DOCSLIB.ORG

Upregulation of COX4-2 Via HIF-1Α in Mitochondrial COX4-1Deficiency

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Upregulation of COX4-2 Via HIF-1Α in Mitochondrial COX4-1Deficiency Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 10 February 2021 Upregulation of COX4-2 via HIF-1α in mitochondrial COX4-1deficiency Liza Douiev1*, Chaya Miller1, Shmuel Ruppo2, Hadar Benyamini2, Bassam Abu-Libdeh3, Ann Saada1,4* Affiliations 1 Department of Genetics, Hadassah Medical Center, Jerusalem 9112001, Israel. 2 Info-CORE, I-CORE Bioinformatics Unit of the Hebrew University of Jerusalem and Hadassah Medical Center 3 Department of Pediatrics, Makassed Hospital and Al-Quds University, Jerusalem 91220, Palestinian Authority 4Faculty of Medicine, Hebrew University of Jerusalem, 9112001, Israel *corresponding authors Prof. Ann Saada (Reisch), Department of Genetics, Hadassah Medical Center, Jerusalem 9112001, Israel. [email protected], [email protected] Liza Douiev, Department of Genetics, Hadassah Medical Center, Jerusalem 9112001, Israel [email protected] Abstract Cytochrome-c-oxidase (COX) subunit 4 (COX4) plays important roles in the function, assembly and regulation of COX (mitochondrial respiratory complex 4), the terminal electron acceptor of the oxidative phosphorylation (OXPHOS) system. The principal COX4 isoform, COX4-1, is expressed in all tissues, whereas COX4-2 is mainly expressed in the lungs, or under hypoxia and other stress conditions. We have previously described a patient with a COX4-1 defect with a relatively mild presentation compared to other primary COX deficiencies, and hypothesized that this could be the result of compensatory upregulation of COX4-2. To this end, COX4-1 was downregulated by shRNAs in human foreskin fibroblasts (HFF), and compared to patient's cells. COX4-1, COX4-2 and HIF-1α were detected by immunocytochemistry. The mRNA transcripts of both COX4 isoforms and HIF-1 target genes were carried out by RT-qPCR. COX activity and OXPHOS function were measured by enzymatic and oxygen consumption assays, respectively. Pathways were analyzed by CEL-Seq2 and by RT-qPCR. We demonstrate elevated COX4-2 levels in the COX4-1-deficient cells with a concomitant HIF-1α stabilization, nuclear localization and upregulated hypoxia and glycolysis pathways. We suggest that COX4-2 and HIF-1α has the are upregulated, also in normoxia as a compensatory mechanism in COX4-1 deficiency. Key Words Mitochondria, cytochrome c oxidase, COX4-1, COX4-2, HIF-1α © 2021 by the author(s). Distributed under a Creative Commons CC BY license. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 10 February 2021 1. Introduction: The mammalian cytochrome c oxidase (COX, mitochondrial respiratory chain complex IV) is a dimeric multi-subunit complex which is comprised of fourteen mitochondrial and nuclear-encoded subunits. COX is considered the rate-limiting complex of the oxidative phosphorylation system (OXPHOS). The two unique regulatory mechanisms (compared to the other OXPHOS complexes) are; the expression of isoforms and the binding of specific regulatory factors to nuclear-encoded subunits [ 2 Arnold. Mitochondrion. 2012]. One important regulatory mechanism involves the COX4 isoforms and feedback inhibition by ATP. COX4 is the largest nuclear encoded subunit and plays important roles in COX function, assembly and regulation. It is allosterically inhibited at high ATP/ADP ratios, and by phosphorylation, allowing fine tuning of the mitochondrial respiratory capacity. COX4 isoform 1 (COX4-1), which is the main subunit 4 of COX, is ubiquitously expressed in mammalian tissues under normoxic conditions. COX4 isoform 2 (COX4-2) the less common isoform, is primarily expressed in the lung and in lower levels in the placenta, heart, brain and pancreas. COX4-2 is preferentially expressed under hypoxia and oxidative stress and it is