Low Dose and Low Dose-Rate Radiation Effects and Models
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Genetic Variations in the PSMA6 and PSMC6 Proteasome Genes Are Associated with Multiple Sclerosis and Response to Interferon‑Β Therapy in Latvians
EXPERIMENTAL AND THERAPEUTIC MEDICINE 21: 478, 2021 Genetic variations in the PSMA6 and PSMC6 proteasome genes are associated with multiple sclerosis and response to interferon‑β therapy in Latvians NATALIA PARAMONOVA1, JOLANTA KALNINA1, KRISTINE DOKANE1, KRISTINE DISLERE1, ILVA TRAPINA1, TATJANA SJAKSTE1 and NIKOLAJS SJAKSTE1,2 1Genomics and Bioinformatics, Institute of Biology of The University of Latvia; 2Department of Medical Biochemistry of The University of Latvia, LV‑1004 Riga, Latvia Received July 8, 2020; Accepted December 8, 2020 DOI: 10.3892/etm.2021.9909 Abstract. Several polymorphisms in genes related to the Introduction ubiquitin‑proteasome system exhibit an association with pathogenesis and prognosis of various human autoimmune Multiple sclerosis (MS) is a lifelong demyelinating disease of diseases. Our previous study reported the association the central nervous system. The clinical onset of MS tends to between multiple sclerosis (MS) and the PSMA3‑rs2348071 be between the second and fourth decade of life. Similarly to polymorphism in the Latvian population. The current study other autoimmune diseases, women are affected 3‑4 times more aimed to evaluate the PSMA6 and PSMC6 genetic variations, frequently than men (1). About 10% of MS patients experience their interaction between each other and with the rs2348071, a primary progressive MS form characterized by the progres‑ on the susceptibility to MS risk and response to therapy in sion of neurological disability from the onset. In about 90% the Latvian population. PSMA6‑rs2277460, ‑rs1048990 and of MS patients, the disease undergoes the relapse‑remitting PSMC6‑rs2295826, ‑rs2295827 were genotyped in the MS MS course (RRMS); in most of these patients, the condition case/control study and analysed in terms of genotype‑protein acquires secondary progressive course (SPMS) (2). -
NPI-0052 and Γ-Radiation Induce a Synergistic Apoptotic Effect In
Frisira et al. Cell Death and Disease (2019) 10:785 https://doi.org/10.1038/s41419-019-2026-y Cell Death & Disease ARTICLE Open Access NPI-0052 and γ-radiation induce a synergistic apoptoticeffectinmedulloblastoma Eleni Frisira1, Fatima Rashid1,SwastinaNathVarma2,SaraBadodi1, Valentine Ayodele Benjamin-Ombo1, David Michod 2 and Maria Victoria Niklison-Chirou 1 Abstract Medulloblastoma (MB) is the most common malignant solid paediatric brain tumour. The standard treatment for MB is surgical resection of the tumour, radiation and chemotherapy. This therapy is associated with high morbidity and adverse side effects. Hence, more targeted and less toxic therapies are vitally needed to improve the quality of life of survivors. NPI-0052 is a novel proteasome inhibitor that irreversibly binds the 20S proteasome subunit. This compound has anti-tumour activity in metastatic solid tumours, glioblastoma and multiple myeloma with a good safety profile. Importantly, NPI-0052 has a lipophilic structure and can penetrate the blood–brain barrier, making it a suitable treatment for brain tumours. In the present study, we performed an in silico gene expression analysis to evaluate the proteasome subunit expression in MB. To evaluate the anticancer activity of NPI-0052, we used a range of MB patient- derived MB cells and cell lines. The synergistic cell death of NPI-0052 with γ-radiation was evaluated in tumour organoids derived from patient-derived MB cells. We show that high expression of proteasome subunits is a poor prognostic factor for MB patients. Also, our preclinical work demonstrated that NPI-0052 can inhibit proteasome activity and activate apoptosis in MB cells. Moreover, we observe that NPI-0052 has a synergistic apoptotic effect with γ-radiation, a component of the current MB therapy. -
