The App-Runx1 Region Is Critical for Birth Defects and Electrocardiographic Dysfunctions Observed in a Down Syndrome Mouse Model
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Activation of ATM Depends on Chromatin Interactions Occurring Before Induction of DNA Damage
LETTERS Activation of ATM depends on chromatin interactions occurring before induction of DNA damage Yong-Chul Kim1,6, Gabi Gerlitz1,6, Takashi Furusawa1, Frédéric Catez1,5, Andre Nussenzweig2, Kyu-Seon Oh3, Kenneth H. Kraemer3, Yosef Shiloh4 and Michael Bustin1,7 Efficient and correct responses to double-stranded breaks the KAP-1 protein9. The local and global changes in chromatin organiza- (DSB) in chromosomal DNA are crucial for maintaining genomic tion facilitate recruitment of damage-response proteins and remodelling stability and preventing chromosomal alterations that lead to factors, which further modify chromatin in the vicinity of the DSB and cancer1,2. The generation of DSB is associated with structural propagate the DNA damage response. Given the extensive changes in chro- changes in chromatin and the activation of the protein kinase matin structure associated with the DSB response, it could be expected ataxia-telangiectasia mutated (ATM), a key regulator of the that architectural chromatin-binding proteins, such as the high mobility signalling network of the cellular response to DSB3,4. The group (HMG) proteins, would be involved in this process10–12. interrelationship between DSB-induced changes in chromatin HMG is a superfamily of nuclear proteins that bind to chromatin architecture and the activation of ATM is unclear4. Here we show without any obvious specificity for a particular DNA sequence and affect that the nucleosome-binding protein HMGN1 modulates the the structure and activity of the chromatin fibre10,12,13. We have previ- interaction of ATM with chromatin both before and after DSB ously reported that HMGN1, an HMG protein that binds specifically to formation, thereby optimizing its activation. -
Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model
Downloaded from http://www.jimmunol.org/ by guest on September 25, 2021 T + is online at: average * The Journal of Immunology , 34 of which you can access for free at: 2016; 197:1477-1488; Prepublished online 1 July from submission to initial decision 4 weeks from acceptance to publication 2016; doi: 10.4049/jimmunol.1600589 http://www.jimmunol.org/content/197/4/1477 Molecular Profile of Tumor-Specific CD8 Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A. Waugh, Sonia M. Leach, Brandon L. Moore, Tullia C. Bruno, Jonathan D. Buhrman and Jill E. Slansky J Immunol cites 95 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html http://www.jimmunol.org/content/suppl/2016/07/01/jimmunol.160058 9.DCSupplemental This article http://www.jimmunol.org/content/197/4/1477.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2016 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 25, 2021. The Journal of Immunology Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A. -
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. -
Methylation Status of Vault RNA 2-1 Promoter Is a Predictor of Glycemic Response To
BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) BMJ Open Diab Res Care SUPPLEMEMTARY DATA Methylation Status of Vault RNA 2-1 Promoter Is a Predictor of Glycemic Response to Glucagon-like Peptide-1 Analogue Therapy in Type 2 Diabetes Mellitus Chia-Hung Lin, Yun-Shien Lee, Yu-Yao Huang, Chi-Neu Tsai List of supplemental Tables Supplemental Table S1 Demographic variables of 10 participants (training group) applied for DNA methylation chip at baselines Supplement Table S2 Demographic variables of participants (validation group) enrolled in this study Supplemental Table S3 Primers used for bisulfite sequencing primers (BSP), pyrosequencing reaction and centromeric CTCF polymorphism Supplemental Table S4 Differentially methylated regions (DMRs) in human genome and association with glycemic response of GLP-1 treatment in training group List of supplemental Figures Supplement Figure S1: A gender difference was identified in Infinium® MethylationEPIC BeadChip analysis in the training group of this study through volcano and heatmap plot. Supplemental Fig. S2: The volcano plots of the differentially methylation comparing responsive and non-responsive groups before and after GLP-1 analogue treatment. Supplemental Fig. S3: Serum level of TGF-1 as a predictor of a glycemic response to GLP-1 analogue treatment and the correlation of VTRNA2-1 RNA expression versus its promoter methylation status. Supplement Figure S4: The association between change in A1C and (A) VTRNA 2-1 methylation level, (B) TGF-beta1 levels, and (C) mRNA levels of VTRNA 2-1 Lin C-H, et al. -