suggested that the isoform switch results in a more efficient COX activity. [2 Arnold, 3 Timon]. In 2017, we reported a novel form of COX deficiency caused by a K101N variant in COX4I1 gene encoding COX4-1 in a patient presented with Fanconi anemia-like features, short stature and mild dysmorphism, while all known Fanconi Anemia (FA) gene sequences were intact. We proved the pathogenicity of the homozygous K101N variant by demonstrating 25% residual COX activity in patients’ fibroblasts homogenate, almost undetectable COX4-1 protein in mitochondria, and by performing complementation studies with the wild-type gene [4Abu-Libdeh, 2017]. Additionally, we verified chromosomal instability by Phospho-Histone H2A.X (γH2AX) staining [5 Douiev 2018]. Recently, an additional pathogenic COX4I1 variant (P152T), associated with a much more severe phenotype resembling Leigh syndrome with developmental regression abnormal MRI and 16% residual COX activity in muscle, was reported by Pilali et al. [6 Pilali]. Notably, the phenotype in our patient was different and relatively mild compared to the COX4-1 P152T patient and other patients with isolated COX deficiencies, and nuclear- encoded mitochondrial diseases in general [7 RAK, 8 shoubridge,9Hock 2020]. Accordingly, we hypothesized that a compensatory isoform switching to COX4-2 is able to, at least partially, compensate for the deficient COX4-1. In this work, we demonstrate elevated COX4-2 in the K101N patient's fibroblasts as well as in a human foreskin fibroblasts cell line (HFF) with stable COX4-1 knockdown. This upregulation is linked to HIF-1α stabilization, nuclear localization and upregulation of both hypoxia and glycolysis pathways. 2. Materials and Methods: 2.1. Tissue cultures Previously established skin primary fibroblasts cultures from the patient (Informed consent was obtained IRB #0485-09) [4Abu-Libdeh 2017] controls and human foreskin fibroblasts (HFF-1 ATCC) were maintained in high-glucose DMEM supplemented with 15% fetal bovine serum, L-glutamine, pyruvate and 50µg/mL uridine (Biological Industries, Beit Ha'emek, Israel). For immunocytochemistry, cells were seeded on u-slide 8 well- ibiTreat sterile tissue culture slides (NBT; New Biotechnology Ltd., Jerusalem, Israel). For western blot or RNA analysis, cells were seeded, cells were grown in tissue culture bottles. For positive hypoxia controls in (Immunostaining and western blot) cells were pre- incubated with 500µL CoCl2 supplemented within a new fresh media, for 6 or 24 hours, at 37°C, 5% CO2 [10 Shteyer2009]. All cells were incubated at 37 °C in a humidified 5% CO2 atmosphere. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 10 February 2021 2.2. RNA interference For the downregulation of COX4I1, we employed the MISSION® shRNA plasmid DNA vector system. The system included five plasmids each is targeted against different site of COX4I1. In addition, we used a non-mammalian shRNA Control Plasmid DNA target as a control vector (Sigma-Aldrich). We introduced each of the DNA plasmids into HEK293FT cells by co-transfection with pLP1, pLP2, and pLP/VSVG plasmids using lipofectamine (ViraPower; Invitrogen, California, USA). Human foreskin fibroblasts were infected with viral supernatant containing polybrene. Stably transfected cells were selected with puromycin (2µg/mL) for three-weeks. Preliminary results showed that shRNA #TRCN0000232554 (COX4-1 shRNA) was the most suitable. 