Altered Mitochondrial Dynamics in Motor Neuron Disease: an Emerging Perspective
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Seq2pathway Vignette
seq2pathway Vignette Bin Wang, Xinan Holly Yang, Arjun Kinstlick May 19, 2021 Contents 1 Abstract 1 2 Package Installation 2 3 runseq2pathway 2 4 Two main functions 3 4.1 seq2gene . .3 4.1.1 seq2gene flowchart . .3 4.1.2 runseq2gene inputs/parameters . .5 4.1.3 runseq2gene outputs . .8 4.2 gene2pathway . 10 4.2.1 gene2pathway flowchart . 11 4.2.2 gene2pathway test inputs/parameters . 11 4.2.3 gene2pathway test outputs . 12 5 Examples 13 5.1 ChIP-seq data analysis . 13 5.1.1 Map ChIP-seq enriched peaks to genes using runseq2gene .................... 13 5.1.2 Discover enriched GO terms using gene2pathway_test with gene scores . 15 5.1.3 Discover enriched GO terms using Fisher's Exact test without gene scores . 17 5.1.4 Add description for genes . 20 5.2 RNA-seq data analysis . 20 6 R environment session 23 1 Abstract Seq2pathway is a novel computational tool to analyze functional gene-sets (including signaling pathways) using variable next-generation sequencing data[1]. Integral to this tool are the \seq2gene" and \gene2pathway" components in series that infer a quantitative pathway-level profile for each sample. The seq2gene function assigns phenotype-associated significance of genomic regions to gene-level scores, where the significance could be p-values of SNPs or point mutations, protein-binding affinity, or transcriptional expression level. The seq2gene function has the feasibility to assign non-exon regions to a range of neighboring genes besides the nearest one, thus facilitating the study of functional non-coding elements[2]. Then the gene2pathway summarizes gene-level measurements to pathway-level scores, comparing the quantity of significance for gene members within a pathway with those outside a pathway. -
Kinetic Analysis of Human DNA Ligase III by Justin R. Mcnally A
Kinetic Analysis of Human DNA Ligase III by Justin R. McNally A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Biological Chemistry) in the University of Michigan 2019 Doctoral Committee: Associate Professor Patrick J. O’Brien, Chair Associate Professor Bruce A. Palfey Associate Professor JoAnn M. Sekiguchi Associate Professor Raymond C. Trievel Professor Thomas E. Wilson Justin R. McNally [email protected] ORCID iD: 0000-0003-2694-2410 © Justin R. McNally 2019 Table of Contents List of Tables iii List of Figures iv Abstract vii Chapter 1 Introduction to the human DNA ligases 1 Chapter 2 Kinetic Analyses of Single-Strand Break Repair by Human DNA Ligase III Isoforms Reveal Biochemical Differences from DNA Ligase I 20 Chapter 3 The LIG3 N-terminus, in its entirety, contributes to single-strand DNA break ligation 56 Chapter 4 Comparative end-joining by human DNA ligases I and III 82 Chapter 5 A real-time DNA ligase assay suitable for high throughput screening 113 Chapter 6 Conclusions and Future Directions 137 ii List of Tables Table 2.1: Comparison of kinetic parameters for multiple turnover ligation by human DNA ligases 31 Table 2.2: Comparison of single-turnover parameters of LIG3β and LIG1 34 Table 3.1: Comparison of LIG3β N-terminal mutant kinetic parameters 67 Table 4.1: Rate constants for sequential ligation by LIG3β 95 Table 5.1: Comparison of multiple turnover kinetic parameters determined by real-time fluorescence assay and reported values 129 iii List of Figures Figure -
Tricarboxylic Acid Cycle Metabolites As Mediators of DNA Methylation Reprogramming in Bovine Preimplantation Embryos
