DOCSLIB.ORG

Chromatin Activation As a Unifying Principle Underlying Pathogenic

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Chromatin Activation As a Unifying Principle Underlying Pathogenic Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Ordoñez&Kulis et al., Chromatin activation in multiple myeloma, 2nd revision, submitted in July 2020 1 Chromatin activation as a unifying principle underlying pathogenic 2 mechanisms in multiple myeloma 3 Raquel Ordoñez1,2*, Marta Kulis3,4*, Nuria Russiñol3, Vicente Chapaprieta5, Arantxa Carrasco- 4 Leon1, Beatriz García-Torre4, Stella Charampopoulou4, Guillem Clot2,4, Renée Beekman2,4, 5 Cem Meydan6, Martí Duran-Ferrer4, Núria Verdaguer-Dot4, Roser Vilarrasa-Blasi4, Paula 6 Soler-Vila4, Leire Garate1,7, Estíbaliz Miranda1,2, Edurne San José-Enériz1,2, Juan R. Rodriguez- 7 Madoz1, Teresa Ezponda1, Rebeca Martínez-Turrilas1, Amaia Vilas-Zornoza1, David Lara- 8 Astiaso1, Daphné Dupéré-Richer8, Joost H.A. Martens9, Halima El-Omri10, Ruba Y Taha10, 9 Maria J. Calasanz1,2, Bruno Paiva1,2,7, Jesus San Miguel1,2,7, Paul Flicek11, Ivo Gut12, Ari 10 Melnick6, Constantine S. Mitsiades13, Jonathan D. Licht8, Elias Campo2,3,4,5, Hendrik G. 11 Stunnenberg9, Xabier Agirre1,2**, Felipe Prosper1,2,7** and Jose I. Martin-Subero2,4,5,14**. 12 13 * Shared first authorship 14 ** Shared senior authorship 15 16 1. Centro de Investigación Médica Aplicada (CIMA), IDISNA, Pamplona, Spain. 17 2. Centro de Investigación Biomédica en Red de Cáncer, CIBERONC. 18 3. Fundació Clínic per a la Recerca Biomèdica, Barcelona, Spain. 19 4. Institut d’Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain. 20 5. Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona, Spain. 21 6. Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, New York, USA. 22 7. Clínica Universidad de Navarra, Pamplona, Spain. 23 8. Division of Hematology/Oncology, University of Florida Health Cancer Center, Gainesville, USA. 24 9. Radboud Institute for Molecular Life Sciences, Nijmegen, Netherlands. 25 10. Department of Hematology & BMT, Hamad Medical Corporation, NCCCR, Doha, Qatar. 26 11. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust 27 Genome Campus, Hinxton, UK. 28 12. CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 29 Barcelona, Spain. 30 13. Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, USA. 31 14. Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain. 32 33 Correspondence: [email protected] (Xabier Agirre), [email protected] (Felipe Prosper) and [email protected] 34 (Jose I Martin-Subero). 35 Word count: 36 ·Abstract: 175 (1,213 characters) 37 ·Manuscript: 4,127 (27,175 characters) 38 ·Methods: 694 (4,901 characters) 39 ·Figure legends: 1,386 (8,812 characters) 40 Figure Count: 4 41 Supplemental figures: 18 42 Supplemental tables: 9 43 1 Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Ordoñez&Kulis et al., Chromatin activation in multiple myeloma, 2nd revision, submitted in July 2020 44 ABSTRACT 45 Multiple myeloma (MM) is a plasma cell neoplasm associated with a broad variety of 46 genetic lesions. In spite of this genetic heterogeneity, MMs share a characteristic malignant 47 phenotype whose underlying molecular basis remains poorly characterized. In the present 48 study, we examined plasma cells from MM using a multi-epigenomics approach and 49 demonstrated that when compared to normal B cells, malignant plasma cells showed an 50 extensive activation of regulatory elements, in part affecting co-regulated adjacent genes. 51 Among target genes upregulated by this process, we found members of the NOTCH, NF-kB, 52 MTOR signaling and TP53 signaling pathways. Other activated genes included sets involved 53 in osteoblast differentiation and response to oxidative stress, all of which have been shown 54 to be associated with the MM phenotype and clinical behavior. We functionally 55 characterized MM specific active distant enhancers controlling the expression of thioredoxin 56 (TXN), a major regulator of cellular redox status, and in addition identified PRDM5 as a novel 57 essential gene for MM. Collectively our data indicates that aberrant chromatin activation is a 58 unifying feature underlying the malignant plasma cell phenotype. 