Loss of the Mir-21 Allele Elevates the Expression of Its Target Genes and Reduces Tumorigenesis
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Sprouty2 Deficiency in Mice Leads to the Development of Achalasia Benjamin Lee Staal Grand Valley State University
Grand Valley State University ScholarWorks@GVSU Masters Theses Graduate Research and Creative Practice 12-2011 Sprouty2 Deficiency in Mice Leads to the Development of Achalasia Benjamin Lee Staal Grand Valley State University Follow this and additional works at: http://scholarworks.gvsu.edu/theses Recommended Citation Staal, Benjamin Lee, "Sprouty2 Deficiency in Mice Leads to the Development of Achalasia" (2011). Masters Theses. 11. http://scholarworks.gvsu.edu/theses/11 This Thesis is brought to you for free and open access by the Graduate Research and Creative Practice at ScholarWorks@GVSU. It has been accepted for inclusion in Masters Theses by an authorized administrator of ScholarWorks@GVSU. For more information, please contact [email protected]. SPROUTY2 DEFICIENCY IN MICE LEADS TO THE DEVELOPMENT OF ACHALASIA Benjamin Lee Staal A Thesis Submitted to the Graduate Faculty of GRAND VALLEY STATE UNIVERSITY In Partial Fulfillment of the Requirements For the Degree of Master of Science Cell and Molecular Biology December 2011 ACKNOWLEDGEMENTS First, I thank God for the privilege of studying His handiwork. I also wish to thank the members of my Graduate Committee for their support and guidance throughout this project. Finally, I thank my family, friends, and colleagues for their continual motivation. iii ABSTRACT SPROUTY2 DEFICIENCY IN MICE LEADS TO THE DEVELOPMENT OF ACHALASIA Sprouty 2 (Spry2), one of the four mammalian Spry family members, is a negative feedback regulator of many receptor tyrosine kinases (RTKs) signaling including Met. It fine-tunes RTKs signaling through multiple levels of regulations starting from RTK itself to several downstream molecules that are crucial for signal transduction. -
Sprouty2 Drives Drug Resistance and Proliferation in Glioblastoma Alice M
Published OnlineFirst May 1, 2015; DOI: 10.1158/1541-7786.MCR-14-0183-T Oncogenes and Tumor Suppressors Molecular Cancer Research Sprouty2 Drives Drug Resistance and Proliferation in Glioblastoma Alice M. Walsh1, Gurpreet S. Kapoor2, Janine M. Buonato3, Lijoy K. Mathew4,5,Yingtao Bi6, Ramana V. Davuluri6, Maria Martinez-Lage7, M. Celeste Simon4,5, Donald M. O'Rourke2,7, and Matthew J. Lazzara3,1 Abstract Glioblastoma multiforme (GBM) is notoriously resistant to demonstrated that SPRY2 protein is definitively expressed in therapy, and the development of a durable cure will require the GBM tissue, that SPRY2 expression is elevated in GBM tumors identification of broadly relevant regulators of GBM cell tumor- expressing EGFR variant III (EGFRvIII), and that elevated igenicity and survival. Here, we identify Sprouty2 (SPRY2), a SPRY2 mRNA expression portends reduced GBM patient sur- known regulator of receptor tyrosine kinases (RTK), as one such vival. Overall, these results identify SPRY2 and the pathways regulator. SPRY2 knockdown reduced proliferation and anchor- it regulates as novel candidate biomarkers and therapeutic age-independent growth in GBM cells and slowed xenograft targets in GBM. tumor growth in mice. SPRY2 knockdown also promoted cell death in response to coinhibition of the epidermal growth factor Implications: SPRY2, counter to its roles in other cancer settings, receptor (EGFR) and the c-MET receptor in GBM cells, an effect promotes glioma cell and tumor growth and cellular resistance to that involved regulation of the ability of the p38 mitogen-acti- targeted inhibitors of oncogenic RTKs, thus making SPRY2 and vated protein kinase (MAPK) to drive cell death in response to the cell signaling processes it regulates potential novel therapeutic inhibitors. -
Spry2 Regulates Signalling Dynamics and Terminal Bud Branching Behaviour During Lung Development
