Mitochondrial Medicine 2018: Nashville
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The Role of PARP1 in Monocyte and Macrophage
cells Review The Role of PARP1 in Monocyte and Macrophage Commitment and Specification: Future Perspectives and Limitations for the Treatment of Monocyte and Macrophage Relevant Diseases with PARP Inhibitors Maciej Sobczak 1, Marharyta Zyma 2 and Agnieszka Robaszkiewicz 1,* 1 Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; [email protected] 2 Department of Immunopathology, Medical University of Lodz, 7/9 Zeligowskiego, Bldg 2, Rm177, 90-752 Lodz, Poland; [email protected] * Correspondence: [email protected]; Tel.: +48-42-6354449; Fax: +48-42-6354449 or +48-42-635-4473 Received: 4 August 2020; Accepted: 4 September 2020; Published: 6 September 2020 Abstract: Modulation of PARP1 expression, changes in its enzymatic activity, post-translational modifications, and inflammasome-dependent cleavage play an important role in the development of monocytes and numerous subtypes of highly specialized macrophages. Transcription of PARP1 is governed by the proliferation status of cells at each step of their development. Higher abundance of PARP1 in embryonic stem cells and in hematopoietic precursors supports their self-renewal and pluri-/multipotency, whereas a low level of the enzyme in monocytes determines the pattern of surface receptors and signal transducers that are functionally linked to the NFκB pathway. In macrophages, the involvement of PARP1 in regulation of transcription, signaling, inflammasome activity, metabolism, and redox balance supports macrophage polarization towards the pro-inflammatory phenotype (M1), which drives host defense against pathogens. On the other hand, it seems to limit the development of a variety of subsets of anti-inflammatory myeloid effectors (M2), which help to remove tissue debris and achieve healing. -
High-Throughput, Pooled Sequencing Identifies Mutations in NUBPL And
ARTICLES High-throughput, pooled sequencing identifies mutations in NUBPL and FOXRED1 in human complex I deficiency Sarah E Calvo1–3,10, Elena J Tucker4,5,10, Alison G Compton4,10, Denise M Kirby4, Gabriel Crawford3, Noel P Burtt3, Manuel Rivas1,3, Candace Guiducci3, Damien L Bruno4, Olga A Goldberger1,2, Michelle C Redman3, Esko Wiltshire6,7, Callum J Wilson8, David Altshuler1,3,9, Stacey B Gabriel3, Mark J Daly1,3, David R Thorburn4,5 & Vamsi K Mootha1–3 Discovering the molecular basis of mitochondrial respiratory chain disease is challenging given the large number of both mitochondrial and nuclear genes that are involved. We report a strategy of focused candidate gene prediction, high-throughput sequencing and experimental validation to uncover the molecular basis of mitochondrial complex I disorders. We created seven pools of DNA from a cohort of 103 cases and 42 healthy controls and then performed deep sequencing of 103 candidate genes to identify 151 rare variants that were predicted to affect protein function. We established genetic diagnoses in 13 of 60 previously unsolved cases using confirmatory experiments, including cDNA complementation to show that mutations in NUBPL and FOXRED1 can cause complex I deficiency. Our study illustrates how large-scale sequencing, coupled with functional prediction and experimental validation, can be used to identify causal mutations in individual cases. Complex I of the mitochondrial respiratory chain is a large ~1-MDa assembly factors are probably required, as suggested by the 20 factors macromolecular machine composed of 45 protein subunits encoded necessary for assembly of the smaller complex IV9 and by cohort by both the nuclear and mitochondrial (mtDNA) genomes. -
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. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
(12) Patent Application Publication (10) Pub. No.: US 2003/0082511 A1 Brown Et Al