Supplementary Materials Tricarboxylic Acid Cycle Metabolites as Mediators of DNA Methylation Reprogramming in Bovine Preimplantation Embryos Figure S1. (A) Total number of cells in fast (FBL) and slow (SBL) blastocysts; (B) Fluorescence intensity for 5-methylcytosine and 5-hydroxymethylcytosine of fast and slow blastocysts of cells from Trophoectoderm (TE) or inner cell mass (ICM). Fluorescence intensity for 5-methylcytosine of cells from the ICM or TE in blastocysts cultured with (C) dimethyl-succinate or (D) dimethyl-α- ketoglutarate. Statistical significance is identified by different letters. Figure S2. Experimental design. Table S1. Selected genes related to metabolism and epigenetic mechanisms from RNA-Seq analysis of bovine blastocysts (slow vs. fast). Genes in blue represent upregulation in slow blastocysts, genes in red represent upregulation in fast blastocysts. log2FoldCh Gene p-value p-Adj ange PDHB −1.425 0.000 0.000 MDH1 −1.206 0.000 0.000 APEX1 −1.193 0.000 0.000 OGDHL −3.417 0.000 0.002 PGK1 −0.942 0.000 0.002 GLS2 1.493 0.000 0.002 AICDA 1.171 0.001 0.005 ACO2 0.693 0.002 0.011 CS −0.660 0.002 0.011 SLC25A1 1.181 0.007 0.032 IDH3A −0.728 0.008 0.035 GSS 1.039 0.013 0.053 TET3 0.662 0.026 0.093 GLUD1 −0.450 0.032 0.108 SDHD −0.619 0.049 0.143 FH −0.547 0.054 0.149 OGDH 0.316 0.133 0.287 ACO1 −0.364 0.141 0.297 SDHC −0.335 0.149 0.311 LIG3 0.338 0.165 0.334 SUCLG −0.332 0.174 0.349 SDHA 0.297 0.210 0.396 SUCLA2 −0.324 0.248 0.439 DNMT1 0.266 0.279 0.486 IDH3B1 −0.269 0.296 0.503 SDHB −0.213 0.339 0.544 DNMT3B 0.181 0.386 0.598 APOBEC1 0.629 0.386 0.598 TDG 0.427 0.398 0.611 IDH3G 0.237 0.468 0.675 NEIL2 0.509 0.572 0.720 IDH2 0.298 0.571 0.720 DNMT3L 1.306 0.590 0.722 GLS 0.120 0.706 0.821 XRCC1 0.108 0.793 0.887 TET1 −0.028 0.879 0.919 DNMT3A 0.029 0.893 0.920 MBD4 −0.056 0.885 0.920 PDHX 0.033 0.890 0.920 SMUG1 0.053 0.936 0.954 TET2 −0.002 0.991 0.991 Table S2. -
Kinase-Dead ATM Protein Is Highly Oncogenic and Can Be Preferentially Targeted by Topo
1 Kinase-dead ATM protein is highly oncogenic and can be preferentially targeted by Topo- 2 isomerase I inhibitors 3 4 Kenta Yamamoto1,2, Jiguang Wang3, Lisa Sprinzen1,2, Jun Xu5, Christopher J. Haddock6, Chen 5 Li1, Brian J. Lee1, Denis G. Loredan1, Wenxia Jiang1, Alessandro Vindigni6, Dong Wang5, Raul 6 Rabadan3 and Shan Zha1,4 7 8 1 Institute for Cancer Genetics, Department of Pathology and Cell Biology, College of Physicians 9 and Surgeons, Columbia University, New York City, NY 10032 10 2 Pathobiology and Molecular Medicine Graduate Program, Department of Pathology and Cell 11 Biology, Columbia University, New York City, NY 10032 12 3 Department of Biomedical Informatics and Department of Systems Biology, College of 13 Physicians & Surgeons, Columbia University, New York City, NY 10032 14 4 Division of Pediatric Oncology, Hematology and Stem Cell Transplantation, Department of 15 Pediatrics, College of Physicians & Surgeons, Columbia University, New York City, NY 10032 16 5 Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 17 La Jolla, CA 92093 18 6 Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University 19 School of Medicine, St. Louis, MO 63104 20 21 Short Title: Topo1 inhibitors target ATM mutated cancers 22 Key Words: ATM, missense mutations, Topo I inhibitors 23 24 Address Correspondence to: Shan Zha at [email protected] 25 26 1 27 ABSTRACT 28 Missense mutations in ATM kinase, a master regulator of DNA damage responses, are 29 found in many cancers, but their impact on ATM function and implications for cancer therapy are 30 largely unknown. -
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 -
Error-Prone DNA Repair As Cancer's Achilles' Heel
cancers Review Alternative Non-Homologous End-Joining: Error-Prone DNA Repair as Cancer’s Achilles’ Heel Daniele Caracciolo, Caterina Riillo , Maria Teresa Di Martino , Pierosandro Tagliaferri and Pierfrancesco Tassone * Department of Experimental and Clinical Medicine, Magna Græcia University, Campus Salvatore Venuta, 88100 Catanzaro, Italy; [email protected] (D.C.); [email protected] (C.R.); [email protected] (M.T.D.M.); [email protected] (P.T.) * Correspondence: [email protected] Simple Summary: Cancer onset and progression lead to a high rate of DNA damage, due to replicative and metabolic stress. To survive