2.3. Quantitative reverse transcription polymerase chain reaction (RT-qPCR) Total RNA was isolated from patient, HFF-shRNA, HFF-CV and healthy control primary fibroblasts with Tri-Reagent (Telron, Isarel) and cDNA from poly(A)+mRNA was generated using Improm II, Promega, Madison, WI, USA. Real time, quantitative PCR for the quantification of COX4I1, COX4I2, PDK1, SLC2A1, HK1, HK2, GUSB and GAPDH transcripts - was performed using Fast SYBR GreenMaster Mix and the ABI PRISM7900HT sequence detection system (Applied Biosystems, Foster City, CA, USA). The following primer sequences were used fo qPCR: Gene Forward primer Reverse primer COX4I1 (NM_001861.6) 5'-TTTCACCGCGCTCGTTAT-3' 5'-CTTCATGTCCAGCATCCTCTT-3' COX4I2 (NM_032609) 5'-GAAGACGAGGGATGCACAG-3' 5'-GGCTCTTCTGGCATGGG-3' PDK1 (NM_001278549.2) 5'- CAGGACACCATCCGTTCAAT-3' 5'- AGCTTTAGCATCCTCAGCAC-3' GLUT1 (NM_006516.4) 5'-GCTACAACACTGGAGTCATCAA-3' 5'-ACTGAGAGGGACCAGAGC-3' HK1 (NM_000188.3) 5'- CCCTAAATGCTGGGAAACAAAG-3' 5'- CCCTTCTTGGTGAAGTCGATTA-3' HK2 (NM_000189.5) 5'- CATCCTCCTCAAGTGGACAAA-3' 5'- ACCACATCCAGGTCAAACTC-3' GUSB (NM_000181.4) 5'-GAAAATATGTGGTTGGAGAGCTCATT-3' 5'-CCGAGTGAAGATCCCCTTTTTA-3' GAPDH (NM_001357943.2) 5'-CAAGAGCACAAGAGGAAGAGAG-3' 5'-CTACATGGCAACTGTGAGGAG-3' 2.4. COX enzymatic activity COX activity in cells disrupted by sonication and solubilization with 0.5mg/mL -dodecyl- β-D-maltoside (Calbiochem, San-Diego, CA, US) on ice, was determined by spectrophotometry monitoring the oxidation of 50µM reduced cytochrome c at 550nm in 10mM potassium phosphate buffer, pH7.0 at 37°C on a Kontron UVICON xs double beam spectrophotometer (Secomam, France) 2.5. Oxygen Consumption rate Oxygen consumption rate (OCR) was measured using Agilent Seahorse XF Cell Mito Stress Test Kit (#103015-100) (Seahorse Biosciences, North Billeric, MA, USA). 10,000 cells/well were seeded on an XF96-well plate. Following 72 hr, the growth medium was changed to an unbuffered DMEM (Agilent Technologies, Inc. Wilmington, USA) supplemented with 10mM glucose 1mM pyruvate and 2mM glutamine and the plate was equilibrated at 37°C for 1 hr before the measurements. In the absence and in the presence of sequentially added 2.5 µM Oligomycin, 2 µM Carbonyl cyanide-4 (trifluoromethoxy) phenylhydrazone (FCCP), 0.5 µM Rotenone and Antimycin), according to the manufacturer's instructions. Oxygen consumption rate (OCR) and extra cellular acidification rate ECAR,
Load more

Recommended publications
  • A Small De Novo 16Q24.1 Duplication in a Woman with Severe Clinical Features
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by HAL-Université de Bretagne Occidentale A small de novo 16q24.1 duplication in a woman with severe clinical features. Sylvia Qu´em´ener-Redon,Caroline B´enech, S´everine Audebert-Bellanger, Ga¨elleFriocourt, Marc Planes, Philippe Parent, Claude F´erec To cite this version: Sylvia Qu´em´ener-Redon, Caroline B´enech, S´everine Audebert-Bellanger, Ga¨elle Friocourt, Marc Planes, et al.. A small de novo 16q24.1 duplication in a woman with severe clini- cal features.. European Journal of Medical Genetics, Elsevier, 2013, epub ahead of print. <10.1016/j.ejmg.2013.01.001>. <inserm-00788405> HAL Id: inserm-00788405 http://www.hal.inserm.fr/inserm-00788405 Submitted on 14 Feb 2013 HAL is a multi-disciplinary open access L'archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destin´eeau d´ep^otet `ala diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publi´esou non, lished or not. The documents may come from ´emanant des ´etablissements d'enseignement et de teaching and research institutions in France or recherche fran¸caisou ´etrangers,des laboratoires abroad, or from public or private research centers. publics ou priv´es. A small de novo 16q24.1 duplication in a woman with severe clinical features Sylvia Quéméner-Redon1,2, Caroline Bénech1,3, Séverine Audebert-Bellanger4, Gaëlle Friocourt1, Marc Planes4, Philippe Parent4 and Claude Férec1,2,3 1 Institut National de la Santé et de la Recherche Médicale (INSERM), UMR1078, Brest, France, 2 Laboratoire de Génétique Moléculaire et d’Histocompatibilité, Centre Hospitalier Universitaire (CHU), Hôpital Morvan, Brest, France, 3 Etablissement Français du Sang (EFS) – Bretagne, Brest, France, 4Service de Pédiatrie et de Génétique Médicale, Centre Hospitalier Universitaire de Brest, Brest, France.