HMGB1 in Health and Disease R
Donald and Barbara Zucker School of Medicine Journal Articles Academic Works 2014 HMGB1 in health and disease R. Kang R. C. Chen Q. H. Zhang W. Hou S. Wu See next page for additional authors Follow this and additional works at: https://academicworks.medicine.hofstra.edu/articles Part of the Emergency Medicine Commons Recommended Citation Kang R, Chen R, Zhang Q, Hou W, Wu S, Fan X, Yan Z, Sun X, Wang H, Tang D, . HMGB1 in health and disease. 2014 Jan 01; 40():Article 533 [ p.]. Available from: https://academicworks.medicine.hofstra.edu/articles/533. Free full text article. This Article is brought to you for free and open access by Donald and Barbara Zucker School of Medicine Academic Works. It has been accepted for inclusion in Journal Articles by an authorized administrator of Donald and Barbara Zucker School of Medicine Academic Works. Authors R. Kang, R. C. Chen, Q. H. Zhang, W. Hou, S. Wu, X. G. Fan, Z. W. Yan, X. F. Sun, H. C. Wang, D. L. Tang, and +8 additional authors This article is available at Donald and Barbara Zucker School of Medicine Academic Works: https://academicworks.medicine.hofstra.edu/articles/533 NIH Public Access Author Manuscript Mol Aspects Med. Author manuscript; available in PMC 2015 December 01. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Mol Aspects Med. 2014 December ; 0: 1–116. doi:10.1016/j.mam.2014.05.001. HMGB1 in Health and Disease Rui Kang1,*, Ruochan Chen1, Qiuhong Zhang1, Wen Hou1, Sha Wu1, Lizhi Cao2, Jin Huang3, Yan Yu2, Xue-gong Fan4, Zhengwen Yan1,5, Xiaofang Sun6, Haichao Wang7, Qingde Wang1, Allan Tsung1, Timothy R. -
Nrg4 and Gpr120 Signalling in Brown Fat Anthony Chukunweike OKOLO
Nrg4 and Gpr120 Signalling in Brown Fat Anthony Chukunweike OKOLO Institute of Reproductive and Developmental Biology Department of Surgery and Cancer Faculty of Medicine Imperial College London A thesis submitted in fulfilment of the requirements for award of the degree of Doctor of Philosophy 1 Statement of Originality All experiments included in this thesis were performed by me unless otherwise stated in the text. 2 Copyright statement The copyright of this thesis rests with the author and is made available under a Creative Commons Attribution Non-Commercial No Directive Licence. Researchers are free to copy, distribute or transmit the thesis on the condition that they attribute it, and they do not use it for commercial purposes, and they do not alter, transform or build upon it. For any re-use or re-distribution, researchers must make clear to others the licence terms of this work. 3 Acknowledgments I would like to thank my supervisors Dr Aylin Hanyaloglu and Dr Mark Christian for giving me the great opportunity to work in their labs. Aylin put in a great deal of effort especially in area of Gpr120 signalling, including having to guide me through the critical imaging procedures. Aylin and Mark contributed a great deal towards the final edition of this thesis. I would also like to thank Dr Mark Christian for bringing me to Imperial College London to start off my PhD in his laboratory, and for being a great mentor and a continuous source of knowledge for me. I am grateful for your enduring patience in trying to bring out the best in me and ensuring that I develop the ‘critical thinking’ that is needed as a scientist. -
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Molecular BioSystems Accepted Manuscript This is an Accepted Manuscript, which has been through the Royal Society of Chemistry peer review process and has been accepted for publication. Accepted Manuscripts are published online shortly after acceptance, before technical editing, formatting and proof reading. Using this free service, authors can make their results available to the community, in citable form, before we publish the edited article. We will replace this Accepted Manuscript with the edited and formatted Advance Article as soon as it is available. You can find more information about Accepted Manuscripts in the Information for Authors. Please note that technical editing may introduce minor changes to the text and/or graphics, which may alter content. The journal’s standard Terms & Conditions and the Ethical guidelines still apply. In no event shall the Royal Society of Chemistry be held responsible for any errors or omissions in this Accepted Manuscript or any consequences arising from the use of any information it contains. www.rsc.org/molecularbiosystems Page 1 of 29 Molecular BioSystems Mutated Genes and Driver Pathways Involved in Myelodysplastic Syndromes—A Transcriptome Sequencing Based Approach Liang Liu1*, Hongyan Wang1*, Jianguo Wen2*, Chih-En Tseng2,3*, Youli Zu2, Chung-che Chang4§, Xiaobo Zhou1§ 1 Center for Bioinformatics and Systems Biology, Division of Radiologic Sciences, Wake Forest University Baptist Medical Center, Winston-Salem, NC 27157, USA. 2 Department of Pathology, the Methodist Hospital Research Institute, -
