Mex3c Regulates Insulin-Like Growth Factor 1 (IGF1) Expression and Promotes Postnatal Growth
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A Novel Approach to Identify Driver Genes Involved in Androgen-Independent Prostate Cancer
Schinke et al. Molecular Cancer 2014, 13:120 http://www.molecular-cancer.com/content/13/1/120 RESEARCH Open Access A novel approach to identify driver genes involved in androgen-independent prostate cancer Ellyn N Schinke1, Victor Bii1, Arun Nalla1, Dustin T Rae1, Laura Tedrick1, Gary G Meadows1 and Grant D Trobridge1,2* Abstract Background: Insertional mutagenesis screens have been used with great success to identify oncogenes and tumor suppressor genes. Typically, these screens use gammaretroviruses (γRV) or transposons as insertional mutagens. However, insertional mutations from replication-competent γRVs or transposons that occur later during oncogenesis can produce passenger mutations that do not drive cancer progression. Here, we utilized a replication-incompetent lentiviral vector (LV) to perform an insertional mutagenesis screen to identify genes in the progression to androgen-independent prostate cancer (AIPC). Methods: Prostate cancer cells were mutagenized with a LV to enrich for clones with a selective advantage in an androgen-deficient environment provided by a dysregulated gene(s) near the vector integration site. We performed our screen using an in vitro AIPC model and also an in vivo xenotransplant model for AIPC. Our approach identified proviral integration sites utilizing a shuttle vector that allows for rapid rescue of plasmids in E. coli that contain LV long terminal repeat (LTR)-chromosome junctions. This shuttle vector approach does not require PCR amplification and has several advantages over PCR-based techniques. Results: Proviral integrations were enriched near prostate cancer susceptibility loci in cells grown in androgen- deficient medium (p < 0.001), and five candidate genes that influence AIPC were identified; ATPAF1, GCOM1, MEX3D, PTRF, and TRPM4. -
Genetic Basis of Simple and Complex Traits with Relevance to Avian Evolution
Genetic basis of simple and complex traits with relevance to avian evolution Małgorzata Anna Gazda Doctoral Program in Biodiversity, Genetics and Evolution D Faculdade de Ciências da Universidade do Porto 2019 Supervisor Miguel Jorge Pinto Carneiro, Auxiliary Researcher, CIBIO/InBIO, Laboratório Associado, Universidade do Porto Co-supervisor Ricardo Lopes, CIBIO/InBIO Leif Andersson, Uppsala University FCUP Genetic basis of avian traits Nota Previa Na elaboração desta tese, e nos termos do número 2 do Artigo 4º do Regulamento Geral dos Terceiros Ciclos de Estudos da Universidade do Porto e do Artigo 31º do D.L.74/2006, de 24 de Março, com a nova redação introduzida pelo D.L. 230/2009, de 14 de Setembro, foi efetuado o aproveitamento total de um conjunto coerente de trabalhos de investigação já publicados ou submetidos para publicação em revistas internacionais indexadas e com arbitragem científica, os quais integram alguns dos capítulos da presente tese. Tendo em conta que os referidos trabalhos foram realizados com a colaboração de outros autores, o candidato esclarece que, em todos eles, participou ativamente na sua conceção, na obtenção, análise e discussão de resultados, bem como na elaboração da sua forma publicada. Este trabalho foi apoiado pela Fundação para a Ciência e Tecnologia (FCT) através da atribuição de uma bolsa de doutoramento (PD/BD/114042/2015) no âmbito do programa doutoral em Biodiversidade, Genética e Evolução (BIODIV). 2 FCUP Genetic basis of avian traits Acknowledgements Firstly, I would like to thank to my all supervisors Miguel Carneiro, Ricardo Lopes and Leif Andersson, for the demanding task of supervising myself last four years. -
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. -
Westminsterresearch ZFP36 Proteins and Mrna Targets in B Cell
WestminsterResearch http://www.westminster.ac.uk/westminsterresearch ZFP36 proteins and mRNA targets in B cell malignancies Alcaraz, A. This is an electronic version of a PhD thesis awarded by the University of Westminster. © Miss Amor Alcaraz, 2015. The WestminsterResearch online digital archive at the University of Westminster aims to make the research output of the University available to a wider audience. Copyright and Moral Rights remain with the authors and/or copyright owners. Whilst further distribution of specific materials from within this archive is forbidden, you may freely distribute the URL of WestminsterResearch: ((http://westminsterresearch.wmin.ac.uk/). In case of abuse or copyright appearing without permission e-mail [email protected] ZFP36 proteins and mRNA targets in B cell malignancies Maria del Amor Alcaraz-Serrano A Thesis submitted in partial fulfilment of the requirements of the University of