    [Show full text]
  • 4-6 Weeks Old Female C57BL/6 Mice Obtained from Jackson Labs Were Used for Cell Isolation
    Methods Mice: 4-6 weeks old female C57BL/6 mice obtained from Jackson labs were used for cell isolation. Female Foxp3-IRES-GFP reporter mice (1), backcrossed to B6/C57 background for 10 generations, were used for the isolation of naïve CD4 and naïve CD8 cells for the RNAseq experiments. The mice were housed in pathogen-free animal facility in the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee. Preparation of cells: Subsets of thymocytes were isolated by cell sorting as previously described (2), after cell surface staining using CD4 (GK1.5), CD8 (53-6.7), CD3ε (145- 2C11), CD24 (M1/69) (all from Biolegend). DP cells: CD4+CD8 int/hi; CD4 SP cells: CD4CD3 hi, CD24 int/lo; CD8 SP cells: CD8 int/hi CD4 CD3 hi, CD24 int/lo (Fig S2). Peripheral subsets were isolated after pooling spleen and lymph nodes. T cells were enriched by negative isolation using Dynabeads (Dynabeads untouched mouse T cells, 11413D, Invitrogen). After surface staining for CD4 (GK1.5), CD8 (53-6.7), CD62L (MEL-14), CD25 (PC61) and CD44 (IM7), naïve CD4+CD62L hiCD25-CD44lo and naïve CD8+CD62L hiCD25-CD44lo were obtained by sorting (BD FACS Aria). Additionally, for the RNAseq experiments, CD4 and CD8 naïve cells were isolated by sorting T cells from the Foxp3- IRES-GFP mice: CD4+CD62LhiCD25–CD44lo GFP(FOXP3)– and CD8+CD62LhiCD25– CD44lo GFP(FOXP3)– (antibodies were from Biolegend). In some cases, naïve CD4 cells were cultured in vitro under Th1 or Th2 polarizing conditions (3, 4).
    [Show full text]
  • Mutation in the COX4I1 Gene Is Associated with Short Stature, Poor Weight Gain and Increased Chromosomal Breaks, Simulating Fanconi Anemia
    European Journal of Human Genetics (2017) 25, 1142–1146 & 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved 1018-4813/17 www.nature.com/ejhg ARTICLE Mutation in the COX4I1 gene is associated with short stature, poor weight gain and increased chromosomal breaks, simulating Fanconi anemia Bassam Abu-Libdeh*,1,4, Liza Douiev2,3,4, Sarah Amro1, Maher Shahrour1, Asaf Ta-Shma2, Chaya Miller2,3, Orly Elpeleg2 and Ann Saada*,2,3 We describe a novel autosomal recessive form of mitochondrial disease in a child with short stature, poor weight gain, and mild dysmorphic features with highly suspected Fanconi anemia due to a mutation in COX4I1 gene. Whole Exome Sequencing was performed then followed by Sanger confirmation, identified a K101N mutation in COX4I1, segregating with the disease. This nuclear gene encodes the common isoform of cytochrome c oxidase (COX) subunit 4 (COX 4-1), an integral regulatory part of COX (respiratory chain complex IV) the terminal electron acceptor of the mitochondrial respiratory chain. The patient’s fibroblasts disclosed decreased COX activity, impaired ATP production, elevated ROS production, decreased expression of COX4I1 mRNA and undetectable (COX4) protein. COX activity and ATP production were restored by lentiviral transfection with the wild-type gene. Our results demonstrate the first human mutation in the COX4I1 gene linked to diseases and confirm its role in the pathogenesis. Thus COX4I1 mutations should be considered in any patient with features suggestive of this diagnosis. European Journal of Human Genetics (2017) 25, 1142–1146; doi:10.1038/ejhg.2017.112; published online 2 August 2017 INTRODUCTION normal vaginal delivery with birth weight of 2.8 kg after an uneventful Mitochondrial cytochrome c oxidase (COX, complex IV) is the terminal pregnancy.