Genet. Res., Camb. (2015), vol. 97, e5. © Cambridge University Press 2015 1 doi:10.1017/S0016672315000026 Spry2 regulates signalling dynamics and terminal bud branching behaviour during lung development 1,2 2 YINGYING ZHAO AND TIMOTHY P. O’BRIEN * 1Shenzhen University Diabetes Center, AstraZeneca-Shenzhen University Joint Institute of Nephrology, Department of Physiology, Shenzhen University Health Science Center, Shenzhen 518060, China 2Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA (Received 7 November 2014; revised 12 January 2015; accepted 3 February 2015) Summary Development of mammalian lung involves reiterative outgrowth and branching of an epithelial tube into the surrounding mesenchymal bed. Each coordinated growth and branching cycle is driven by reciprocal signal- ling between epithelial and adjacent mesenchymal cells. This signalling network includes FGF, SHH, BMP4 and other pathways. We have characterized lung defects in 36Pub mice carrying a deletion that removes an antagonist of FGF signalling, Spry2. Spry2 deficient mice show an enlarged cystic structure located in the ter- minus of each lobes. Our study shows that Spry2 deficient lungs have reduced lung branching and the cystic structure forms in the early lung development stage. Furthermore, mice carrying a targeted disruption of Spry2 fail to complement the lung phenotype characterized in 36Pub mice. A Spry2-BAC transgene rescues the defect. Interestingly, cystic structure growth is accompanied by the reduced and spatially disorganized ex- pression of Fgf10 and elevated expression of Shh and Bmp4. Altered signalling balance due to the loss of Spry2 causes a delayed branch cycle and cystic growth. Our data underscores the importance of restricting cellular responsiveness to signalling and highlights the interplay between morphogenesis events and spatial localization of gene expression. -
Non-Coding Rnas As Cancer Hallmarks in Chronic Lymphocytic Leukemia
International Journal of Molecular Sciences Review Non-Coding RNAs as Cancer Hallmarks in Chronic Lymphocytic Leukemia Linda Fabris 1, Jaroslav Juracek 2 and George Calin 1,* 1 Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; [email protected] 2 Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; [email protected] * Correspondence: [email protected] Received: 24 July 2020; Accepted: 10 September 2020; Published: 14 September 2020 Abstract: The discovery of non-coding RNAs (ncRNAs) and their role in tumor onset and progression has revolutionized the way scientists and clinicians study cancers. This discovery opened new layers of complexity in understanding the fine-tuned regulation of cellular processes leading to cancer. NcRNAs represent a heterogeneous group of transcripts, ranging from a few base pairs to several kilobases, that are able to regulate gene networks and intracellular pathways by interacting with DNA, transcripts or proteins. Deregulation of ncRNAs impinge on several cellular responses and can play a major role in each single hallmark of cancer. This review will focus on the most important short and long non-coding RNAs in chronic lymphocytic leukemia (CLL), highlighting their implications as potential biomarkers and therapeutic targets as they relate to the well-established hallmarks of cancer. The key molecular events in the onset of CLL will be contextualized, taking into account the role of the “dark matter” of the genome. Keywords: chronic lymphocytic leukemia; lncRNA; miRNA; hallmarks 1. Introduction: Current Status of Chronic Lymphocytic Leukemia Research Chronic lymphocytic leukemia (CLL) is the most common leukemia in adults in the Western world, representing more than 30% of all leukemia cases [1]. -
Open Dogan Phdthesis Final.Pdf
