase deficiency in siblings with impaired pyruvate dehydrogenase complex (PDC) and other oxidative Boston Children’s Hospital enzymes in skeletal muscle without mtDNA depletion Cleveland Medical Center Xiaoping Huanga,, Jirair K. Bedoyanb,c,d,j, Didem Demirbasa, David J. Harrisa,e, Alexander Mironc, Simone Edelheitc, George Grahamed, Suzanne D. DeBrossebc,j, Lee-Jun Wongf, Charles L. Hoppeld,g,h, Douglas S. Kerrd,j, Irina Anselmi, and Gerard T. Berrya,e a Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital (BCH), Boston, MA, USA; b Center for Human Genetics, University Hospitals Cleveland Medical Center (UHCMC), Cleveland, OH, USA; c Department of Genetics and Genome Sciences, Case Western Reserve University (CWRU), Cleveland, OH, USA; d Center for Inherited Disorders of Energy Metabolism (CIDEM), UHCMC, Cleveland, OH, USA; e Department of Pediatrics, Harvard Medical School, Boston, MA, USA; f Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; g Department of Pharmacology, CWRU, Cleveland, OH, USA; h Department of Medicine, CWRU, Cleveland, OH, USA; I Department of Neurology, BCH, Boston, MA USA; and j Department of Pediatrics, CWRU, Cleveland, OH, USA. SUMMARY These authors contributed equally to this work. Mutations in SUCLA2 result in succinyl-CoA ligase (ATP-forming) or succinyl-CoA synthetase (ADP-forming) (A-SCS) deficiency, a mitochondrial tricarboxylic acid cycle disorder (Fig. 1). The phenotype associated with this gene defect is largely encephalomyopathy. We describe two siblings compound heterozygous for SUCLA2 mutations, c.985A>G (p.M329V) and c.920C>T (p.A307V), with parents confirmed as carriers of each mutation.