59 60 Keywords. Multiple myeloma, epigenomics, chromatin. 61 62 2 Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Ordoñez&Kulis et al., Chromatin activation in multiple myeloma, 2nd revision, submitted in July 2020 63 INTRODUCTION 64 MM is an aggressive hematological neoplasm characterized by the uncontrolled expansion 65 and accumulation of malignant plasma cells (PCs) in the bone marrow (San Miguel 2014; Kumar et al. 66 2017). Given the central role of genomic alterations in cancer development, the study of molecular 67 mechanisms underlying MM pathogenesis has mostly focused on the genetic aberrations of these 68 tumors (Stratton et al. 2009). Such studies have revealed that MM patients are genetically 69 heterogeneous, without a single and unifying genetic event identified in all patients (Robiou du Pont 70 et al. 2017), but nevertheless the central paradox of MM remains, i.e. terminally-differentiated 71 plasma cells normally do not divide. This indicates that the essential aspects of the gene regulatory 72 networks within the malignant plasma cell are dysfunctional and suggests that epigenetic 73 deregulation of gene expression may be a root cause of the disease. Over the last decades, a greater 74 understanding of the role of histone, DNA and other chromatin modifications in the epigenetic 75 control of gene expression has transformed our understanding of transcriptional patterns in normal 76 and neoplastic cells (Allis and Jenuwein 2016). In spite of the multifaceted nature of the epigenome 77 (Stricker et al. 2017), the cancer epigenomics field has been mostly focused on the association 78 between DNA methylation and transcription (Esteller 2008). However, recent whole-genome DNA 79 methylation studies indicate that this association is less clear than previously appreciated (Kulis et al. 80 2012; Kretzmer et al. 2015; Kulis et al. 2015), and that understanding gene deregulation in cancer 81 requires the integrative analysis of various epigenetic marks including histone modifications and 82 chromatin accessibility (Martens et al. 2010; Ooi et al. 2016; Beekman et al. 2018). In MM, although 83 several reports have identified alterations in the DNA methylome of malignant plasma cells (Walker 84 et al. 2011; Heuck et al. 2013; Kaiser et al. 2013; Agirre et al. 2015), their pathogenic impact has been 85 uncertain and the chromatin regulatory network underlying aberrant cellular functions in MM has 86 just started to be characterized (Agarwal et al. 2016; Jin et al. 2018). 87 3 Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Ordoñez&Kulis et al., Chromatin activation in multiple myeloma, 2nd revision, submitted in July 2020 88 RESULTS 89 Integrative analysis of multiple epigenetic layers in MM 90 We performed an integrative analysis of multiple epigenetic layers in purified plasma cells 91 from 3 MM patients, including whole-genome maps of six core histone modifications (i.e. H3K27ac, 92 H3K4me1, H3K4me3, H3K36me3, H3K27me3, and H3K9me3) by ChIP-seq, chromatin accessibility by 93 ATAC-seq, DNA methylation by whole-genome bisulfite sequencing (WGBS) and gene expression by 94 RNA-seq. The major limiting factor for such multi-omics characterization was the high amount of 95 starting material needed from each individual patient. To overcome this limitation, we also analyzed 96 the chromatin regulatory landscape of an extended series of MM patients, including additional 97 profiles for H3K27ac (n=11), H3K4me1 (n=7), ATAC-seq (n=14) and RNA-seq data (n=37). Normal 98 control consisted of reference epigenomes from B cell subpopulations at different maturation stages, 99 including naive B cells (both from peripheral blood, pb-NBCs, and tonsils, t-NBCs), germinal center B 100 cells (GCBCs), memory B cells (MBCs) and tonsillar PCs (t-PCs) (Beekman et al. 2018) (Fig. 1A, 101 Supplemental Tables S1 and S2). Additionally, we were able to characterize the H3K27ac and 102 transcriptional profiles of bone marrow plasma cells (bm-PCs), the normal counterpart of MM, from 103 which a complete reference epigenome could not be generated due to the scarcity of this cell 104 subpopulation in healthy bone marrow. 