in this dangerous condition, cancer cells switch the DNA repair machinery from faithful systems to error-prone pathways, strongly increasing the mutational rate that, in turn, supports the disease progression and drug resistance. Although DNA repair de-regulation boosts genomic instability, it represents, at the same time, a critical cancer vulnerability that can be exploited for synthetic lethality-based therapeutic intervention. We here discuss the role of the error-prone DNA repair, named Alternative Non-Homologous End Joining (Alt-NHEJ), as inducer of genomic instability and as a potential therapeutic target. We portray different strategies to drug Alt-NHEJ and discuss future challenges for selecting patients who could benefit from Alt-NHEJ inhibition, with the aim of precision oncology. Abstract: Error-prone DNA repair pathways promote genomic instability which leads to the onset of cancer hallmarks by progressive genetic aberrations in tumor cells. The molecular mechanisms which Citation: Caracciolo, D.; Riillo, C.; Di foster this process remain mostly undefined, and breakthrough advancements are eagerly awaited. Martino, M.T.; Tagliaferri, P.; Tassone, In this context, the alternative non-homologous end joining (Alt-NHEJ) pathway is considered P. -
Targeting the Ubiquitin-Proteasome System for Cancer Therapeutics by Small-Molecule Inhibitors
cancers Review Targeting the Ubiquitin-Proteasome System for Cancer Therapeutics by Small-Molecule Inhibitors Gabriel LaPlante 1 and Wei Zhang 1,2,* 1 Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, 50 Stone Rd E, Guelph, ON N1G2W1, Canada; [email protected] 2 CIFAR Azrieli Global Scholars Program, Canadian Institute for Advanced Research, MaRS Centre West Tower, 661 University Avenue, Toronto, ON M5G1M1, Canada * Correspondence: [email protected] Simple Summary: The ubiquitin-proteasome system regulates multiple facets of protein homeostasis to modulate signal transduction in numerous biological processes. Not surprisingly, dysregulation of this delicately balanced system is frequently observed in cancer progression. In the past two decades, researchers in both academia and industry have made significant progress in developing small-molecule inhibitors targeting various components in the ubiquitin-proteasome system for cancer therapy. Here, we aim to provide a comprehensive summary of these efforts. Additionally, we overview the advancements of targeted protein degradation, a recently emerging drug discovery concept in cancer therapy. Abstract: The ubiquitin-proteasome system (UPS) is a critical regulator of cellular protein levels and activity. It is, therefore, not surprising that its dysregulation is implicated in numerous human diseases, including many types of cancer. Moreover, since cancer cells exhibit increased rates of protein turnover, their heightened dependence on the UPS makes it an attractive target for inhibition Citation: LaPlante, G.; Zhang, W. via targeted therapeutics. Indeed, the clinical application of proteasome inhibitors in treatment Targeting the Ubiquitin-Proteasome System for Cancer Therapeutics by of multiple myeloma has been very successful, stimulating the development of small-molecule Small-Molecule Inhibitors. -
DNA Strand Break Repair and Neurodegeneration
DNA strand break repair and neurodegeneration. Article (Accepted Version) Rulten, Stuart L and Caldecott, Keith W (2013) DNA strand break repair and neurodegeneration. DNA repair, 12 (8). pp. 558-567. ISSN 1568-7856 This version is available from Sussex Research Online: http://sro.sussex.ac.uk/id/eprint/47369/ This document is made available in accordance with publisher policies and may differ from the published version or from the version of record. If you wish to cite this item you are advised to consult the publisher’s version. Please see the URL above for details on accessing the published version. Copyright and reuse: Sussex Research