A Multi-Scale Structural Interactome Browser for Genomic Studies
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Deficiency in Protein Tyrosine Phosphatase PTP1B Shortens Lifespan and Leads to Development of Acute Leukemia
Author Manuscript Published OnlineFirst on November 9, 2017; DOI: 10.1158/0008-5472.CAN-17-0946 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Deficiency in protein tyrosine phosphatase PTP1B shortens lifespan and leads to development of acute leukemia Samantha Le Sommer1, Nicola Morrice1, Martina Pesaresi1, Dawn Thompson1, Mark A. Vickers1, Graeme I. Murray1, Nimesh Mody1, Benjamin G Neel2, Kendra K Bence3,4, Heather M Wilson1*, & Mirela Delibegovic1* 1Institute of Medical Sciences, University of Aberdeen, United Kingdom 2Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York University, New York, New York 10016, USA. 3 Dept. of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, USA. 4 Current address: Internal Medicine Research Unit (IMRU), Pfizer Inc, 610 Main St. Cambridge, MA 02139 USA *corresponding authors: Prof. Mirela Delibegovic ([email protected]) and Dr. Heather Wilson ([email protected] ) Running Title: PTP1B deficiency shortens lifespan and leads to leukaemia Key Words: PTP1B, lifespan, leukaemia, myeloid, STAT3 Additional information: This work was performed with the funds from the Wellcome Trust ISSF grant to M. Delibegovic and BHF project grant to M. Delibegovic (PG/11/8/28703). S. Le Sommer is a recipient of the University of Aberdeen Institute of Medical Sciences PhD studentship. Conflict of interest: Authors declare there are no conflicts of interests. Word Count: 5,000 Figure Count: 6 Figures, 1 Table (Supplemental Figures: 6, Supplemental Tables: 4) 1 Downloaded from cancerres.aacrjournals.org on September 29, 2021. © 2017 American Association for Cancer Research. -
Cancer-Testis Antigens MAGEA Proteins Are Incorporated Into Extracellular Vesicles Released by Cells
www.oncotarget.com Oncotarget, 2019, Vol. 10, (No. 38), pp: 3694-3708 Research Paper Cancer-testis antigens MAGEA proteins are incorporated into extracellular vesicles released by cells Anneli Kuldkepp1, Magda Karakai1, Eve Toomsoo1, Olavi Reinsalu1 and Reet Kurg1 1Institute of Technology, University of Tartu, Tartu, Estonia Correspondence to: Reet Kurg, email: [email protected] Keywords: cancer-testis antigens; MAGEA; extracellular vesicles; microvesicles Received: December 13, 2018 Accepted: May 13, 2019 Published: June 04, 2019 Copyright: Kuldkepp et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT Melanoma-associated antigen A (MAGEA) family proteins represent a class of tumor antigens that are expressed in a variety of malignant tumors, but their expression in normal tissues is restricted to germ cells. MAGEA family consists of eleven proteins that are highly conserved sharing the common MAGE homology domain (MHD). In the current study, we show that MAGEA4 and MAGEA10 proteins are incorporated into extracellular vesicles released by mouse fibroblast and human osteosarcoma U2OS cells and are expressed, at least partly, on the surface of released EVs. The C-terminal part of the protein containing MHD domain is required for this activity. Expression of MAGEA proteins induced the budding of cells and formation of extracellular vesicles with 150 to 1500 nm in diameter. Our data suggest that the release of MAGEA-positive EVs is at least to some extent induced by the expression of MAGEA proteins itself. -
Environmental Influences on Endothelial Gene Expression