Radioresistance of Brain Tumors
cancers Review Radioresistance of Brain Tumors Kevin Kelley 1, Jonathan Knisely 1, Marc Symons 2,* and Rosamaria Ruggieri 1,2,* 1 Radiation Medicine Department, Hofstra Northwell School of Medicine, Northwell Health, Manhasset, NY 11030, USA; [email protected] (K.K.); [email protected] (J.K.) 2 The Feinstein Institute for Molecular Medicine, Hofstra Northwell School of Medicine, Northwell Health, Manhasset, NY 11030, USA * Correspondence: [email protected] (M.S.); [email protected] (R.R.); Tel.: +1-516-562-1193 (M.S.); +1-516-562-3410 (R.R.) Academic Editor: Zhe-Sheng (Jason) Chen Received: 17 January 2016; Accepted: 24 March 2016; Published: 30 March 2016 Abstract: Radiation therapy (RT) is frequently used as part of the standard of care treatment of the majority of brain tumors. The efficacy of RT is limited by radioresistance and by normal tissue radiation tolerance. This is highlighted in pediatric brain tumors where the use of radiation is limited by the excessive toxicity to the developing brain. For these reasons, radiosensitization of tumor cells would be beneficial. In this review, we focus on radioresistance mechanisms intrinsic to tumor cells. We also evaluate existing approaches to induce radiosensitization and explore future avenues of investigation. Keywords: radiation therapy; radioresistance; brain tumors 1. Introduction 1.1. Radiotherapy and Radioresistance of Brain Tumors Radiation therapy is a mainstay in the treatment of the majority of primary tumors of the central nervous system (CNS). However, the efficacy of this therapeutic approach is significantly limited by resistance to tumor cell killing after exposure to ionizing radiation. This phenomenon, termed radioresistance, can be mediated by factors intrinsic to the cell or by the microenvironment. -
Serpin Peptidase Inhibitor Clade a Member 1 As a Potential Marker for Malignancy in Insulinomas
Human Cancer Biology Serpin Peptidase Inhibitor Clade A Member 1as a Potential Marker for Malignancy in Insulinomas Sandra Vale¤ riadeSa¤ ,1, 2 Maria Lu¤ cia Corre“ a-Giannella,1, 3 Ma¤ rcio Carlos Machado,3 Karin Krogh,4 Madson Queiroz de Almeida, 3 Maria AdelaideAlbergaria Pereira,3 4 4 1 Sheila Aparecida Coelho Siqueira, RoselyAntunes Patzina, FelI¤cia Satie Ibuki, Mari Cleide Sogayar,5 Marcel Cerqueira Ce¤ sar Machado,2 and Daniel Giannella-Neto1, 3 Abstract Purpose: The biological behavior of insulinomas cannot be predicted based on histopathologic criteria in which the diagnosis of malignancy is confirmed by the presence of metastases. In this study, microarray and quantitative real-time reverse transcription-PCR were applied to identify differentially expressed genes between malignant and nonmalignant insulinomas to search for useful biomarkers to recognize the metastatic potential of insulinomas. Experimental Design: CodeLink human bioarrays were used to analyze differences in f20,000 genes between six well-differentiated endocrine tumors of benign behavior compared with one well-differentiated endocrine carcinoma (WDEC) and three metastases of endocrine carcinomas (MEC). Quantitative real-time reverse transcription-PCR was used to validate differ- ential expressions of five genes in a series of 35 sporadic insulinomas. Serpin peptidase inhibitor cladeA member1 (SERPINA1; a-1-antitrypsin) expression, identified as up-regulated in malignant insulinomas, was also evaluated by immunohistochemistry. Results: Analysis of microarray -