105 Unsupervised principal component analysis indicated that MM displays a distinct epigenetic 106 configuration than normal B cell subpopulations, which is reflected in every single layer of the 107 epigenome (Fig. 1B). As B cell differentiation entails modulation of all studied epigenetic layers, we 108 focused our analysis on the genome fraction changing in MM but showing stable chromatin profiles 109 across the normal B cell maturation program. This strategy shall allow us to identify chromatin 110 changes specifically altered during myelomagenesis (Fig. 1C and Supplemental Fig. S1 and S2). 111 Overall, we observed that each histone modification undergoes more gains than losses in MM, but at 112 different degrees, being the H3K27ac, H3K4me1 and H3K4me3 regulatory marks those with the 4 Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Ordoñez&Kulis et al., Chromatin activation in multiple myeloma,
Load more

Recommended publications
  • Mitoxplorer, a Visual Data Mining Platform To
    mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations Annie Yim, Prasanna Koti, Adrien Bonnard, Fabio Marchiano, Milena Dürrbaum, Cecilia Garcia-Perez, José Villaveces, Salma Gamal, Giovanni Cardone, Fabiana Perocchi, et al. To cite this version: Annie Yim, Prasanna Koti, Adrien Bonnard, Fabio Marchiano, Milena Dürrbaum, et al.. mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dy- namics and mutations. Nucleic Acids Research, Oxford University Press, 2020, 10.1093/nar/gkz1128. hal-02394433 HAL Id: hal-02394433 https://hal-amu.archives-ouvertes.fr/hal-02394433 Submitted on 4 Dec 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License Nucleic Acids Research, 2019 1 doi: 10.1093/nar/gkz1128 Downloaded from https://academic.oup.com/nar/advance-article-abstract/doi/10.1093/nar/gkz1128/5651332 by Bibliothèque de l'université la Méditerranée user on 04 December 2019 mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations Annie Yim1,†, Prasanna Koti1,†, Adrien Bonnard2, Fabio Marchiano3, Milena Durrbaum¨ 1, Cecilia Garcia-Perez4, Jose Villaveces1, Salma Gamal1, Giovanni Cardone1, Fabiana Perocchi4, Zuzana Storchova1,5 and Bianca H.
    [Show full text]
  • Zebrafish Oxr1a Knockout Reveals Its Role in Regulating Antioxidant
    G C A T T A C G G C A T genes Article Zebrafish Oxr1a Knockout Reveals Its Role in Regulating Antioxidant Defenses and Aging Hao Xu 1, Yu Jiang 2, Sheng Li 2, Lang Xie 1, Yi-Xi Tao 1 and Yun Li 1,2,* 1 Institute of Three Gorges Ecological Fisheries of Chongqing, College of Fisheries, Southwest University, Chongqing 400715, China; [email protected] (H.X.); [email protected] (L.X.); [email protected] (Y.-X.T.) 2 Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing 400715, China; [email protected] (Y.J.); [email protected] (S.L.) * Correspondence: [email protected]; Tel.: +86-2368-2519-62 Received: 19 August 2020; Accepted: 21 September 2020; Published: 24 September 2020 Abstract: Oxidation resistance gene 1 (OXR1) is essential for protection against oxidative stress in mammals, but its functions in non-mammalian vertebrates, especially in fish, remain uncertain. Here, we created a homozygous oxr1a-knockout zebrafish via the CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein 9) system. Compared with / wild-type (WT) zebrafish, oxr1a− − mutants exhibited higher mortality and more apoptotic cells under oxidative stress, and multiple antioxidant genes (i.e., gpx1b, gpx4a, gpx7 and sod3a) involved in detoxifying cellular reactive oxygen species were downregulated significantly. Based on these observations, we conducted a comparative transcriptome analysis of early oxidative stress response. The results show that oxr1a mutation caused more extensive changes in transcriptional networks / compared to WT zebrafish, and several stress response and pro-inflammatory pathways in oxr1a− − mutant zebrafish were strongly induced.