    [Show full text]
  • Loss of COX4I1 Leads to Combined Respiratory Chain Deficiency And
    cells Article Loss of COX4I1 Leads to Combined Respiratory Chain Deficiency and Impaired Mitochondrial Protein Synthesis Kristýna Cunˇ átová 1,2, David Pajuelo Reguera 1 , Marek Vrbacký 1, Erika Fernández-Vizarra 3 , Shujing Ding 3, Ian M. Fearnley 3, Massimo Zeviani 3 , Josef Houštˇek 1 , Tomáš Mráˇcek 1,* and Petr Pecina 1,* 1 Laboratory of Bioenergetics, Institute of Physiology, Czech Academy of Sciences, 142 00 Prague, Czech Republic; [email protected] (K.C.);ˇ [email protected] (D.P.R.); [email protected] (M.V.); [email protected] (J.H.) 2 Department of Cell Biology, Faculty of Science, Charles University, 128 00 Prague, Czech Republic 3 MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; [email protected] (E.F.-V.); [email protected] (S.D.); [email protected] (I.M.F.); [email protected] (M.Z.) * Correspondence: [email protected] (T.M.); [email protected] (P.P.) Abstract: The oxidative phosphorylation (OXPHOS) system localized in the inner mitochondrial membrane secures production of the majority of ATP in mammalian organisms. Individual OXPHOS complexes form supramolecular assemblies termed supercomplexes. The complexes are linked not only by their function but also by interdependency of individual complex biogenesis or maintenance. For instance, cytochrome c oxidase (cIV) or cytochrome bc1 complex (cIII) deficiencies affect the level of fully assembled NADH dehydrogenase (cI) in monomeric as well as supercomplex forms. It was hypothesized that cI is affected at the level of enzyme assembly as well as at the level of cI stability and maintenance.
    [Show full text]
  • Hypoxia Inducible Factors Modulate Mitochondrial Oxygen Consumption and Transcriptional Regulation of Nuclear-Encoded Electron T
    Article pubs.acs.org/biochemistry Hypoxia Inducible Factors Modulate Mitochondrial Oxygen Consumption and Transcriptional Regulation of Nuclear-Encoded Electron Transport Chain Genes † § † ‡ ∥ † † ‡ † Hye Jin Hwang, , Scott G. Lynn, , , Ajith Vengellur, Yogesh Saini, , Elizabeth A. Grier, † § † § ‡ Shelagh M. Ferguson-Miller, , and John J. LaPres*, , , † ‡ § Department of Biochemistry and Molecular Biology, Center for Integrative Toxicology, and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, Michigan 48824-1319, United States *S Supporting Information ABSTRACT: Hypoxia inducible factor-1 (HIF1) is a stress-responsive nuclear transcription factor that is activated with a decrease in oxygen availability. HIF1 regulates the expression of genes involved in a cell’s adaptation to hypoxic stress, including those with mitochondrial specific function. To gain a more comprehensive understanding of the role of HIF1 in mitochondrial homeostasis, we studied the link between hypoxia, HIF1 transactivation, and electron transport chain (ETC) function. We established immortalized mouse embryonic fibroblasts (MEFs) for HIF1α wild-type (WT) and null cells and tested whether HIF1α regulates mitochondrial respiration by modulating gene expressions of nuclear-encoded ETC components. High- throughput quantitative real-time polymerase chain reaction was performed to screen nuclear- encoded mitochondrial genes related to the ETC to identify those whose regulation was HIF1α- dependent. Our data suggest that HIF1α regulates transcription of cytochrome c oxidase (CcO) heart/muscle isoform 7a1 (Cox7a1) under hypoxia, where it is induced 1.5−2.5-fold, whereas Cox4i2 hypoxic induction was HIF1α-independent. We propose that adaptation to hypoxic stress of CcO as the main cellular oxygen consumer is mediated by induction of hypoxia-sensitive tissue-specific isoforms.
    [Show full text]
  • THE FUNCTIONAL SIGNIFICANCE of MITOCHONDRIAL SUPERCOMPLEXES in C. ELEGANS by WICHIT SUTHAMMARAK Submitted in Partial Fulfillment
    THE FUNCTIONAL SIGNIFICANCE OF MITOCHONDRIAL SUPERCOMPLEXES in C. ELEGANS by WICHIT SUTHAMMARAK Submitted in partial fulfillment of the requirements For the degree of Doctor of Philosophy Dissertation Advisor: Drs. Margaret M. Sedensky & Philip G. Morgan Department of Genetics CASE WESTERN RESERVE UNIVERSITY January, 2011 CASE WESTERN RESERVE UNIVERSITY SCHOOL OF GRADUATE STUDIES We hereby approve the thesis/dissertation of _____________________________________________________ candidate for the ______________________degree *. (signed)_______________________________________________ (chair of the committee) ________________________________________________ ________________________________________________ ________________________________________________ ________________________________________________ ________________________________________________ (date) _______________________ *We also certify that written approval has been obtained for any proprietary material contained therein. Dedicated to my family, my teachers and all of my beloved ones for their love and support ii ACKNOWLEDGEMENTS My advanced academic journey began 5 years ago on the opposite side of the world. I traveled to the United States from Thailand in search of a better understanding of science so that one day I can return to my homeland and apply the knowledge and experience I have gained to improve the lives of those affected by sickness and disease yet unanswered by science. Ultimately, I hoped to make the academic transition into the scholarly community by proving myself through scientific research and understanding so that I can make a meaningful contribution to both the scientific and medical communities. The following dissertation would not have been possible without the help, support, and guidance of a lot of people both near and far. I wish to thank all who have aided me in one way or another on this long yet rewarding journey. My sincerest thanks and appreciation goes to my advisors Philip Morgan and Margaret Sedensky.