ENDOTHELIAL CELL GENE EXPRESSION John Matthew Jeff Herbert Supervisors: Prof. Roy Bicknell and Dr. Victoria Heath PhD thesis University of Birmingham August 2012 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 Tumour angiogenesis is a vital process in the pathology of tumour development and metastasis. Targeting markers of tumour endothelium provide a means of targeted destruction of a tumours oxygen and nutrient supply via destruction of tumour vasculature, which in turn ultimately leads to beneficial consequences to patients. Although current anti -angiogenic and vascular targeting strategies help patients, more potently in combination with chemo therapy, there is still a need for more tumour endothelial marker discoveries as current treatments have cardiovascular and other side effects. For the first time, the analyses of in-vivo biotinylation of an embryonic system is performed to obtain putative vascular targets. Also for the first time, deep sequencing is applied to freshly isolated tumour and normal endothelial cells from lung, colon and bladder tissues for the identification of pan-vascular-targets. Integration of the proteomic, deep sequencing, public cDNA libraries and microarrays, delivers 5,892 putative vascular targets to the science community. -
Expanding the Genetic Basis of Copy Number Variation in Familial Breast
Masson et al. Hereditary Cancer in Clinical Practice 2014, 12:15 http://www.hccpjournal.com/content/12/1/15 RESEARCH Open Access Expanding the genetic basis of copy number variation in familial breast cancer Amy L Masson1,4, Bente A Talseth-Palmer1,4, Tiffany-Jane Evans1,4, Desma M Grice1,2, Garry N Hannan2 and Rodney J Scott1,3,4* Abstract Introduction: Familial breast cancer (fBC) is generally associated with an early age of diagnosis and a higher frequency of disease among family members. Over the past two decades a number of genes have been identified that are unequivocally associated with breast cancer (BC) risk but there remain a significant proportion of families that cannot be accounted for by these genes. Copy number variants (CNVs) are a form of genetic variation yet to be fully explored for their contribution to fBC. CNVs exert their effects by either being associated with whole or partial gene deletions or duplications and by interrupting epigenetic patterning thereby contributing to disease development. CNV analysis can also be used to identify new genes and loci which may be associated with disease risk. Methods: The Affymetrix Cytogenetic Whole Genome 2.7 M (Cyto2.7 M) arrays were used to detect regions of genomic re-arrangement in a cohort of 129 fBC BRCA1/BRCA2 mutation negative patients with a young age of diagnosis (<50 years) compared to 40 unaffected healthy controls (>55 years of age). Results: CNV analysis revealed the presence of 275 unique rearrangements that were not present in the control population suggestive of their involvement in BC risk. -
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. -
Transcriptome-Wide Profiling of Cerebral Cavernous Malformations
www.nature.com/scientificreports OPEN Transcriptome-wide Profling of Cerebral Cavernous Malformations Patients Reveal Important Long noncoding RNA molecular signatures Santhilal Subhash 2,8, Norman Kalmbach3, Florian Wegner4, Susanne Petri4, Torsten Glomb5, Oliver Dittrich-Breiholz5, Caiquan Huang1, Kiran Kumar Bali6, Wolfram S. Kunz7, Amir Samii1, Helmut Bertalanfy1, Chandrasekhar Kanduri2* & Souvik Kar1,8* Cerebral cavernous malformations (CCMs) are low-fow vascular malformations in the brain associated with recurrent hemorrhage and seizures. The current treatment of CCMs relies solely on surgical intervention. Henceforth, alternative non-invasive therapies are urgently needed to help prevent subsequent hemorrhagic episodes. Long non-coding RNAs (lncRNAs) belong to the class of non-coding RNAs and are known to regulate gene transcription and involved in chromatin remodeling via various mechanism. Despite accumulating evidence demonstrating