    [Show full text]
  • Oxr1 Improves Pathogenic Cellular Features of ALS-Associated FUS
    Human Molecular Genetics, 2015, Vol. 24, No. 12 3529–3544 doi: 10.1093/hmg/ddv104 Advance Access Publication Date: 19 March 2015 Original Article ORIGINAL ARTICLE Oxr1 improves pathogenic cellular features of ALS-associated FUS and TDP-43 mutations Downloaded from https://academic.oup.com/hmg/article/24/12/3529/623195 by guest on 26 July 2021 Mattéa J. Finelli†, Kevin X. Liu†, Yixing Wu, Peter L. Oliver* and Kay E. Davies* MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford OX1 3PT, UK *To whom correspondence should be addressed. Tel: +44 1865285880/79; Email: [email protected] (K.E.D.); [email protected] (P.L.O.) Abstract Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by the loss of motor neuron-like cells. Mutations in the RNA- and DNA-binding proteins, fused in sarcoma (FUS) and transactive response DNA-binding protein 43 kDa (TDP-43), are responsible for 5–10% of familial and 1% of sporadic ALS cases. Importantly, aggregation of misfolded FUS or TDP- 43 is also characteristic of several neurodegenerative disorders in addition to ALS, including frontotemporal lobar degeneration. Moreover, splicing deregulation of FUS and TDP-43 target genes as well as mitochondrial abnormalities are associated with disease-causing FUS and TDP-43 mutants. While progress has been made to understand the functions of these proteins, the exact mechanisms by which FUS and TDP-43 cause ALS remain unknown. Recently, we discovered that, in addition to being up-regulated in spinal cords of ALS patients, the novel protein oxidative resistance 1 (Oxr1) protects neurons from oxidative stress-induced apoptosis.
    [Show full text]
  • Transcriptome Analysis of Human OXR1 Depleted Cells Reveals Its Role
    www.nature.com/scientificreports OPEN Transcriptome analysis of human OXR1 depleted cells reveals its role in regulating the p53 signaling Received: 28 July 2015 Accepted: 23 October 2015 pathway Published: 30 November 2015 Mingyi Yang1,2, Xiaolin Lin2,5, Alexander Rowe2, Torbjørn Rognes1,3, Lars Eide2 & Magnar Bjørås1,2,4 The oxidation resistance gene 1 (OXR1) is crucial for protecting against oxidative stress; however, its molecular function is unknown. We employed RNA sequencing to examine the role of human OXR1 for genome wide transcription regulation. In total, in non-treated and hydrogen peroxide exposed HeLa cells, OXR1 depletion resulted in down-regulation of 554 genes and up-regulation of 253 genes. These differentially expressed genes include transcription factors (i.e. HIF1A, SP6, E2F8 and TCF3), antioxidant genes (PRDX4, PTGS1 and CYGB) and numerous genes of the p53 signaling pathway involved in cell-cycle arrest (i.e. cyclin D, CDK6 and RPRM) and apoptosis (i.e. CytC and CASP9). We demonstrated that OXR1 depleted cells undergo cell cycle arrest in G2/M phase during oxidative stress and increase protein expression of the apoptosis initiator protease CASP9. In summary, OXR1 may act as a sensor of cellular oxidative stress to regulate the transcriptional networks required to detoxify reactive oxygen species and modulate cell cycle and apoptosis. Reactive oxygen species (ROS) are readily formed in aerobic organisms and constitute a heterogene- ous group comprising superoxide anions, hydrogen peroxide, hydroxyl radicals and other free radicals, which differ in level between compartments inside the cell. In the cell, ROS may attack DNA causing accumulation of oxidative DNA damage and mutations, which are implicated in diseases such as cancer and neurodegeneration1–3.
    [Show full text]
  • Next-Generation DNA Sequencing Identifies Novel Gene Variants And
    www.nature.com/scientificreports OPEN Next-generation DNA sequencing identifies novel gene variants and pathways involved in specific Received: 15 November 2016 Accepted: 08 March 2017 language impairment Published: 25 April 2017 Xiaowei Sylvia Chen1, Rose H. Reader2, Alexander Hoischen3, Joris A. Veltman3,4,5, Nuala H. Simpson2, Clyde Francks1,5, Dianne F. Newbury2,6 & Simon E. Fisher1,5 A significant proportion of children have unexplained problems acquiring proficient linguistic skills despite adequate intelligence and opportunity. Developmental language disorders are highly heritable with substantial societal impact. Molecular studies have begun to identify candidate loci, but much of the underlying genetic architecture remains undetermined. We performed whole-exome sequencing of 43 unrelated probands affected by severe specific language impairment, followed by independent validations with Sanger sequencing, and analyses of segregation patterns in parents and siblings, to shed new light on aetiology. By first focusing on a pre-defined set of known candidates from the literature, we identified potentially pathogenic variants in genes already implicated in diverse language-related syndromes, including ERC1, GRIN2A, and SRPX2. Complementary analyses suggested novel putative candidates carrying validated variants which were predicted to have functional effects, such as OXR1, SCN9A and KMT2D. We also searched for potential “multiple-hit” cases; one proband carried a rare AUTS2 variant in combination with a rare inherited haplotype affectingSTARD9 , while another carried a novel nonsynonymous variant in SEMA6D together with a rare stop-gain in SYNPR. On broadening scope to all rare and novel variants throughout the exomes, we identified biological themes that were enriched for such variants, including microtubule transport and cytoskeletal regulation.