The Pennsylvania State University The Graduate School Eberly College of Science ELUCIDATING BIOLOGICAL FUNCTION OF GENOMIC DNA WITH ROBUST SIGNALS OF BIOCHEMICAL ACTIVITY: INTEGRATIVE GENOME-WIDE STUDIES OF ENHANCERS A Dissertation in Biochemistry, Microbiology and Molecular Biology by Nergiz Dogan © 2014 Nergiz Dogan Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy August 2014 ii The dissertation of Nergiz Dogan was reviewed and approved* by the following: Ross C. Hardison T. Ming Chu Professor of Biochemistry and Molecular Biology Dissertation Advisor Chair of Committee David S. Gilmour Professor of Molecular and Cell Biology Anton Nekrutenko Professor of Biochemistry and Molecular Biology Robert F. Paulson Professor of Veterinary and Biomedical Sciences Philip Reno Assistant Professor of Antropology Scott B. Selleck Professor and Head of the Department of Biochemistry and Molecular Biology *Signatures are on file in the Graduate School iii ABSTRACT Genome-wide measurements of epigenetic features such as histone modifications, occupancy by transcription factors and coactivators provide the opportunity to understand more globally how genes are regulated. While much effort is being put into integrating the marks from various combinations of features, the contribution of each feature to accuracy of enhancer prediction is not known. We began with predictions of 4,915 candidate erythroid enhancers based on genomic occupancy by TAL1, a key hematopoietic transcription factor that is strongly associated with gene induction in erythroid cells. Seventy of these DNA segments occupied by TAL1 (TAL1 OSs) were tested by transient transfections of cultured hematopoietic cells, and 56% of these were active as enhancers. Sixty-six TAL1 OSs were evaluated in transgenic mouse embryos, and 65% of these were active enhancers in various tissues. -
The Malignant Phenotype in Breast Cancer Is Driven by Eif4a1-Mediated Changes in the Translational Landscape
Citation: Cell Death and Disease (2015) 6, e1603; doi:10.1038/cddis.2014.542 OPEN & 2015 Macmillan Publishers Limited All rights reserved 2041-4889/15 www.nature.com/cddis The malignant phenotype in breast cancer is driven by eIF4A1-mediated changes in the translational landscape A Modelska1, E Turro1,2, R Russell1, J Beaton1, T Sbarrato3, K Spriggs4, J Miller1, S Gräf1,2,5, E Provenzano6,7, F Blows8, P Pharoah6,8, C Caldas1,6 and J Le Quesne*,1,3 Human mRNA DeXD/H-box helicases are ubiquitous molecular motors that are required for the majority of cellular processes that involve RNA metabolism. One of the most abundant is eIF4A, which is required during the initiation phase of protein synthesis to unwind regions of highly structured mRNA that would otherwise impede the scanning ribosome. Dysregulation of protein synthesis is associated with tumorigenesis, but little is known about the detailed relationships between RNA helicase function and the malignant phenotype in solid malignancies. Therefore, immunohistochemical analysis was performed on over 3000 breast tumors to investigate the relationship among expression of eIF4A1, the helicase-modulating proteins eIF4B, eIF4E and PDCD4, and clinical outcome. We found eIF4A1, eIF4B and eIF4E to be independent predictors of poor outcome in ER-negative disease, while in contrast, the eIF4A1 inhibitor PDCD4 was related to improved outcome in ER-positive breast cancer. Consistent with these data, modulation of eIF4A1, eIF4B and PCDC4 expression in cultured MCF7 cells all restricted breast cancer cell growth and cycling. The eIF4A1-dependent translatome of MCF7 cells was defined by polysome profiling, and was shown to be highly enriched for several classes of oncogenic genes, including G-protein constituents, cyclins and protein kinases, and for mRNAs with G/C-rich 5′UTRs with potential to form G-quadruplexes and with 3′UTRs containing microRNA target sites. -
Gene Section Review
Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Gene Section Review MIRN21 (microRNA 21) Sadan Duygu Selcuklu, Mustafa Cengiz Yakicier, Ayse Elif Erson Biology Department, Room: 141, Middle East Technical University, Ankara 06531, Turkey Published in Atlas Database: March 2007 Online updated version: http://AtlasGeneticsOncology.org/Genes/MIRN21ID44019ch17q23.html DOI: 10.4267/2042/38450 This work is licensed under a Creative Commons Attribution-Non-commercial-No Derivative Works 2.0 France Licence. © 2007 Atlas of Genetics and Cytogenetics in Oncology and Haematology sequences of MIRN21 showed enrichment for Pol II Identity but not Pol III. Hugo: MIRN21 MIRN21 gene was shown to harbor a 5' promoter Other names: hsa-mir-21; miR-21 element. 