the role of lncRNAs in cerebrovascular disorders, their identifcation in CCMs pathology remains unknown. The objective of the current study was to identify lncRNAs associated with CCMs pathogenesis using patient cohorts having 10 CCM patients and 4 controls from brain. Executing next generation sequencing, we performed whole transcriptome sequencing (RNA-seq) analysis and identifed 1,967 lncRNAs and 4,928 protein coding genes (PCGs) to be diferentially expressed in CCMs patients. Among these, we selected top 6 diferentially expressed lncRNAs each having signifcant correlative expression with more than 100 diferentially expressed PCGs. The diferential expression status of the top lncRNAs, SMIM25 and LBX2-AS1 in CCMs was further confrmed by qRT-PCR analysis. Additionally, gene set enrichment analysis of correlated PCGs revealed critical pathways related to vascular signaling and important biological processes relevant to CCMs pathophysiology. -
Small Cell Carcinoma of the Ovary, Hypercalcemic Type (SCCOHT) Beyond SMARCA4 Mutations: a Comprehensive Genomic Analysis
cells Article Small Cell Carcinoma of the Ovary, Hypercalcemic Type (SCCOHT) beyond SMARCA4 Mutations: A Comprehensive Genomic Analysis Aurélie Auguste 1,Félix Blanc-Durand 2 , Marc Deloger 3 , Audrey Le Formal 1, Rohan Bareja 4,5, David C. Wilkes 4 , Catherine Richon 6,Béatrice Brunn 2, Olivier Caron 6, Mojgan Devouassoux-Shisheboran 7,Sébastien Gouy 2, Philippe Morice 2, Enrica Bentivegna 2, Andrea Sboner 4,5,8, Olivier Elemento 4,8, Mark A. Rubin 9 , Patricia Pautier 2, Catherine Genestie 10, Joanna Cyrta 4,9,11 and Alexandra Leary 1,2,* 1 Medical Oncologist, Gynecology Unit, Lead Translational Research Team, INSERM U981, Gustave Roussy, 94805 Villejuif, France; [email protected] (A.A.); [email protected] (A.L.F.) 2 Gynecological Unit, Department of Medicine, Gustave Roussy, 94805 Villejuif, France; [email protected] (F.B.-D.); [email protected] (B.B.); [email protected] (S.G.); [email protected] (P.M.); [email protected] (E.B.); [email protected] (P.P.) 3 Bioinformatics Core Facility, Gustave Roussy Cancer Center, UMS CNRS 3655/INSERM 23 AMMICA, 94805 Villejuif, France; [email protected] 4 Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10001, USA; [email protected] (R.B.); [email protected] (D.C.W.); [email protected] (A.S.); [email protected] (O.E.); [email protected] (J.C.) 5 Institute for Computational Biomedicine, Weill Cornell -
Chromatin Immunoprecipitation and DNA Sequencing Identified A
CANCER GENOMICS & PROTEOMICS 15 : 165-174 (2018) doi:10.21873/cgp.20074 Chromatin Immunoprecipitation and DNA Sequencing Identified a LIMS1/ILK Pathway Regulated by LMO1 in Neuroblastoma NORIHISA SAEKI 1* , AKIRA SAITO 2, YUKI SUGAYA 2, MITSUHIRO AMEMIYA 2, HIROE ONO 1, RIE KOMATSUZAKI 3, KAZUYOSHI YANAGIHARA 4 and HIROKI SASAKI 3 1Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan; 2Statistical Genetics Analysis Division, StaGen Co. Ltd., Tokyo, Japan; 3Department of Translational Oncology, National Cancer Center Research Institute, Tokyo, Japan; 4Division of Pathology, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center Hospital East, Chiba, Japan Abstract. Background/Aim: Overall survival for the high- malignancies in patients younger than 15, it is a cause for risk group of neuroblastoma (NB) remains at 40-50%. An approximately 15% of all pediatric cancer deaths (1). NB integrative genomics study revealed that LIM domain only 1 cells develop from a sympathicoadrenal linage of the neural (LMO1) encoding a transcriptional regulator to be an NB- crest and form solid tumors in the adrenal medulla or susceptibility gene with a tumor-promoting activity, that paraspinal regions, which cause variable symptoms by needs to be revealed. Materials and