Online is a digital repository of the research output of the University. Copyright and all moral rights to the version of the paper presented here belong to the individual author(s) and/or other copyright owners. To the extent reasonable and practicable, the material made available in SRO has been checked for eligibility before being made available. Copies of full text items generally can be reproduced, displayed or performed and given to third parties in any format or medium for personal research or study, educational, or not-for-profit purposes without prior permission or charge, provided that the authors, title and full bibliographic details are credited, a hyperlink and/or URL is given for the original metadata page and the content is not changed in any way. http://sro.sussex.ac.uk DNA Strand Break Repair and Neurodegeneration Stuart L. Rulten and Keith W. Caldecott Genome Damage and Stability Centre, Science Park Road, Falmer, Brighton, BN1 9RQ, UK Correspondence: Stuart L. -
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ANNEX F DNA repair and mutagenesis CONTENTS Page INTRODUCTION..................................................... 2 I. DNADAMAGEANDREPAIR...................................... 2 A. THEROLEOFDNAREPAIRGENESINCELLFUNCTION .......... 2 B. TYPESOFDAMAGEANDPATHWAYSOFREPAIR ............... 3 C. SUMMARY................................................. 8 II. REPAIRPROCESSESANDRADIOSENSITIVITY ...................... 9 A. RADIOSENSITIVITYINMAMMALIANCELLSANDHUMANS...... 9 1. The identification of radiosensitive cell lines and disorders ......... 9 2. Mechanisms of enhanced sensitivity in human disorders .......... 11 3. Analysis of genes determining radiosensitivity .................. 12 4. Summary ............................................. 17 B. RELATIONSHIP BETWEEN REPAIR AND OTHERCELLREGULATORYPROCESSES...................... 18 1. Radiosensitivity and defective recombination in the immune system: non-homologousendjoiningofDNAdouble-strandbreaks........ 18 2. Radiosensitivity and the cell cycle ........................... 21 3. Apoptosis:analternativetorepair?.......................... 23 4. Summary.............................................. 25 III. HUMAN RADIATION RESPONSES ................................. 26 A. CONTRIBUTION OF MUTANT GENES TOHUMANRADIOSENSITIVITY ............................. 26 B. INFLUENCEOFREPAIRONRADIATIONRESPONSES............ 29 C. SUMMARY................................................ 32 IV. MECHANISMSOFRADIATIONMUTAGENESIS ..................... 33 A. MUTATIONASAREPAIR-RELATEDRESPONSE................ 33 B. THESPECTRUMOFRADIATION-INDUCEDMUTATIONS........ -
Rational Design of Human DNA Ligase Inhibitors That Target Cellular DNA Replication and Repair
Research Article Rational Design of Human DNA Ligase Inhibitors that Target Cellular DNA Replication and Repair Xi Chen,1 Shijun Zhong,3 Xiao Zhu,3 Barbara Dziegielewska,1 Tom Ellenberger,4 Gerald M. Wilson,2 Alexander D. MacKerell, Jr.,3 and Alan E. Tomkinson1 1Radiation Oncology Research Laboratory and Marlene and Stewart Greenebaum Cancer Center, 2Department of Biochemistry and Molecular Biology, School of Medicine, 3Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland; and 4Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri Abstract exert their cytotoxic effects by damaging DNA. Unfortunately, these Based on the crystal structure of human DNA ligase I agents also kill normal cells, thereby limiting their utility. There is complexed with nicked DNA, computer-aided drug design growing interest in the identification of DNA repair inhibitors that was used to identify compounds in a database of 1.5 million will enhance the cytotoxicity of DNA-damaging agents because commercially available low molecular weight chemicals that combinations of DNA-damaging agents and DNA repair inhibitors were predicted to bind to a DNA-binding pocket within the have the potential to concomitantly increase the killing of cancer DNA-binding domain of DNA ligase I, thereby inhibiting DNA cells and reduce damage to normal tissues and cells if either the joining. Ten of 192 candidates specifically inhibited purified damaging agent or the inhibitor could be selectively delivered to human DNA ligase I. Notably, a subset of these compounds the cancer cells (1). Because DNA ligation is required during replication and is the was also active against the other human DNA ligases. -