    [Show full text]
  • Endocrine System Local Gene Expression
    Copyright 2008 By Nathan G. Salomonis ii Acknowledgments Publication Reprints The text in chapter 2 of this dissertation contains a reprint of materials as it appears in: Salomonis N, Hanspers K, Zambon AC, Vranizan K, Lawlor SC, Dahlquist KD, Doniger SW, Stuart J, Conklin BR, Pico AR. GenMAPP 2: new features and resources for pathway analysis. BMC Bioinformatics. 2007 Jun 24;8:218. The co-authors listed in this publication co-wrote the manuscript (AP and KH) and provided critical feedback (see detailed contributions at the end of chapter 2). The text in chapter 3 of this dissertation contains a reprint of materials as it appears in: Salomonis N, Cotte N, Zambon AC, Pollard KS, Vranizan K, Doniger SW, Dolganov G, Conklin BR. Identifying genetic networks underlying myometrial transition to labor. Genome Biol. 2005;6(2):R12. Epub 2005 Jan 28. The co-authors listed in this publication developed the hierarchical clustering method (KP), co-designed the study (NC, AZ, BC), provided statistical guidance (KV), co- contributed to GenMAPP 2.0 (SD) and performed quantitative mRNA analyses (GD). The text of this dissertation contains a reproduction of a figure from: Yeo G, Holste D, Kreiman G, Burge CB. Variation in alternative splicing across human tissues. Genome Biol. 2004;5(10):R74. Epub 2004 Sep 13. The reproduction was taken without permission (chapter 1), figure 1.3. iii Personal Acknowledgments The achievements of this doctoral degree are to a large degree possible due to the contribution, feedback and support of many individuals. To all of you that helped, I am extremely grateful for your support.
    [Show full text]
  • Oxidation Resistance 1 Is a Novel Senolytic Target
    Lawrence Berkeley National Laboratory Recent Work Title Oxidation resistance 1 is a novel senolytic target. Permalink https://escholarship.org/uc/item/3055r19w Journal Aging cell, 17(4) ISSN 1474-9718 Authors Zhang, Xin Zhang, Suping Liu, Xingui et al. Publication Date 2018-08-01 DOI 10.1111/acel.12780 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Accepted: 1 April 2018 DOI: 10.1111/acel.12780 ORIGINAL ARTICLE Oxidation resistance 1 is a novel senolytic target Xin Zhang1,† | Suping Zhang1,2,† | Xingui Liu1 | Yingying Wang1 | Jianhui Chang1 | Xuan Zhang1 | Samuel G. Mackintosh3 | Alan J. Tackett3 | Yonghan He1 | Dongwen Lv1 | Remi-Martin Laberge4 | Judith Campisi5,6 | Jianrong Wang2,† | Guangrong Zheng1,7,† | Daohong Zhou1,8,† 1Department of Pharmaceutical Sciences, College of Pharmacy, University of Summary Arkansas for Medical Sciences, Little Rock, The selective depletion of senescent cells (SCs) by small molecules, termed senolytic Arkansas agents, is a promising therapeutic approach for treating age-related diseases and 2Hematology Center of Cyrus Tang Medical Institute, Collaborative Innovation Center of chemotherapy- and radiotherapy-induced side effects. Piperlongumine (PL) was Hematology, Soochow University School of recently identified as a novel senolytic agent. However, its mechanism of action and Medicine, Suzhou, China 3Department of Biochemistry and molecular targets in SCs was unknown and thus was investigated. Specifically, we Molecular Biology, College of Medicine, used a PL-based chemical probe to pull-down PL-binding proteins from live cells and University of Arkansas for Medical Sciences, Little Rock, Arkansas then mass spectrometry-based proteomic analysis to identify potential molecular tar- 4Unity Biotechnology, Brisbane, California gets of PL in SCs.