Genome-Wide Transcript and Protein Analysis Reveals Distinct Features of Aging in the Mouse Heart
bioRxiv preprint doi: https://doi.org/10.1101/2020.08.28.272260; this version posted April 21, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Genome-wide transcript and protein analysis reveals distinct features of aging in the mouse heart Isabela Gerdes Gyuricza1, Joel M. Chick2, Gregory R. Keele1, Andrew G. Deighan1, Steven C. Munger1, Ron Korstanje1, Steven P. Gygi3, Gary A. Churchill1 1The Jackson Laboratory, Bar Harbor, Maine 04609 USA; 2Vividion Therapeutics, San Diego, California 92121, USA; 3Harvard Medical School, Boston, Massachusetts 02115, USA Corresponding author: [email protected] Key words for online indexing: Heart Aging Transcriptomics Proteomics eQTL pQTL Stoichiometry ABSTRACT Investigation of the molecular mechanisms of aging in the human heart is challenging due to confounding factors, such as diet and medications, as well limited access to tissues. The laboratory mouse provides an ideal model to study aging in healthy individuals in a controlled environment. However, previous mouse studies have examined only a narrow range of the genetic variation that shapes individual differences during aging. Here, we analyzed transcriptome and proteome data from hearts of genetically diverse mice at ages 6, 12 and 18 months to characterize molecular changes that occur in the aging heart. Transcripts and proteins reveal distinct biological processes that are altered through the course of natural aging. Transcriptome analysis reveals a scenario of cardiac hypertrophy, fibrosis, and reemergence of fetal gene expression patterns. -
A Peripheral Blood Gene Expression Signature to Diagnose Subclinical Acute Rejection
CLINICAL RESEARCH www.jasn.org A Peripheral Blood Gene Expression Signature to Diagnose Subclinical Acute Rejection Weijia Zhang,1 Zhengzi Yi,1 Karen L. Keung,2 Huimin Shang,3 Chengguo Wei,1 Paolo Cravedi,1 Zeguo Sun,1 Caixia Xi,1 Christopher Woytovich,1 Samira Farouk,1 Weiqing Huang,1 Khadija Banu,1 Lorenzo Gallon,4 Ciara N. Magee,5 Nader Najafian,5 Milagros Samaniego,6 Arjang Djamali ,7 Stephen I. Alexander,2 Ivy A. Rosales,8 Rex Neal Smith,8 Jenny Xiang,3 Evelyne Lerut,9 Dirk Kuypers,10,11 Maarten Naesens ,10,11 Philip J. O’Connell,2 Robert Colvin,8 Madhav C. Menon,1 and Barbara Murphy1 Due to the number of contributing authors, the affiliations are listed at the end of this article. ABSTRACT Background In kidney transplant recipients, surveillance biopsies can reveal, despite stable graft function, histologic features of acute rejection and borderline changes that are associated with undesirable graft outcomes. Noninvasive biomarkers of subclinical acute rejection are needed to avoid the risks and costs associated with repeated biopsies. Methods We examined subclinical histologic and functional changes in kidney transplant recipients from the prospective Genomics of Chronic Allograft Rejection (GoCAR) study who underwent surveillance biopsies over 2 years, identifying those with subclinical or borderline acute cellular rejection (ACR) at 3 months (ACR-3) post-transplant. We performed RNA sequencing on whole blood collected from 88 indi- viduals at the time of 3-month surveillance biopsy to identify transcripts associated with ACR-3, developed a novel sequencing-based targeted expression assay, and validated this gene signature in an independent cohort. -
Theranostics the PSMD14 Inhibitor Thiolutin As a Novel Therapeutic