Westminster for the degree of Doctor of Philosophy September 2015 Abstract The ZFP36 proteins are a family of post-transcriptional regulator proteins that bind to adenine uridine rich elements (AREs) in 3’ untranslated (3’UTR) regions of mRNAs. The members of the human family, ZFP36L1, ZFP36L2 and ZFP36 are able to degrade mRNAs of important cell regulators that include cytokines, cell signalling proteins and transcriptional factors. This project investigated two proposed targets for the protein family that have important roles in B cell biology, BCL2 and CD38 mRNAs. BCL2 is an anti-apoptotic protein with key roles in cell survival and carcinogenesis; CD38 is a membrane protein differentially expressed in B cells and with a prognostic value in B chronic lymphocytic leukaemia (B-CLL), patients positive for CD38 are considered to have a poor prognosis. -
Revostmm Vol 10-4-2018 Ingles Maquetaciûn 1
108 ORIGINALS / Rev Osteoporos Metab Miner. 2018;10(4):108-18 Roca-Ayats N1, Falcó-Mascaró M1, García-Giralt N2, Cozar M1, Abril JF3, Quesada-Gómez JM4, Prieto-Alhambra D5,6, Nogués X2, Mellibovsky L2, Díez-Pérez A2, Grinberg D1, Balcells S1 1 Departamento de Genética, Microbiología y Estadística - Facultad de Biología - Universidad de Barcelona - Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) - Instituto de Salud Carlos III (ISCIII) - Instituto de Biomedicina de la Universidad de Barcelona (IBUB) - Instituto de Investigación Sant Joan de Déu (IRSJD) - Barcelona (España) 2 Unidad de Investigación en Fisiopatología Ósea y Articular (URFOA); Instituto Hospital del Mar de Investigaciones Médicas (IMIM) - Parque de Salud Mar - Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES); Instituto de Salud Carlos III (ISCIII) - Barcelona (España) 3 Departamento de Genética, Microbiología y Estadística; Facultad de Biología; Universidad de Barcelona - Instituto de Biomedicina de la Universidad de Barcelona (IBUB) - Barcelona (España) 4 Unidad de Metabolismo Mineral; Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC); Hospital Universitario Reina Sofía - Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES); Instituto de Salud Carlos III (ISCIII) - Córdoba (España) 5 Grupo de Investigación en Enfermedades Prevalentes del Aparato Locomotor (GREMPAL) - Instituto de Investigación en Atención Primaria (IDIAP) Jordi Gol - Centro de Investigación -
Oncogenic Potential of the Dual-Function Protein MEX3A
biology Review Oncogenic Potential of the Dual-Function Protein MEX3A Marcell Lederer 1,*, Simon Müller 1, Markus Glaß 1 , Nadine Bley 1, Christian Ihling 2, Andrea Sinz 2 and Stefan Hüttelmaier 1 1 Charles Tanford Protein Center, Faculty of Medicine, Institute of Molecular Medicine, Section for Molecular Cell Biology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle, Germany; [email protected] (S.M.).; [email protected] (M.G.).; [email protected] (N.B.); [email protected] (S.H.) 2 Center for Structural Mass Spectrometry, Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany; [email protected] (C.I.); [email protected] (A.S.) * Correspondence: [email protected] Simple Summary: RNA-binding proteins (RBPs) are involved in the post-transcriptional control of gene expression, modulating the splicing, turnover, subcellular sorting and translation of (m)RNAs. Dysregulation of RBPs, for instance, by deregulated expression in cancer, disturbs key cellular processes such as proliferation, cell cycle progression or migration. Accordingly, RBPs contribute to tumorigenesis. Members of the human MEX3 protein family harbor RNA-binding capacity and E3 ligase activity. Thus, they presumably combine post-transcriptional and post-translational regulatory mechanisms. In this review, we discuss recent studies to emphasize emerging evidence for a pivotal role of the MEX3 protein family, in particular MEX3A, in human cancer. Citation: Lederer, M.; Müller, S.; Glaß, M.; Bley, N.; Ihling, C.; Sinz, A.; Abstract: MEX3A belongs to the MEX3 (Muscle EXcess) protein family consisting of four members Hüttelmaier, S. -
Epigenomic Analysis Reveals DNA Motifs Regulating Histone Modifications in Human and Mouse