    [Show full text]
  • Microrna-29A Mitigates Osteoblast Senescence and Counteracts Bone Loss Through Oxidation Resistance-1 Control of Foxo3 Methylation
    antioxidants Article MicroRNA-29a Mitigates Osteoblast Senescence and Counteracts Bone Loss through Oxidation Resistance-1 Control of FoxO3 Methylation Wei-Shiung Lian 1,2,†, Re-Wen Wu 3,† , Yu-Shan Chen 1, Jih-Yang Ko 3, Shao-Yu Wang 1, Holger Jahr 4,5 and Feng-Sheng Wang 1,2,* 1 Core Laboratory for Phenomics and Diagnostic, Department of Medical Research, College of Medicine, Chang Gung University, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; [email protected] (W.-S.L.); [email protected] (Y.-S.C.); [email protected] (S.-Y.W.) 2 Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan 3 Department of Orthopedic Surgery, College of Medicine, Chang Gung University, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan; [email protected] (R.-W.W.); [email protected] (J.-Y.K.) 4 Department of Anatomy and Cell Biology, University Hospital RWTH Aachen, 52074 Aachen, Germany; [email protected] 5 Department of Orthopedic Surgery, Maastricht University Medical Center, 6229 ER Maastricht, The Netherlands * Correspondence: [email protected]; Tel.: +886-7-731-7123 † W.-S.L. and R.-W.W. contribute to this article equally. Abstract: Senescent osteoblast overburden accelerates bone mass loss. Little is understood about Citation: Lian, W.-S.; Wu, R.-W.; microRNA control of oxidative stress and osteoblast senescence in osteoporosis. We revealed an asso- Chen, Y.-S.; Ko, J.-Y.; Wang, S.-Y.; Jahr, ciation between microRNA-29a (miR-29a) loss, oxidative stress marker 8-hydroxydeoxyguanosine H.; Wang, F.-S. MicroRNA-29a (8-OHdG), DNA hypermethylation marker 5-methylcystosine (5mC), and osteoblast senescence in Mitigates Osteoblast Senescence and human osteoporosis.
    [Show full text]
  • 393LN V 393P 344SQ V 393P Probe Set Entrez Gene
    393LN v 393P 344SQ v 393P Entrez fold fold probe set Gene Gene Symbol Gene cluster Gene Title p-value change p-value change chemokine (C-C motif) ligand 21b /// chemokine (C-C motif) ligand 21a /// chemokine (C-C motif) ligand 21c 1419426_s_at 18829 /// Ccl21b /// Ccl2 1 - up 393 LN only (leucine) 0.0047 9.199837 0.45212 6.847887 nuclear factor of activated T-cells, cytoplasmic, calcineurin- 1447085_s_at 18018 Nfatc1 1 - up 393 LN only dependent 1 0.009048 12.065 0.13718 4.81 RIKEN cDNA 1453647_at 78668 9530059J11Rik1 - up 393 LN only 9530059J11 gene 0.002208 5.482897 0.27642 3.45171 transient receptor potential cation channel, subfamily 1457164_at 277328 Trpa1 1 - up 393 LN only A, member 1 0.000111 9.180344 0.01771 3.048114 regulating synaptic membrane 1422809_at 116838 Rims2 1 - up 393 LN only exocytosis 2 0.001891 8.560424 0.13159 2.980501 glial cell line derived neurotrophic factor family receptor alpha 1433716_x_at 14586 Gfra2 1 - up 393 LN only 2 0.006868 30.88736 0.01066 2.811211 1446936_at --- --- 1 - up 393 LN only --- 0.007695 6.373955 0.11733 2.480287 zinc finger protein 1438742_at 320683 Zfp629 1 - up 393 LN only 629 0.002644 5.231855 0.38124 2.377016 phospholipase A2, 1426019_at 18786 Plaa 1 - up 393 LN only activating protein 0.008657 6.2364 0.12336 2.262117 1445314_at 14009 Etv1 1 - up 393 LN only ets variant gene 1 0.007224 3.643646 0.36434 2.01989 ciliary rootlet coiled- 1427338_at 230872 Crocc 1 - up 393 LN only coil, rootletin 0.002482 7.783242 0.49977 1.794171 expressed sequence 1436585_at 99463 BB182297 1 - up 393
    [Show full text]
  • Characterisation of Human and Mouse SOD1-ALS Proteins in Vivo and in Vitro