    [Show full text]
  • Upregulation of COX4-2 Via HIF-1 in Mitochondrial COX4-1 Deficiency
    cells Article Upregulation of COX4-2 via HIF-1α in Mitochondrial COX4-1 Deficiency Liza Douiev 1,*, Chaya Miller 1, Shmuel Ruppo 2 , Hadar Benyamini 2, Bassam Abu-Libdeh 3 and Ann Saada 1,4,* 1 Department of Genetics, Hadassah Medical Center, Jerusalem 9112001, Israel; [email protected] 2 Info-CORE, I-CORE Bioinformatics Unit of the Hebrew, University of Jerusalem and Hadassah Medical Center, Jerusalem 91120011, Israel; [email protected] (S.R.); [email protected] (H.B.) 3 Department of Pediatrics and Genetics, Makassed Hospital and Al-Quds University, East Jerusalem 91220, Palestine; [email protected] 4 Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112001, Israel * Correspondence: [email protected] (L.D.); [email protected] or [email protected] (A.S.) Abstract: Cytochrome-c-oxidase (COX) subunit 4 (COX4) plays important roles in the function, assembly and regulation of COX (mitochondrial respiratory complex 4), the terminal electron acceptor of the oxidative phosphorylation (OXPHOS) system. The principal COX4 isoform, COX4-1, is expressed in all tissues, whereas COX4-2 is mainly expressed in the lungs, or under hypoxia and other stress conditions. We have previously described a patient with a COX4-1 defect with a relatively mild presentation compared to other primary COX deficiencies, and hypothesized that this could be the result of a compensatory upregulation of COX4-2. To this end, COX4-1 was downregulated by shRNAs in human foreskin fibroblasts (HFF) and compared to the patient’s cells. COX4-1, COX4-2 and HIF-1α were detected by immunocytochemistry.
    [Show full text]
  • Supplementary Table 1
    Supplementary Table 1. 492 genes are unique to 0 h post-heat timepoint. The name, p-value, fold change, location and family of each gene are indicated. Genes were filtered for an absolute value log2 ration 1.5 and a significance value of p ≤ 0.05. Symbol p-value Log Gene Name Location Family Ratio ABCA13 1.87E-02 3.292 ATP-binding cassette, sub-family unknown transporter A (ABC1), member 13 ABCB1 1.93E-02 −1.819 ATP-binding cassette, sub-family Plasma transporter B (MDR/TAP), member 1 Membrane ABCC3 2.83E-02 2.016 ATP-binding cassette, sub-family Plasma transporter C (CFTR/MRP), member 3 Membrane ABHD6 7.79E-03 −2.717 abhydrolase domain containing 6 Cytoplasm enzyme ACAT1 4.10E-02 3.009 acetyl-CoA acetyltransferase 1 Cytoplasm enzyme ACBD4 2.66E-03 1.722 acyl-CoA binding domain unknown other containing 4 ACSL5 1.86E-02 −2.876 acyl-CoA synthetase long-chain Cytoplasm enzyme family member 5 ADAM23 3.33E-02 −3.008 ADAM metallopeptidase domain Plasma peptidase 23 Membrane ADAM29 5.58E-03 3.463 ADAM metallopeptidase domain Plasma peptidase 29 Membrane ADAMTS17 2.67E-04 3.051 ADAM metallopeptidase with Extracellular other thrombospondin type 1 motif, 17 Space ADCYAP1R1 1.20E-02 1.848 adenylate cyclase activating Plasma G-protein polypeptide 1 (pituitary) receptor Membrane coupled type I receptor ADH6 (includes 4.02E-02 −1.845 alcohol dehydrogenase 6 (class Cytoplasm enzyme EG:130) V) AHSA2 1.54E-04 −1.6 AHA1, activator of heat shock unknown other 90kDa protein ATPase homolog 2 (yeast) AK5 3.32E-02 1.658 adenylate kinase 5 Cytoplasm kinase AK7
    [Show full text]
  • Chromosomal Microarray Analysis in Turkish Patients with Unexplained Developmental Delay and Intellectual Developmental Disorders