Methods: We conducted compressing and/or invading to adjacent organs depending chromatin immunoprecipitation and DNA sequencing on their location (1-3). NB cells are heterogenous, and analyses and cell proliferation assays on two NB cell lines. patient age at the time of diagnosis is one of the major Results: We identified three genes regulated by LMO1 in the factors that contribute to the determination of their biological cells, LIM and senescent cell antigen-like domains 1 characters; patients older than 18 months are considered to (LIMS1), Ras suppressor protein 1 (RSU1) and relaxin 2 have a poorer prognosis when associated with dissemination (RLN2). -
Seromic Profiling of Ovarian and Pancreatic Cancer
Seromic profiling of ovarian and pancreatic cancer Sacha Gnjatica,1, Erika Rittera, Markus W. Büchlerb, Nathalia A. Gieseb, Benedikt Brorsc, Claudia Freid, Anne Murraya, Niels Halamad, Inka Zörnigd, Yao-Tseng Chene, Christopher Andrewsf, Gerd Rittera, Lloyd J. Olda,1, Kunle Odunsig,2, and Dirk Jägerd,2 aLudwig Institute for Cancer Research Ltd, Memorial-Sloan Kettering Cancer Center, New York, NY 10065; bDepartment of General Surgery, cDepartment of Theoretical Bioinformatics, and dMedizinische Onkologie, Nationales Centrum für Tumorerkrankungen, University Hospital Heidelberg, Heidelberg D-69120, Germany; eDepartment of Pathology, Weill Medical College of Cornell University, New York, NY 10065; and fDepartment of Biostatistics and gDepartment of Gynecologic Oncology, Roswell Park Cancer Institute, Buffalo, NY 14263 Contributed by Lloyd J. Old, December 10, 2009 (sent for review August 20, 2009) Autoantibodies, a hallmark of both autoimmunity and cancer, analyzing a series of lung cancer and healthy control sera on a represent an easily accessible surrogate for measuring adaptive small array (329 proteins) for antigen reactivity using this anti- immune responses to cancer. Sera can now be assayed for re- body profiling method, referred to here as “seromics,” we were activity against thousands of proteins using microarrays, but there able to detect known antigens with sensitivity and specificity is no agreed-upon standard to analyze results. We developed a set comparable to ELISA, as well as new antigens that are now of tailored quality control and normalization procedures based on under further investigation. Contrary to gene microarrays where ELISA validation to allow patient comparisons and determination changes in the pattern of gene expression are detected in clus- of individual cutoffs for specificity and sensitivity. -
(12) United States Patent (10) Patent No.: US 7,662,561 B2 Godfrey Et Al
USOO7662561 B2 (12) United States Patent (10) Patent No.: US 7,662,561 B2 Godfrey et al. (45) Date of Patent: Feb. 16, 2010 (54) IDENTIFICATION OF MARKERS IN 6,440,725 B1 8/2002 Pourahmadi et al. ESOPHAGEAL CANCER, COLON CANCER, 7,101,663 B2 9/2006 Godfrey et al. HEAD AND NECK CANCER, AND 2001/005.1344 A1* 12/2001 Shalon et al. .................. 435/6 MELANOMA 2006/0068418 A1* 3/2006 Godfrey et al. ................ 435/6 (75) Inventors: Tony E. Godfrey, Bronxville, NY (US); FOREIGN PATENT DOCUMENTS Liqiang Xi, Plainsboro, NJ (US); Siva EP 105O587 11, 2000 Raja, Jamaica Plain, MA (US); Steven WO WO95/11687 5, 1995 J. Hughes, Blawnox, PA (US); William WO WO98,0897O 3, 1998 E. Gooding, Pittsburgh, PA (US) WO WO99, 13104 3, 1999 WO WOOOf 44774 8, 2000 (73) Assignee: University of Pittsburgh-Of the WO WOOOf 72970 12/2000 commonwealth System of Higher WO WOOOf73412 12/2000 WO WOOOf73413 12/2000 Education, Pittsburgh, PA (US) WO WOO1/O1129 1, 2001 WO WOO1? 45845 6, 2001 (*) Notice: Subject to any disclaimer, the term of this WO WO O1, 57253 8, 2001 patent is extended or adjusted under 35 WO WOO1 (84.463 11, 2001 U.S.C. 154(b) by 159 days. WO WO O2, 18902 3, 2002 WO WO O2/O52030 T 2002 (21) Appl. No.: 11/178,134 WO WO O2/O70751 9, 2002 WO WOO3/O55973 T 2003 (22) Filed: Jul. 8, 2005 WO WOO3,O72253 9, 2003 WO WOO3,O77O55 9, 2003 (65) Prior Publication Data WO WO 2004/048931 6, 2004 US 2006/OO1929.0 A1 Jan. -