Theranostics 2021, Vol. 11, Issue 12 5847 Ivyspring International Publisher Theranostics 2021; 11(12): 5847-5862. doi: 10.7150/thno.46109 Research Paper The PSMD14 inhibitor Thiolutin as a novel therapeutic approach for esophageal squamous cell carcinoma through facilitating SNAIL degradation Chao Jing1*, Xingchen Li1*, Mengqian Zhou1*, Shengchi Zhang1,2*, Qingchuan Lai1, Dandan Liu1, Beibei Ye1, Linqi Li1, Yue Wu1, Hong Li1, Kai Yue1, Peng Chen1, Xiaofeng Yao1, Yansheng Wu1, Yuansheng Duan1, Xudong Wang1 1. Department of Maxillofacial and Otorhinolaryngological Oncology, Tianjin Medical University Cancer Institute and Hospital, Key Laboratory of Cancer Prevention and Therapy, Tianjin Cancer Institute, National Clinical Research Center of Cancer, Tianjin 300060, China. 2. Department of Ear, Nose and Throat, Tianjin 1st Centre Hospital, Tianjin 300192, China. * These authors contributed equally to this work. Corresponding authors: Dr. Xudong Wang ([email protected]), Ms Yuansheng Duan ([email protected]) and Dr. Yansheng Wu ([email protected]). Department of Maxillofacial and Otorhinolaryngological Oncology, Tianjin Medical University Cancer Institute and Hospital, Key Laboratory of Cancer Prevention and Therapy, Tianjin Cancer Institute, National Clinical Research Center of Cancer, 18 Huanhuxi Road, Tianjin 300060, China. Tel: +86-22-23340123. © The author(s). This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/). See http://ivyspring.com/terms for full terms and conditions. Received: 2020.03.17; Accepted: 2021.03.11; Published: 2021.04.03 Abstract Metastasis and chemoresistance are major causes of poor prognosis in patients with esophageal squamous cell carcinoma (ESCC), manipulated by multiple factors including deubiquitinating enzyme (DUB). -
Biocreative 2012 Proceedings
Proceedings of 2012 BioCreative Workshop April 4 -5, 2012 Washington, DC USA Editors: Cecilia Arighi Kevin Cohen Lynette Hirschman Martin Krallinger Zhiyong Lu Carolyn Mattingly Alfonso Valencia Thomas Wiegers John Wilbur Cathy Wu 2012 BioCreative Workshop Proceedings Table of Contents Preface…………………………………………………………………………………….......... iv Committees……………………………………………………………………………………... v Workshop Agenda…………………………………………………………………………….. vi Track 1 Collaborative Biocuration-Text Mining Development Task for Document Prioritization for Curation……………………………………..……………………………………………….. 2 T Wiegers, AP Davis, and CJ Mattingly System Description for the BioCreative 2012 Triage Task ………………………………... 20 S Kim, W Kim, CH Wei, Z Lu and WJ Wilbur Ranking of CTD articles and interactions using the OntoGene pipeline ……………..….. 25 F Rinaldi, S Clematide and S Hafner Selection of relevant articles for curation for the Comparative Toxicogenomic Database…………………………………………………………………………………………. 31 D Vishnyakova, E Pasche and P Ruch CoIN: a network exploration for document triage………………………………................... 39 YY Hsu and HY Kao DrTW: A Biomedical Term Weighting Method for Document Recommendation ………... 45 JH Ju, YD Chen and JH Chiang C2HI: a Complete CHemical Information decision system……………………………..….. 52 CH Ke, TLM Lee and JH Chiang Track 2 Overview of BioCreative Curation Workshop Track II: Curation Workflows….…………... 59 Z Lu and L Hirschman WormBase Literature Curation Workflow ……………………………………………………. 66 KV Auken, T Bieri, A Cabunoc, J Chan, Wj Chen, P Davis, A Duong, R Fang, C Grove, Tw Harris, K Howe, R Kishore, R Lee, Y Li, Hm Muller, C Nakamura, B Nash, P Ozersky, M Paulini, D Raciti, A Rangarajan, G Schindelman, Ma Tuli, D Wang, X Wang, G Williams, K Yook, J Hodgkin, M Berriman, R Durbin, P Kersey, J Spieth, L Stein and Pw Sternberg Literature curation workflow at The Arabidopsis Information Resource (TAIR)…..……… 72 D Li, R Muller, TZ Berardini and E Huala Summary of Curation Process for one component of the Mouse Genome Informatics Database Resource ………………………………………………………………………….... -
Human Radiosensitivity and Radiosusceptibility: What Are the Differences?