Epigenomic analysis reveals DNA motifs regulating histone modifications in human and mouse Vu Ngoa,1, Zhao Chenb,1, Kai Zhanga, John W. Whitakerb, Mengchi Wanga, and Wei Wanga,b,c,2 aGraduate Program of Bioinformatics and Systems Biology, University of California, San Diego, La Jolla, CA 92093-0359; bDepartment of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0359; and cDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0359 Edited by Steven Henikoff, Fred Hutchinson Cancer Research Center, Seattle, WA, and approved January 3, 2019 (received for review August 6, 2018) Histones are modified by enzymes that act in a locus, cell-type, and An analogy is that a transcription factor (TF) recognizes the same developmental stage-specific manner. The recruitment of enzymes DNA motif but its binding sites are cell-type–dependent. However, if to chromatin is regulated at multiple levels, including interaction we identify all motifs enriched in the TF binding sites across a large with sequence-specific DNA-binding factors. However, the DNA- and diverse set of cell types, the most common motif is likely the one binding specificity of the regulatory factors that orchestrate spe- recognized by the TF. Histone modifications are more complicated cific histone modifications has not been broadly mapped. We have than a single TF binding and one histone mark can be regulated by analyzed 6 histone marks (H3K4me1, H3K4me3, H3K27ac, H3K27me3, K3H9me3, H3K36me3) across 121 human cell types and tissues from multiple factors recognizing different motifs. Therefore, a compar- the NIH Roadmap Epigenomics Project as well as 8 histone marks ative analysis across diverse cell types/tissues is critical. -
Alterations of the Pro-Survival Bcl-2 Protein Interactome in Breast Cancer
bioRxiv preprint doi: https://doi.org/10.1101/695379; this version posted July 12, 2019. 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. 1 Alterations of the pro-survival Bcl-2 protein interactome in 2 breast cancer at the transcriptional, mutational and 3 structural level 4 5 Simon Mathis Kønig1, Vendela Rissler1, Thilde Terkelsen1, Matteo Lambrughi1, Elena 6 Papaleo1,2 * 7 1Computational Biology Laboratory, Danish Cancer Society Research Center, 8 Strandboulevarden 49, 2100, Copenhagen 9 10 2Translational Disease Systems Biology, Faculty of Health and Medical Sciences, Novo 11 Nordisk Foundation Center for Protein Research University of Copenhagen, Copenhagen, 12 Denmark 13 14 Abstract 15 16 Apoptosis is an essential defensive mechanism against tumorigenesis. Proteins of the B-cell 17 lymphoma-2 (Bcl-2) family regulates programmed cell death by the mitochondrial apoptosis 18 pathway. In response to intracellular stresses, the apoptotic balance is governed by interactions 19 of three distinct subgroups of proteins; the activator/sensitizer BH3 (Bcl-2 homology 3)-only 20 proteins, the pro-survival, and the pro-apoptotic executioner proteins. Changes in expression 21 levels, stability, and functional impairment of pro-survival proteins can lead to an imbalance 22 in tissue homeostasis. Their overexpression or hyperactivation can result in oncogenic effects. 23 Pro-survival Bcl-2 family members carry out their function by binding the BH3 short linear 24 motif of pro-apoptotic proteins in a modular way, creating a complex network of protein- 25 protein interactions. -
Small Noncoding RNA Signatures for Determining the Developmental Potential of an Embryo at the Morula Stage
International Journal of Molecular Sciences Article Small Noncoding RNA Signatures for Determining the Developmental Potential of an Embryo at the Morula Stage Angelika Timofeeva * , Yulia Drapkina, Ivan Fedorov, Vitaliy Chagovets, Nataliya Makarova, Maria Shamina, Elena Kalinina and Gennady Sukhikh Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, Ministry of Health of Russia, Ac. Oparina 4, 117997 Moscow, Russia; [email protected] (Y.D.); [email protected] (I.F.); [email protected] (V.C.); [email protected] (N.M.); [email protected] (M.S.); [email protected] (E.K.); [email protected] (G.S.) * Correspondence: [email protected]; Tel.: +7-495-531-4444 Received: 7 November 2020; Accepted: 8 December 2020; Published: 10 December 2020 Abstract: As part of the optimization of assisted reproductive technology programs, the aim of the study was to identify key small noncoding RNA (sncRNA) molecules that participate in maternal-to-zygotic transition and determine development potential and competence to form a healthy fetus. Small RNA deep sequencing followed by quantitative real-time RT-PCR was used to profile sncRNAs in 50 samples of spent culture medium from morula with different development potentials (no potential (degradation/developmental arrest), low potential (poor-quality blastocyst), and high potential (good/excellent quality blastocyst capable of implanting and leading to live birth)) obtained from 27 subfertile couples who underwent in vitro fertilization. We have shown that the quality of embryos at the morula stage is determined by secretion/uptake rates of certain sets of piRNAs and miRNAs, namely hsa_piR_011291, hsa_piR_019122, hsa_piR_001311, hsa_piR_015026, hsa_piR_015462, hsa_piR_016735, hsa_piR_019675, hsa_piR_020381, hsa_piR_020485, hsa_piR_004880, hsa_piR_000807, hsa-let-7b-5p, and hsa-let-7i-5p. -
Comparative Analysis of Chicken Chromosome 28 Provides New Clues to the Evolutionary Fragility of Gene-Rich Vertebrate Regions