(12) Patent Application Publication (10) Pub. No.: US 2016/0280759 A1 MAHR Et Al
US 20160280759A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2016/0280759 A1 MAHR et al. (43) Pub. Date: Sep. 29, 2016 (54) NOVEL PEPTIDES AND COMBINATION OF Publication Classification PEPTDES FOR USE IN IMMUNOTHERAPY AGAINST VARIOUS TUMIORS (51) Int. Cl. C07K I4/74 (2006.01) (71) Applicant: immatics biotechnologies GmbH, C07K 6/28 (2006.01) Tuebingen (DE) C07K 14/725 (2006.01) CI2O I/68 (2006.01) (72) Inventors: Andrea MAHR, Tuebingen (DE); Toni A6139/00 (2006.01) WEINSCHENK, Aichwald (DE); (52) U.S. Cl. Oliver SCHOOR, Tuebingen (DE): CPC ....... C07K 14/70539 (2013.01); C12O 1/6886 Jens FRITSCHE, Dusslingen (DE): (2013.01); A61K 39/00II (2013.01); C07K Harpreet SINGH, Muenchen (DE): 14/7051 (2013.01); C07K 16/2833 (2013.01); Lea STEVERMANN, Tuebingen (DE) CI2O 2600/106 (2013.01); C12O 2600/158 (2013.01); A61K 2039/5158 (2013.01); C07K 2317/34 (2013.01) Assignee: immatics biotechnologies GmbH (73) (57) ABSTRACT The present invention relates to peptides, proteins, nucleic (21) Appl. No.: 15/083,075 acids and cells for use in immunotherapeutic methods. In particular, the present invention relates to the immuno (22) Filed: Mar. 28, 2016 therapy of cancer. The present invention furthermore relates to tumor-associated T-cell peptide epitopes, alone or in combination with other tumor-associated peptides that can Related U.S. Application Data for example serve as active pharmaceutical ingredients of (60) Provisional application No. 62/139,189, filed on Mar. vaccine compositions that stimulate anti-tumor immune 27, 2015. responses, or to stimulate T cells ex vivo and transfer into patients. -
Frequent MAGE Mutations in Human Melanoma
Frequent MAGE Mutations in Human Melanoma Otavia L. Caballero1*.¤, Qi Zhao2., Donata Rimoldi3, Brian J. Stevenson3, Suzanne Svobodova´ 4, Sylvie Devalle1, Ute F. Ro¨ hrig3, Anna Pagotto5, Olivier Michielin3, Daniel Speiser3, Jedd D. Wolchok1,6, Cailian Liu6, Tanja Pejovic7, Kunle Odunsi8, Francis Brasseur9, Benoit J. Van den Eynde9, Lloyd J. Old1, Xin Lu5, Jonathan Cebon4, Robert L. Strausberg10, Andrew J. Simpson10 1 Ludwig Institute for Cancer Research Ltd, New York Branch at Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America, 2 J. Craig Venter Institute, Rockville, Maryland, United States of America, 3 Ludwig Institute for Cancer Research Ltd, Lausanne Branch, Lausanne, Switzerland, 4 Ludwig Institute for Cancer Research Ltd, Melbourne Centre for Clinical Sciences, Austin Health, Heidelberg, Victoria, Australia, 5 Nuffield Department of Clinical Medicine, University of Oxford, Ludwig Institute for Cancer Research Ltd, Oxford Branch, Headington, Oxford, United Kingdom, 6 Department of Medicine and Ludwig Center for Cancer Immunotherapy, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America, 7 Division of Gynecologic Oncology and the Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, United States of America, 8 Department of Gynecological Oncology and Center for Immunotherapy, Roswell Park Cancer Institute, Buffalo, New York, United States of America, 9 Ludwig Institute for Cancer Research Ltd, Brussels Branch, Universite´ catholique de Louvain, Brussels, Belgium, 10 Ludwig Institute for Cancer Research Ltd, New York, New York, United States of America Abstract Background: Cancer/testis (CT) genes are expressed only in the germ line and certain tumors and are most frequently located on the X-chromosome (the CT-X genes).