International Journal of Molecular Sciences Review Human Radiosensitivity and Radiosusceptibility: What Are the Differences? Laura El-Nachef 1, Joelle Al-Choboq 1, Juliette Restier-Verlet 1, Adeline Granzotto 1, Elise Berthel 1,2, Laurène Sonzogni 1,Mélanie L. Ferlazzo 1, Audrey Bouchet 1 , Pierre Leblond 3, Patrick Combemale 3, Stéphane Pinson 4, Michel Bourguignon 1,5 and Nicolas Foray 1,* 1 Inserm, U1296 unit, Radiation: Defense, Health and Environment, Centre Léon-Bérard, 28, rue Laennec, 69008 Lyon, France; [email protected] (L.E.-N.); [email protected] (J.A.-C.); Juliette.Restier–[email protected] (J.R.-V.); [email protected] (A.G.); [email protected] (E.B.); [email protected] (L.S.); [email protected] (M.L.F.); [email protected] (A.B.); [email protected] (M.B.) 2 Neolys Diagnostics, 67960 Entzheim, France 3 Centre Léon-Bérard, 28, rue Laennec, 69008 Lyon, France; [email protected] (P.L.); [email protected] (P.C.) 4 Hospices Civils de Lyon, Quai des Célestins, 69002 Lyon, France; [email protected] 5 Université Paris Saclay Versailles St Quentin en Yvelines, 78035 Versailles, France * Correspondence: [email protected]; Tel.: +33-4-78-78-28-28 Abstract: The individual response to ionizing radiation (IR) raises a number of medical, scientific, and societal issues. While the term “radiosensitivity” was used by the pioneers at the beginning Citation: El-Nachef, L.; Al-Choboq, of the 20st century to describe only the radiation-induced adverse tissue reactions related to cell J.; Restier-Verlet, J.; Granzotto, A.; death, a confusion emerged in the literature from the 1930s, as “radiosensitivity” was indifferently Berthel, E.; Sonzogni, L.; Ferlazzo, used to describe the toxic, cancerous, or aging effect of IR. -
Interaction Profiling of RNA-Binding Ubiquitin Ligases Reveals A
www.nature.com/scientificreports OPEN Interaction profling of RNA- binding ubiquitin ligases reveals a link between posttranscriptional Received: 7 March 2017 Accepted: 14 September 2017 regulation and the ubiquitin system Published: xx xx xxxx Andrea Hildebrandt1, Gregorio Alanis-Lobato1,2, Andrea Voigt1, Kathi Zarnack3, Miguel A. Andrade-Navarro1,2, Petra Beli1 & Julian König1 RNA-binding ubiquitin ligases (RBULs) have the potential to link RNA-mediated mechanisms to protein ubiquitylation. Despite this, the cellular functions, substrates and interaction partners of most RBULs remain poorly characterized. Afnity purifcation (AP) combined with quantitative mass spectrometry (MS)-based proteomics is a powerful approach for analyzing protein functions. Mapping the physiological interaction partners of RNA-binding proteins has been hampered by their intrinsic properties, in particular the existence of low-complexity regions, which are prone to engage in non- physiological interactions. Here, we used an adapted AP approach to identify the interaction partners of human RBULs harboring diferent RNA-binding domains. To increase the likelihood of recovering physiological interactions, we combined control and bait-expressing cells prior to lysis. In this setup, only stable interactions that were originally present in the cell will be identifed. We exploit gene function similarity between the bait proteins and their interactors to benchmark our approach in its ability to recover physiological interactions. We reveal that RBULs engage in stable interactions with RNA-binding proteins involved in diferent steps of RNA metabolism as well as with components of the ubiquitin conjugation machinery and ubiquitin-binding proteins. Our results thus demonstrate their capacity to link posttranscriptional regulation with the ubiquitin system. -
A High-Throughput Approach to Uncover Novel Roles of APOBEC2, a Functional Orphan of the AID/APOBEC Family