Downloaded from genome.cshlp.org on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press Letter Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions Laurie Gordon,1,2,5 Shan Yang,1,5 Mary Tran-Gyamfi,1,2 Dan Baggott,1 Mari Christensen,1,2 Aaron Hamilton,1 Richard Crooijmans,3 Martien Groenen,3 Susan Lucas,2 Ivan Ovcharenko,2,4 and Lisa Stubbs1,6 1Genome Biology Group, Lawrence Livermore National Laboratory, Livermore, California 94550, USA; 2Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA; 3Wageningen University, Wageningen 6709 PG, The Netherlands; 4Computations Group, Lawrence Livermore National Laboratory, Livermore, California 94550, USA The chicken genome draft sequence has provided a valuable resource for studies of an important agricultural and experimental model species and an important data set for comparative analysis. However, some of the most gene-rich segments are missing from chicken genome draft assemblies, limiting the analysis of a substantial number of genes and preventing a closer look at regions that are especially prone to syntenic rearrangements. To facilitate the functional and evolutionary analysis of one especially gene-rich, rearrangement-prone genomic region, we analyzed sequence from BAC clones spanning chicken microchromosome GGA28; as a complement we also analyzed a gene-sparse, stable region from GGA11. In these two regions we documented the conservation and lineage-specific gain and loss of protein-coding genes and precisely mapped the locations of 31 major human-chicken syntenic breakpoints. Altogether, we identified 72 lineage-specific genes, many of which are found at or near syntenic breaks, implicating evolutionary breakpoint regions as major sites of genetic innovation and change. -
(NF1) As a Breast Cancer Driver
INVESTIGATION Comparative Oncogenomics Implicates the Neurofibromin 1 Gene (NF1) as a Breast Cancer Driver Marsha D. Wallace,*,† Adam D. Pfefferle,‡,§,1 Lishuang Shen,*,1 Adrian J. McNairn,* Ethan G. Cerami,** Barbara L. Fallon,* Vera D. Rinaldi,* Teresa L. Southard,*,†† Charles M. Perou,‡,§,‡‡ and John C. Schimenti*,†,§§,2 *Department of Biomedical Sciences, †Department of Molecular Biology and Genetics, ††Section of Anatomic Pathology, and §§Center for Vertebrate Genomics, Cornell University, Ithaca, New York 14853, ‡Department of Pathology and Laboratory Medicine, §Lineberger Comprehensive Cancer Center, and ‡‡Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27514, and **Memorial Sloan-Kettering Cancer Center, New York, New York 10065 ABSTRACT Identifying genomic alterations driving breast cancer is complicated by tumor diversity and genetic heterogeneity. Relevant mouse models are powerful for untangling this problem because such heterogeneity can be controlled. Inbred Chaos3 mice exhibit high levels of genomic instability leading to mammary tumors that have tumor gene expression profiles closely resembling mature human mammary luminal cell signatures. We genomically characterized mammary adenocarcinomas from these mice to identify cancer-causing genomic events that overlap common alterations in human breast cancer. Chaos3 tumors underwent recurrent copy number alterations (CNAs), particularly deletion of the RAS inhibitor Neurofibromin 1 (Nf1) in nearly all cases. These overlap with human CNAs including NF1, which is deleted or mutated in 27.7% of all breast carcinomas. Chaos3 mammary tumor cells exhibit RAS hyperactivation and increased sensitivity to RAS pathway inhibitors. These results indicate that spontaneous NF1 loss can drive breast cancer. This should be informative for treatment of the significant fraction of patients whose tumors bear NF1 mutations. -
Wo2018/232195
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2018/232195 Al 20 December 2018 (20.12.2018) W !P O PCT (51) International Patent Classification: MANIAN, Ayshwarya; 77 Massachusetts Ave., Cam A61K 31/00 (2006.01) C07K 16/28 (2006.01) bridge, MA 02139 (US). C07K 14/705 (2006.01) C12Q 1/68 (2018.01) (72) Inventor: ROZENBLATT-ROSEN, Orit; 415 Main C07K 16/24 (2006.01) G06F 19/00 (2018.01) Street, Cambridge, MA 02142 (US). (21) International Application Number: (74) Agent: NIX, F., Brent et al.; Johnson, Marcou & Isaacs, PCT/US20 18/037662 LLC, P.O. Box 691, Hoschton, GA 30548 (US). (22) International Filing Date: (81) Designated States (unless otherwise indicated, for every 14 June 2018 (14.06.2018) kind of national protection available): AE, AG, AL, AM, (25) Filing Language: English AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, (26) Publication Langi English DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, (30) Priority Data: HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, 62/5 19,788 14 June 2017 (14.06.2017) US KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, [US/US]; (71) Applicants: THE BROAD INSTITUTE, INC. OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, 415 Main Street, Cambridge, MA 02142 (US).