Mechanism of Hepatitis B Virus Cccdna Formation
viruses Review Mechanism of Hepatitis B Virus cccDNA Formation Lei Wei and Alexander Ploss * 110 Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-609-258-7128 Abstract: Hepatitis B virus (HBV) remains a major medical problem affecting at least 257 million chronically infected patients who are at risk of developing serious, frequently fatal liver diseases. HBV is a small, partially double-stranded DNA virus that goes through an intricate replication cycle in its native cellular environment: human hepatocytes. A critical step in the viral life-cycle is the conversion of relaxed circular DNA (rcDNA) into covalently closed circular DNA (cccDNA), the latter being the major template for HBV gene transcription. For this conversion, HBV relies on multiple host factors, as enzymes capable of catalyzing the relevant reactions are not encoded in the viral genome. Combinations of genetic and biochemical approaches have produced findings that provide a more holistic picture of the complex mechanism of HBV cccDNA formation. Here, we review some of these studies that have helped to provide a comprehensive picture of rcDNA to cccDNA conversion. Mechanistic insights into this critical step for HBV persistence hold the key for devising new therapies that will lead not only to viral suppression but to a cure. Keywords: hepatitis B virus; HBV; viral replication; cccDNA biogenesis; rcDNA; DNA repair Citation: Wei, L.; Ploss, A. 1. Overview of HBV Life Cycle and cccDNA Biogenesis Mechanism of Hepatitis B Virus cccDNA Formation. Viruses 2021, 13, The hepatotropic HBV belongs to the Hepadnaviridae family and is a blood-borne 1463. -
Polymerase Is a Robust Terminal Transferase That Oscillates Between
RESEARCH ARTICLE Polymerase is a robust terminal transferase that oscillates between three different mechanisms during end-joining Tatiana Kent1,2, Pedro A Mateos-Gomez3,4, Agnel Sfeir3,4, Richard T Pomerantz1,2* 1Fels Institute for Cancer Research, Temple University Lewis Katz School of Medicine, Philadelphia, United States; 2Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, United States; 3Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, United States; 4Department of Cell Biology, New York University School of Medicine, New York, United States Abstract DNA polymerase q (Polq) promotes insertion mutations during alternative end-joining (alt-EJ) by an unknown mechanism. Here, we discover that mammalian Polq transfers nucleotides to the 3’ terminus of DNA during alt-EJ in vitro and in vivo by oscillating between three different modes of terminal transferase activity: non-templated extension, templated extension in cis, and templated extension in trans. This switching mechanism requires manganese as a co-factor for Polq template-independent activity and allows for random combinations of templated and non- templated nucleotide insertions. We further find that Polq terminal transferase activity is most efficient on DNA containing 3’ overhangs, is facilitated by an insertion loop and conserved residues that hold the 3’ primer terminus, and is surprisingly more proficient than terminal deoxynucleotidyl transferase. In summary, this report identifies an unprecedented switching mechanism used by Polq to generate genetic diversity during alt-EJ and characterizes Polq as among the most proficient terminal transferases known. DOI: 10.7554/eLife.13740.001 *For correspondence: richard.