Rockefeller University Digital Commons @ RU Student Theses and Dissertations 2018 A High-Throughput Approach to Uncover Novel Roles of APOBEC2, a Functional Orphan of the AID/APOBEC Family Linda Molla Follow this and additional works at: https://digitalcommons.rockefeller.edu/ student_theses_and_dissertations Part of the Life Sciences Commons A HIGH-THROUGHPUT APPROACH TO UNCOVER NOVEL ROLES OF APOBEC2, A FUNCTIONAL ORPHAN OF THE AID/APOBEC FAMILY A Thesis Presented to the Faculty of The Rockefeller University in Partial Fulfillment of the Requirements for the degree of Doctor of Philosophy by Linda Molla June 2018 © Copyright by Linda Molla 2018 A HIGH-THROUGHPUT APPROACH TO UNCOVER NOVEL ROLES OF APOBEC2, A FUNCTIONAL ORPHAN OF THE AID/APOBEC FAMILY Linda Molla, Ph.D. The Rockefeller University 2018 APOBEC2 is a member of the AID/APOBEC cytidine deaminase family of proteins. Unlike most of AID/APOBEC, however, APOBEC2’s function remains elusive. Previous research has implicated APOBEC2 in diverse organisms and cellular processes such as muscle biology (in Mus musculus), regeneration (in Danio rerio), and development (in Xenopus laevis). APOBEC2 has also been implicated in cancer. However the enzymatic activity, substrate or physiological target(s) of APOBEC2 are unknown. For this thesis, I have combined Next Generation Sequencing (NGS) techniques with state-of-the-art molecular biology to determine the physiological targets of APOBEC2. Using a cell culture muscle differentiation system, and RNA sequencing (RNA-Seq) by polyA capture, I demonstrated that unlike the AID/APOBEC family member APOBEC1, APOBEC2 is not an RNA editor. Using the same system combined with enhanced Reduced Representation Bisulfite Sequencing (eRRBS) analyses I showed that, unlike the AID/APOBEC family member AID, APOBEC2 does not act as a 5-methyl-C deaminase. -
Thesis to My Family, for the Joy in Everyday Life
From DEPARTMENT OF ONCOLOGY AND PATHOLOGY Karolinska Institutet, Stockholm, Sweden STEREOTACTIC BODY RADIATION THERAPY OF PRIMARY LUNG CANCER AND METASTASES Karin Lindberg Stockholm 2015 All previously published papers were reproduced with permission from the publisher. Published by Karolinska Institutet. Printed by AJ E-print AB © Karin Lindberg, 2015 ISBN 978-91-7549-942-0 Institutionen för Onkologi-Patologi Stereotactic Body Radiation Therapy of Primary Lung cancer and Metastases AKADEMISK AVHANDLING som för avläggande av medicine doktorsexamen vid Karolinska Institutet offentligen försvaras i Radiumhemmets föreläsningssal, plan 01 (P1:01), Karolinska Universitetssjukhuset Solna Fredagen den 29:e maj 2015, kl 10.00 Av Karin Lindberg Leg läkare Huvudhandledare: Fakultetsopponent: Rolf Lewensohn, MD, PhD, Professor Matthias Guckenberger, MD, PhD, Professor Karolinska Institutet University Hospital Zürich (USZ) Department of Radiation Oncology Institutionen för Onkologi-Patologi Bihandledare: Betygsnämnd: Peter Wersäll, MD, PhD, Docent Magnus Sköld, MD, PhD, Professor Karolinska Institutet Karolinska Institutet Institutionen för Onkologi-Patologi Institutionen för Medicin Solna Signe Friesland, MD, PhD Thomas Asklund, MD, PhD, Docent Karolinska Institutet Umeå Universitet Institutionen för Onkologi-Patologi Institutionen för strålningsvetenskaper Anders Montelius, PhD, Docent Uppsala Universitet Institutionen för Immunologi, Genetik och Patologi I dedicate this thesis to my family, for the joy in everyday life. ...”Kärlek som är att vakna tillsammans och möta den blåögda morgonen att utbyta leenden som värmer och värnar och den nya dagens framtid att på resan genom dagen vila tillsammans på klockslagens små väntstationer och intaga gemensamma måltider upplysta av lingonsyltens röda glädje”... Ur Den dagliga kärleken av Maria Wine ABSTRACT Stereotactic body radiation therapy (SBRT) has been assessed by both retrospective and prospective studies showing excellent treatment outcome with acceptable toxicity and high grade of local control.