The Pathogenetic Role of Β-Cell Mitochondria in Type 2 Diabetes
236 3 Journal of M Fex et al. Mitochondria in β-cells 236:3 R145–R159 Endocrinology REVIEW The pathogenetic role of β-cell mitochondria in type 2 diabetes Malin Fex1, Lisa M Nicholas1, Neelanjan Vishnu1, Anya Medina1, Vladimir V Sharoyko1, David G Nicholls1, Peter Spégel1,2 and Hindrik Mulder1 1Department of Clinical Sciences in Malmö, Unit of Molecular Metabolism, Lund University Diabetes Centre, Clinical Research Center, Malmö University Hospital, Lund University, Malmö, Sweden 2Department of Chemistry, Center for Analysis and Synthesis, Lund University, Sweden Correspondence should be addressed to H Mulder: [email protected] Abstract Mitochondrial metabolism is a major determinant of insulin secretion from pancreatic Key Words β-cells. Type 2 diabetes evolves when β-cells fail to release appropriate amounts f TCA cycle of insulin in response to glucose. This results in hyperglycemia and metabolic f coupling signal dysregulation. Evidence has recently been mounting that mitochondrial dysfunction f oxidative phosphorylation plays an important role in these processes. Monogenic dysfunction of mitochondria is a f mitochondrial transcription rare condition but causes a type 2 diabetes-like syndrome owing to β-cell failure. Here, f genetic variation we describe novel advances in research on mitochondrial dysfunction in the β-cell in type 2 diabetes, with a focus on human studies. Relevant studies in animal and cell models of the disease are described. Transcriptional and translational regulation in mitochondria are particularly emphasized. The role of metabolic enzymes and pathways and their impact on β-cell function in type 2 diabetes pathophysiology are discussed. The role of genetic variation in mitochondrial function leading to type 2 diabetes is highlighted. -
(WCPG): Poster Abstracts: Sunday
ARTICLE IN PRESS JID: NEUPSY [m6+; October 2, 2018;12:59 ] European Neuropsychopharmacology (2018) 000, 1–75 www.elsevier.com/locate/euroneuro Abstracts of the 26th World Congress of Psychiatric Genetics (WCPG): Poster Abstracts: Sunday Sunday, October 14, 2018 with a 2kb upstream and 1kb downstream region was consid- ered for each gene. Gene-set analysis was conducted using MAGMA, with a principal components regression model for gene-based analyses. Sex, age, the 10 first and otherwise as- Poster Session III sociated principal components were included as covariates 4:00 p.m. - 6:00 p.m. in this step. We retrieved a “Hallmark Androgen response” gene-set from MSigDB to be tested in a case-control asso- SU1 ciation study. This gene-set contains 98 curated genes in- ANDROGEN RECEPTOR SIGNALING PATHWAYS IN- volved in the response to androgen receptor signaling. Also, FLUENCE IN ATTENTION-DEFICIT/HYPERACTIVITY a list of 534 annotated genes with at least one occurrence DISORDER of potential transcription factor binding sites (TFBS) for AR was created to investigate potential gene targets related to Djenifer Kappel 1, Bruna da Silva 1, Renata B. Cupertino 1, ADHD susceptibility. Diana Müller 1, Vitor Breda 2, Stefania Pigatto Teche 2, Results: No genome-wide association was observed at the Rogério Margis 1, Luis Augusto Rohde 2, Nina Roth Mota 3, SNPs or gene level. In the gene-set analysis, we found evi- Diego L. Rovaris 1, Eugênio H. Grevet 1, Claiton Bau 1 dence that the “Hallmark Androgen response” gene-set was significantly associated with ADHD susceptibility in our sam- 1 Universidade Federal do Rio Grande do Sul ple (p = 0.039). -
Modulation of Mitochondrial DNA Copy Number in a Model of Glioblastoma
Sun and St John Epigenetics & Chromatin (2018) 11:53 https://doi.org/10.1186/s13072-018-0223-z Epigenetics & Chromatin RESEARCH Open Access Modulation of mitochondrial DNA copy number in a model of glioblastoma induces changes to DNA methylation and gene expression of the nuclear genome in tumours Xin Sun1,2 and Justin C. St John1,2* Abstract Background: There are multiple copies of mitochondrial DNA (mtDNA) present in each cell type, and they are strictly regulated in a cell-specifc manner by a group of nuclear-encoded mtDNA-specifc replication factors. This strict regu- lation of mtDNA copy number is mediated by cell-specifc DNA methylation of these replication factors. Glioblastoma multiforme, HSR-GBM1, cells are hyper-methylated and maintain low mtDNA copy number to support their tumori- genic status. We have previously shown that when HSR-GBM1 cells with 50% of their original mtDNA content were inoculated into mice, tumours