    177 Arch Neuropsychitry 2020;57:177−191 RESEARCH ARTICLE https://doi.org/10.29399/npa.24890 Chromosomal Microarray Analysis in Turkish Patients with Unexplained Developmental Delay and Intellectual Developmental Disorders Hakan GÜRKAN1 , Emine İkbal ATLI1 , Engin ATLI1 , Leyla BOZATLI2 , Mengühan ARAZ ALTAY2 , Sinem YALÇINTEPE1 , Yasemin ÖZEN1 , Damla EKER1 , Çisem AKURUT1 , Selma DEMİR1 , Işık GÖRKER2 1Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey 2Faculty of Medicine, Department of Child and Adolescent Psychiatry, Trakya University, Edirne, Turkey ABSTRACT Introduction: Aneuploids, copy number variations (CNVs), and single in 39 (39/123=31.7%) patients. Twelve CNV variant of unknown nucleotide variants in specific genes are the main genetic causes of significance (VUS) (9.75%) patients and 7 CNV benign (5.69%) patients developmental delay (DD) and intellectual disability disorder (IDD). were reported. In 6 patients, one or more pathogenic CNVs were These genetic changes can be detected using chromosome analysis, determined. Therefore, the diagnostic efficiency of CMA was found to chromosomal microarray (CMA), and next-generation DNA sequencing be 31.7% (39/123). techniques. Therefore; In this study, we aimed to investigate the Conclusion: Today, genetic analysis is still not part of the routine in the importance of CMA in determining the genomic etiology of unexplained evaluation of IDD patients who present to psychiatry clinics. A genetic DD and IDD in 123 patients. diagnosis from CMA can eliminate genetic question marks and thus Method: For 123 patients, chromosome analysis, DNA fragment analysis alter the clinical management of patients. Approximately one-third and microarray were performed. Conventional G-band karyotype of the positive CMA findings are clinically intervenable.
    [Show full text]
  • Role of Cytochrome C Oxidase Nuclear-Encoded Subunits in Health and Disease
    Physiol. Res. 69: 947-965, 2020 https://doi.org/10.33549/physiolres.934446 REVIEW Role of Cytochrome c Oxidase Nuclear-Encoded Subunits in Health and Disease Kristýna ČUNÁTOVÁ1, David PAJUELO REGUERA1, Josef HOUŠTĚK1, Tomáš MRÁČEK1, Petr PECINA1 1Department of Bioenergetics, Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic Received February 2, 2020 Accepted September 13, 2020 Epub Ahead of Print November 2, 2020 Summary [email protected] and Tomáš Mráček, Department of Cytochrome c oxidase (COX), the terminal enzyme of Bioenergetics, Institute of Physiology CAS, Vídeňská 1083, 142 mitochondrial electron transport chain, couples electron transport 20 Prague 4, Czech Republic. E-mail: [email protected] to oxygen with generation of proton gradient indispensable for the production of vast majority of ATP molecules in mammalian Cytochrome c oxidase cells. The review summarizes current knowledge of COX structure and function of nuclear-encoded COX subunits, which may Energy demands of mammalian cells are mainly modulate enzyme activity according to various conditions. covered by ATP synthesis carried out by oxidative Moreover, some nuclear-encoded subunits possess tissue-specific phosphorylation apparatus (OXPHOS) located in the and development-specific isoforms, possibly enabling fine-tuning central bioenergetic organelle, mitochondria. OXPHOS is of COX function in individual tissues. The importance of nuclear- composed of five multi-subunit complexes embedded in encoded subunits is emphasized by recently discovered the inner mitochondrial membrane (IMM). Electron pathogenic mutations in patients with severe mitopathies. In transport from reduced substrates of complexes I and II to addition, proteins substoichiometrically associated with COX were cytochrome c oxidase (COX, complex IV, CIV) is found to contribute to COX activity regulation and stabilization of achieved by increasing redox potential of individual the respiratory supercomplexes.