US 20030082511A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2003/0082511 A1 Brown et al. (43) Pub. Date: May 1, 2003 (54) IDENTIFICATION OF MODULATORY Publication Classification MOLECULES USING INDUCIBLE PROMOTERS (51) Int. Cl." ............................... C12O 1/00; C12O 1/68 (52) U.S. Cl. ..................................................... 435/4; 435/6 (76) Inventors: Steven J. Brown, San Diego, CA (US); Damien J. Dunnington, San Diego, CA (US); Imran Clark, San Diego, CA (57) ABSTRACT (US) Correspondence Address: Methods for identifying an ion channel modulator, a target David B. Waller & Associates membrane receptor modulator molecule, and other modula 5677 Oberlin Drive tory molecules are disclosed, as well as cells and vectors for Suit 214 use in those methods. A polynucleotide encoding target is San Diego, CA 92121 (US) provided in a cell under control of an inducible promoter, and candidate modulatory molecules are contacted with the (21) Appl. No.: 09/965,201 cell after induction of the promoter to ascertain whether a change in a measurable physiological parameter occurs as a (22) Filed: Sep. 25, 2001 result of the candidate modulatory molecule. Patent Application Publication May 1, 2003 Sheet 1 of 8 US 2003/0082511 A1 KCNC1 cDNA F.G. 1 Patent Application Publication May 1, 2003 Sheet 2 of 8 US 2003/0082511 A1 49 - -9 G C EH H EH N t R M h so as se W M M MP N FIG.2 Patent Application Publication May 1, 2003 Sheet 3 of 8 US 2003/0082511 A1 FG. 3 Patent Application Publication May 1, 2003 Sheet 4 of 8 US 2003/0082511 A1 KCNC1 ITREXCHO KC 150 mM KC 2000000 so 100 mM induced Uninduced Steady state O 100 200 300 400 500 600 700 Time (seconds) FIG. -
Antiviral Properties of Chalcones and Their Synthetic Derivatives: a Mini Review
Pharmacia 67(4): 325–337 DOI 10.3897/pharmacia.67.e53842 Review Article Antiviral properties of chalcones and their synthetic derivatives: a mini review Radoslav Marinov1, Nadezhda Markova2, Stefka Krumova1, Kamelia Yotovska3, Maya M. Zaharieva4, Petia Genova-Kalou1 1 Department of Virology, National Centre of Infectious and Parasitic Diseases, 44A Gen. Stoletov Blvd., 1233 Sofia, Bulgaria 2 Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., bl. 9, 1113 Sofia, Bulgaria 3 Faculty of Biology, Sofia University St. Kliment Ohridski, 8 Dragan Tzankov Blvd., 1164 Sofia, Bulgaria 4 Department of Infectious Microbiology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., bl. 25, 1113 Sofia, Bulgaria Corresponding author: Petia Genova-Kalou ([email protected]) Received 2 May 2020 ♦ Accepted 24 May 2020 ♦ Published 27 November 2020 Citation: Marinov R, Markova N, Krumova S, Yotovska K, Zaharieva MM, Genova-Kalou P (2020) Antiviral properties of chalcones and their synthetic derivatives: a mini review. Pharmacia 67(4): 325–337. https://doi.org/10.3897/pharmacia.67.e53842 Abstract Chalcones (natural or synthetic derivatives) are aromatic ketones possessing a central backbone that form a core for variety import- ant compounds with different substitutions. Recent scientific advances show that chalcones exhibit different bio-medical activities, including antiviral, which is related to the variety substitutions. This review provides general information on the origin, sources, virucidal and direct antiviral properties of chalcones in vitro, as well as a brief overview of the possible application and molecular modes of action of these compounds. -
The Green Alga Chlamydomonas Reinhardtii: a New Model System To
THE GREEN ALGA CHLAMYDOMONAS REINHARDTII: A NEW MODEL SYSTEM TO UNRAVEL THE ASSEMBLY PROCESS OF RESPIRATORY COMPLEXES DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By María del Rosario Barbieri Graduate Program in Plant Cellular and Molecular Biology The Ohio State University 2010 Dissertation Committee Professor Patrice P. Hamel, Adviser Professor Iris Meier Professor Erich Grotewold Professor Juan D. Alfonzo ABSTRACT The general purpose of this research is to contribute to a better understanding of the mitochondrial NADH: ubiquinone oxidoreductase (Complex I) and to illustrate the current view of its assembly process. I propose to use the green alga Chlamydomonas reinhardtii as a novel model system to carry out the molecular dissection of Complex I assembly. The main objective is to discover novel genes controlling the assembly process of this