grew more aggressively than non-depleted cells. However, when the cells possessed only 3% and 0.2% of their original mtDNA content, tumour formation was less frequent and the initiation of tumori- genesis was signifcantly delayed. Importantly, the process of tumorigenesis was dependent on mtDNA copy number being restored to pre-depletion levels. Results: By performing whole genome MeDIP-Seq and RNA-Seq on tumours generated from cells possessing 100%, 50%, 0.3% and 0.2% of their original mtDNA content, we determined that restoration of mtDNA copy number caused signifcant changes to both the nuclear methylome and its transcriptome for each tumour type. The afected genes were specifcally associated with gene networks and pathways involving behaviour, nervous system development, cell diferentiation and regulation of transcription and cellular processes. -
Association of Sequence Alterations in the Putative Promoter of RAB7L1 with a Reduced Parkinson Disease Risk
ORIGINAL CONTRIBUTION Association of Sequence Alterations in the Putative Promoter of RAB7L1 With a Reduced Parkinson Disease Risk Ziv Gan-Or, BMedSci; Anat Bar-Shira, PhD; Dvir Dahary, MSc; Anat Mirelman, PhD; Merav Kedmi, PhD; Tanya Gurevich, MD; Nir Giladi, MD; Avi Orr-Urtreger, MD, PhD Objective: To examine whether PARK16, which was re- Results: All tested SNPs were significantly associated with cently identified as a protective locus for Parkinson dis- PD (odds ratios=0.64-0.76; P=.0002-.014). Two of them, ease (PD) in Asian, white, and South American popula- rs1572931 and rs823144, were localized to the putative pro- tions, is also associated with PD in the genetically moter region of RAB7L1 and their sequence variations al- homogeneous Ashkenazi Jewish population. teredthepredictedtranscriptionfactorbindingsitesofCdxA, p300, GATA-1, Sp1, and c-Ets-1. Only 0.4% of patients were Design: Case-control study. homozygous for the protective rs1572931 genotype (T/T), comparedwith3.0%amongcontrols(P=5ϫ10−5).ThisSNP was included in a haplotype that reduced the risk for PD by Setting: A medical center affiliated with a university. 10- to 12-fold (P=.002-.01) in all patients with PD and in a subgroupofpatientswhodonotcarrytheAshkenazifounder Subjects: Five single-nucleotide polymorphisms (SNPs) mutations in the GBA or LRRK2 genes. located between RAB7L1 and SLC41A1 were analyzed in 720 patients with PD and 642 controls, all of Ashkenazi Conclusions: Our data demonstrate that specific SNP Jewish origin. variations and haplotypes in the PARK16 locus are asso- ciated with reduced risk for PD in Ashkenazim. Al- Main Outcome Measures: Haplotypes were defined though it is possible that alterations in the putative pro- and risk estimates were determined for each SNP and hap- moter of RAB7L1 are associated with this effect, the role lotype. -
Newly Identified Gon4l/Udu-Interacting Proteins
www.nature.com/scientificreports OPEN Newly identifed Gon4l/ Udu‑interacting proteins implicate novel functions Su‑Mei Tsai1, Kuo‑Chang Chu1 & Yun‑Jin Jiang1,2,3,4,5* Mutations of the Gon4l/udu gene in diferent organisms give rise to diverse phenotypes. Although the efects of Gon4l/Udu in transcriptional regulation have been demonstrated, they cannot solely explain the observed characteristics among species. To further understand the function of Gon4l/Udu, we used yeast two‑hybrid (Y2H) screening to identify interacting proteins in zebrafsh and mouse systems, confrmed the interactions by co‑immunoprecipitation assay, and found four novel Gon4l‑interacting proteins: BRCA1 associated protein‑1 (Bap1), DNA methyltransferase 1 (Dnmt1), Tho complex 1 (Thoc1, also known as Tho1 or HPR1), and Cryptochrome circadian regulator 3a (Cry3a). Furthermore, all known Gon4l/Udu‑interacting proteins—as found in this study, in previous reports, and in online resources—were investigated by Phenotype Enrichment Analysis. The most enriched phenotypes identifed include increased embryonic tissue cell apoptosis, embryonic lethality, increased T cell derived lymphoma incidence, decreased cell proliferation, chromosome instability, and abnormal dopamine level, characteristics that largely resemble those observed in reported Gon4l/udu mutant animals. Similar to the expression pattern of udu, those of bap1, dnmt1, thoc1, and cry3a are also found in the brain region and other tissues. Thus, these fndings indicate novel mechanisms of Gon4l/ Udu in regulating CpG methylation, histone expression/modifcation, DNA repair/genomic stability, and RNA binding/processing/export. Gon4l is a nuclear protein conserved among species. Animal models from invertebrates to vertebrates have shown that the protein Gon4-like (Gon4l) is essential for regulating cell proliferation and diferentiation.