    [Show full text]
  • Human Mitochondrial Pathologies of the Respiratory Chain and ATP Synthase: Contributions from Studies of Saccharomyces Cerevisiae
    life Review Human Mitochondrial Pathologies of the Respiratory Chain and ATP Synthase: Contributions from Studies of Saccharomyces cerevisiae Leticia V. R. Franco 1,2,* , Luca Bremner 1 and Mario H. Barros 2 1 Department of Biological Sciences, Columbia University, New York, NY 10027, USA; [email protected] 2 Department of Microbiology,Institute of Biomedical Sciences, Universidade de Sao Paulo, Sao Paulo 05508-900, Brazil; [email protected] * Correspondence: [email protected] Received: 27 October 2020; Accepted: 19 November 2020; Published: 23 November 2020 Abstract: The ease with which the unicellular yeast Saccharomyces cerevisiae can be manipulated genetically and biochemically has established this organism as a good model for the study of human mitochondrial diseases. The combined use of biochemical and molecular genetic tools has been instrumental in elucidating the functions of numerous yeast nuclear gene products with human homologs that affect a large number of metabolic and biological processes, including those housed in mitochondria. These include structural and catalytic subunits of enzymes and protein factors that impinge on the biogenesis of the respiratory chain. This article will review what is currently known about the genetics and clinical phenotypes of mitochondrial diseases of the respiratory chain and ATP synthase, with special emphasis on the contribution of information gained from pet mutants with mutations in nuclear genes that impair mitochondrial respiration. Our intent is to provide the yeast mitochondrial specialist with basic knowledge of human mitochondrial pathologies and the human specialist with information on how genes that directly and indirectly affect respiration were identified and characterized in yeast. Keywords: mitochondrial diseases; respiratory chain; yeast; Saccharomyces cerevisiae; pet mutants 1.
    [Show full text]
  • Supplementary Table S1. List of Differentially Expressed
    Supplementary table S1. List of differentially expressed transcripts (FDR adjusted p‐value < 0.05 and −1.4 ≤ FC ≥1.4). 1 ID Symbol Entrez Gene Name Adj. p‐Value Log2 FC 214895_s_at ADAM10 ADAM metallopeptidase domain 10 3,11E‐05 −1,400 205997_at ADAM28 ADAM metallopeptidase domain 28 6,57E‐05 −1,400 220606_s_at ADPRM ADP‐ribose/CDP‐alcohol diphosphatase, manganese dependent 6,50E‐06 −1,430 217410_at AGRN agrin 2,34E‐10 1,420 212980_at AHSA2P activator of HSP90 ATPase homolog 2, pseudogene 6,44E‐06 −1,920 219672_at AHSP alpha hemoglobin stabilizing protein 7,27E‐05 2,330 aminoacyl tRNA synthetase complex interacting multifunctional 202541_at AIMP1 4,91E‐06 −1,830 protein 1 210269_s_at AKAP17A A‐kinase anchoring protein 17A 2,64E‐10 −1,560 211560_s_at ALAS2 5ʹ‐aminolevulinate synthase 2 4,28E‐06 3,560 212224_at ALDH1A1 aldehyde dehydrogenase 1 family member A1 8,93E‐04 −1,400 205583_s_at ALG13 ALG13 UDP‐N‐acetylglucosaminyltransferase subunit 9,50E‐07 −1,430 207206_s_at ALOX12 arachidonate 12‐lipoxygenase, 12S type 4,76E‐05 1,630 AMY1C (includes 208498_s_at amylase alpha 1C 3,83E‐05 −1,700 others) 201043_s_at ANP32A acidic nuclear phosphoprotein 32 family member A 5,61E‐09 −1,760 202888_s_at ANPEP alanyl aminopeptidase, membrane 7,40E‐04 −1,600 221013_s_at APOL2 apolipoprotein L2 6,57E‐11 1,600 219094_at ARMC8 armadillo repeat containing 8 3,47E‐08 −1,710 207798_s_at ATXN2L ataxin 2 like 2,16E‐07 −1,410 215990_s_at BCL6 BCL6 transcription repressor 1,74E‐07 −1,700 200776_s_at BZW1 basic leucine zipper and W2 domains 1 1,09E‐06 −1,570 222309_at
    [Show full text]