    Characterisation of human and mouse SOD1-ALS proteins in vivo and in vitro Rachele Saccon A thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy to the University of London Department of Neurodegenerative Disease Institute of Neurology University College London 1 Declaration I, Rachele Saccon, confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated in the thesis. 2 Abstract Amyotrophic lateral sclerosis (ALS) is a fatal progressive neurodegenerative disease affecting motor neurons (MNs). It is primarily sporadic, however a proportion of cases are inherited and of these ~20 % are caused by mutations in the superoxide dismutase 1 (SOD1) gene. The work described in this thesis has focused on the characterisation of the role that the SOD1 protein plays in ALS, investigating the human and the mouse variants in vivo and in vitro. SOD1 mutations result in ALS by an unknown gain of function mechanism, although mouse models suggest that complete loss of SOD1 is also detrimental to MN function. To investigate a possible role of SOD1 loss of function in SOD1-ALS, a meta-analysis was carried out on the literature reviewing measures of SOD1 activity from patients carrying SOD1 familial ALS mutations and the phenotype of Sod1 knockout mice. The first set of experiments aimed to phenotypically characterise a novel mouse model, Sod1D83G, carrying a pathological mutation in the mouse Sod1 gene. Sod1D83G/D83G mice have no SOD1 activity, low levels of SOD1 protein, develop central MN degeneration and a distal peripheral neuropathy.
    [Show full text]
  • A Network Inference Approach to Understanding Musculoskeletal
    A NETWORK INFERENCE APPROACH TO UNDERSTANDING MUSCULOSKELETAL DISORDERS by NIL TURAN A thesis submitted to The University of Birmingham for the degree of Doctor of Philosophy College of Life and Environmental Sciences School of Biosciences The University of Birmingham June 2013 University of Birmingham Research Archive e-theses repository This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder. ABSTRACT Musculoskeletal disorders are among the most important health problem affecting the quality of life and contributing to a high burden on healthcare systems worldwide. Understanding the molecular mechanisms underlying these disorders is crucial for the development of efficient treatments. In this thesis, musculoskeletal disorders including muscle wasting, bone loss and cartilage deformation have been studied using systems biology approaches. Muscle wasting occurring as a systemic effect in COPD patients has been investigated with an integrative network inference approach. This work has lead to a model describing the relationship between muscle molecular and physiological response to training and systemic inflammatory mediators. This model has shown for the first time that oxygen dependent changes in the expression of epigenetic modifiers and not chronic inflammation may be causally linked to muscle dysfunction.
    [Show full text]
  • A Novel Gene-By-Environment Quantitative Trait Locus on Mouse Chromosome 15 Underlies
    bioRxiv preprint doi: https://doi.org/10.1101/2021.05.20.445039; this version posted May 20, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. A novel gene-by-environment quantitative trait locus on mouse chromosome 15 underlies susceptibility to acute ozone-induced lung injury Adelaide Tovar,a,b Gregory J. Smith,a,c Joseph M. Thomas,a Kathryn M. McFadden,a and Samir N. P. Kelada.a,b,c,1 aDepartment of Genetics, bCurriculum in Genetics & Molecular Biology, cCurriculum in Toxicology & Environmental Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. 1To whom correspondence should be addressed at Department of Genetics, The University of North Carolina, 120 Mason Farm Road, Chapel Hill, NC 27599, E-mail: [email protected]. Keywords: ozone, air pollution, genetic variation, lung, injury, mouse, quantitative trait loci, genetic mapping Running head: A locus on mouse chromosome 15 is associated with ozone-induced lung injury bioRxiv preprint doi: https://doi.org/10.1101/2021.05.20.445039; this version posted May 20, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Respiratory toxicity caused by the common urban air pollutant ozone (O3) varies considerably within the human population and across inbred mouse strains, suggestive of gene-environment interactions (GxE). Though previous studies genetic mapping studies using classical inbred strains have identified several and quantitative trait locus (QTL) and candidate genes underlying responses to O3 exposure, precise mechanisms of susceptibility remain incompletely described.
    [Show full text]