multimeric enzyme. Several reasons including patient death at young age, strict regulations, and ethical concerns make the study of Complex I on humans highly difficult. Although traditionally well established model systems such as the fungi Yarrowia lipolytica and Neurospora crassa and human cell lines have proven useful to understand the role of specific subunits in the assembly process, forward genetic approaches leading to discovery of novel assembly factors have been limited by the lack of straightforward screening methodologies (REMACLE et al. 2008). The process of plant Complex I assembly is largely obscure at present, despite the progress achieved in recent years. In plants, similarly to other eukaryotes, there is no simple strategy to approach the issue of assembly. -
A Novel Familial Case of Diffuse Leukodystrophy Related to NDUFV1 Compound Heterozygous Mutations
Mitochondrion 13 (2013) 749–754 Contents lists available at ScienceDirect Mitochondrion journal homepage: www.elsevier.com/locate/mito A novel familial case of diffuse leukodystrophy related to NDUFV1 compound heterozygous mutations Oscar Ortega-Recalde a,1, Dora Janeth Fonseca a,b,1, Liliana Catherine Patiño a, Juan Jaime Atuesta c, Carolina Rivera-Nieto a, Carlos Martín Restrepo a,b, Heidi Eliana Mateus a, Marjo S. van der Knaap d, Paul Laissue a,b,⁎ a Unidad de Genética, Escuela de Medicina y Ciencias de la Salud, Universidad del Rosario, Bogotá, Colombia b Genética Molecular de Colombia, Departamento de Genética Molecular, Bogotá, Colombia c Centro Dermatológico Federico Lleras Acosta, Bogotá, Colombia d Department of Child Neurology, VU University Medical Center, Amsterdam, The Netherlands article info abstract Article history: NDUFV1 mutations have been related to encephalopathic phenotypes due to mitochondrial energy metabo- Received 13 December 2012 lism disturbances. In this study, we report two siblings affected by a diffuse leukodystrophy, who carry the Received in revised form 25 March 2013 NDUFV1 c.1156C>T (p.Arg386Cys) missense mutation and a novel 42-bp deletion. Bioinformatic and molec- Accepted 27 March 2013 ular analysis indicated that this deletion lead to the synthesis of mRNA molecules carrying a premature stop Available online 4 April 2013 codon, which might be degraded by the nonsense-mediated decay system. Our results add information on the molecular basis and the phenotypic features of mitochondrial disease caused by NDUFV1 mutations. Keywords: Mitochondrial disease © 2013 Elsevier B.V. and Mitochondria Research Society. All rights reserved. Diffuse leukodystrophy NDUFV1 mutations Genetics 1. -
The Evolutionary Diversity of Uracil DNA Glycosylase Superfamily
Clemson University TigerPrints All Dissertations Dissertations December 2017 The Evolutionary Diversity of Uracil DNA Glycosylase Superfamily Jing Li Clemson University, [email protected] Follow this and additional works at: https://tigerprints.clemson.edu/all_dissertations Recommended Citation Li, Jing, "The Evolutionary Diversity of Uracil DNA Glycosylase Superfamily" (2017). All Dissertations. 2546. https://tigerprints.clemson.edu/all_dissertations/2546 This Dissertation is brought to you for free and open access by the Dissertations at TigerPrints. It has been accepted for inclusion in All Dissertations by an authorized administrator of TigerPrints. For more information, please contact [email protected]. THE EVOLUTIONARY DIVERSITY OF URACIL DNA GLYCOSYLASE SUPERFAMILY A Dissertation Presented to the Graduate School of Clemson University In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy Biochemistry and Molecular Biology by Jing Li December 2017 Accepted by: Dr. Weiguo Cao, Committee Chair Dr. Alex Feltus Dr. Cheryl Ingram-Smith Dr. Jeremy Tzeng ABSTRACT Uracil DNA glycosylase (UDG) is a crucial member in the base excision (BER) pathway that is able to specially recognize and cleave the deaminated DNA bases, including uracil (U), hypoxanthine (inosine, I), xanthine (X) and oxanine (O). Currently, based on the sequence similarity of 3 functional motifs, the UDG superfamily is divided into 6 families. Each family has evolved distinct substrate specificity and properties. In this thesis, I broadened the UDG superfamily by characterization of three new groups of enzymes. In chapter 2, we identified a new subgroup of enzyme in family 3 SMUG1 from Listeria Innocua. This newly found SMUG1-like enzyme has distinct catalytic residues and exhibits strong preference on single-stranded DNA substrates. -
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. -
(12) Patent Application Publication (10) Pub. No.: US 2014/0079836A1 Mcdaniel (43) Pub
US 20140079836A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2014/0079836A1 McDaniel (43) Pub. Date: Mar. 20, 2014 (54) METHODS AND COMPOSITIONS FOR (52) U.S. Cl. ALTERING HEALTH, WELLBEING AND CPC ............... A61K 36/74 (2013.01); A61 K3I/122 LIFESPAN (2013.01) USPC ............. 424/777; 514/690: 435/375; 506/16; (71) Applicant: LifeSpan Extension, LLC, Virginia 435/6.12 Beach, VA (US) (72) Inventor: David H. McDaniel, Virginia Beach, VA (57) ABSTRACT (US) Described herein are the results of comprehensive genetic (73) Assignee: LifeSpan Extension, LLC expression and other molecular analysis p the effect s anti oxidants on biological systems, including specifically differ (21) Appl. No.: 14/084,553 ent human cells. Based on these analyses, methods and com (22) Filed: Nov. 19, 2013 positions are described for modifying or influencing the lifespan of cells, tissues, organs, and organisms. In various Related U.S. Application Data embodiments, there are provided methods for modulating the activity of the gene maintenance process in order to influence (60) Continuation of application No. 13/898.307, filed on the length and/or structural integrity of the telomere in living May 20, 2013, which is a division of application No. cells, as well as methods for modulating the rate/efficiency of 12/629,040, filed on Dec. 1, 2009, now abandoned. the cellular respiration provided by the mitochondria, mito (60) Provisional application No. 61/118,945, filed on Dec. chondrial biogenesis, and maintenance of the mitochondrial 1, 2008. membrane potential. Exemplary lifespan altering compounds include natural and synthetic antioxidants, such as plant anti Publication Classification oxidant and polyphenol compounds derived from coffee cherry, tea, berry, and so forth, including but not limited to (51) Int. -
Respiratory Chain Complex I Deficiency Caused by Mitochondrial DNA
European Journal of Human Genetics (2011) 19, 769–775 & 2011 Macmillan Publishers Limited All rights reserved 1018-4813/11 www.nature.com/ejhg ARTICLE Respiratory chain complex I deficiency caused by mitochondrial DNA mutations Helen Swalwell1, Denise M Kirby2, Emma L Blakely1, Anna Mitchell1, Renato Salemi2,6, Canny Sugiana2,3,7, Alison G Compton2, Elena J Tucker2,3, Bi-Xia Ke2, Phillipa J Lamont4, Douglass M Turnbull1, Robert McFarland1, Robert W Taylor1 and David R Thorburn*,2,3,5 Defects of the mitochondrial respiratory chain are associated with a diverse spectrum of clinical phenotypes, and may be caused by mutations in either the nuclear or the mitochondrial genome (mitochondrial DNA (mtDNA)). Isolated complex I deficiency is the most common enzyme defect in mitochondrial disorders, particularly in children in whom family history is often consistent with sporadic or autosomal recessive inheritance, implicating a nuclear genetic cause. In contrast, although a number of recurrent, pathogenic mtDNA mutations have been described, historically, these have been perceived as rare causes of paediatric complex I deficiency. We reviewed the clinical and genetic findings in a large cohort of 109 paediatric patients with isolated complex I deficiency from 101 families. Pathogenic mtDNA mutations were found in 29 of 101 probands (29%), 21 in MTND subunit genes and 8 in mtDNA tRNA genes. Nuclear gene defects were inferred in 38 of 101 (38%) probands based on cell hybrid studies, mtDNA sequencing or mutation analysis (nuclear gene mutations were identified in 22 probands). Leigh or Leigh-like disease was the most common clinical presentation in both mtDNA and nuclear genetic defects.