1008 bp DNA fragment for MIRN21 gene Location: 17q23.1 was cloned (-959 to +49 relative to T1 transcription Location base pair: MIRN21 is located on chr17: site, see Figure 1; A). Analysis of the sequence showed 55273409-55273480 (+). a candidate 'CCAAT' box transcription control element Local order: Based on Mapviewer, genes flanking located approximately about 200 nt upstream of the T1 MIRN21 oriented from centromere to telomere on site. T1 transcription site was found to be located in a 17q23 are: sequence similar to 'TATA' box - TMEM49, transmembrane protein 49, 17q23.1. (ATAAACCAAGGCTCTTACCATAGCTG). To test - MIRN21, microRNA 21, 17q23.1. the activity of the element, about 1kb DNA fragment - TUBD1, tubulin, delta 1, 17q23.1. was inserted into the 5' end of firefly luciferase - LOC729565, similar to NADH dehydrogenase indicator gene and transfected into 293T cells. The (ubiquinone) 1 beta subcomplex, 8, 19 kDa, 17q23.1. -
Distinct Roles of Different Fragments of PDCD4 in Regulating the Metastatic Behavior of B16 Melanoma Cells
INTERNATIONAL JOURNAL OF ONCOLOGY 42: 1725-1733, 2013 Distinct roles of different fragments of PDCD4 in regulating the metastatic behavior of B16 melanoma cells DI WANG, SHU GUO, SI-YUAN HAN, NAN XU, JIA-YAN GUO and QING SUN Department of Plastic Surgery, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China Received December 12, 2012; Accepted January 29, 2013 DOI: 10.3892/ijo.2013.1841 Abstract. Melanoma is an aggressive cutaneous malignancy. In mice (7,8). As shown in Fig. 1, full length human PDCD4 this study, we demonstrated that the levels of the programmed contains an N-terminal putative RNA-binding domain cell death 4 (PDCD4) protein and mRNA were lower in tumor (residues 1-140) and two tandem MA3 domains, designated tissues compared with normal tissues. In order to further as nMA3 (residues 164-275) and cMA3 (residues 327-440) investigate the effects of PDCD4 and its fragments in B16 (9). The two MA3 domains have very similar structure and melanoma cells, we established B16 clones with expression of eIF4A-binding surfaces (10). The molecular basis for PDCD4- different PDCD4 fragments. Intact PDCD4, PDCD4∆164-469 mediated suppression has been linked to its high affinity and PDCD4∆327-440 expression, respectively, decreased MA-3 domains (11,12). NMR binding analysis has shown proliferation and migration and increased apoptosis in B16 that both MA3 domains of PDCD4 interacted with eIF4A cells in vitro. We found that intact PDCD4, PDCD4∆164-469 and prevented translation (10,11). However, another study has or PDCD4∆327-440 can inhibit the activity of MMP-2 and the demonstrated that the cMA3 domain alone is sufficient for expression of CXCR4. -
Micrornas Mediated Regulation of the Ribosomal Proteins and Its Consequences on the Global Translation of Proteins
cells Review microRNAs Mediated Regulation of the Ribosomal Proteins and Its Consequences on the Global Translation of Proteins Abu Musa Md Talimur Reza 1,2 and Yu-Guo Yuan 1,3,* 1 Jiangsu Co-Innovation Center of Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; [email protected] 2 Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawi´nskiego5a, 02-106 Warsaw, Poland 3 Jiangsu Key Laboratory of Zoonosis/Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China * Correspondence: [email protected]; Tel.: +86-514-8797-9228 Abstract: Ribosomal proteins (RPs) are mostly derived from the energy-consuming enzyme families such as ATP-dependent RNA helicases, AAA-ATPases, GTPases and kinases, and are important structural components of the ribosome, which is a supramolecular ribonucleoprotein complex, composed of Ribosomal RNA (rRNA) and RPs, coordinates the translation and synthesis of proteins with the help of transfer RNA (tRNA) and other factors. Not all RPs are indispensable; in other words, the ribosome could be functional and could continue the translation of proteins instead of lacking in some of the RPs. However, the lack of many RPs could result in severe defects in the biogenesis of ribosomes, which could directly influence the overall translation processes and global expression of the proteins leading to the emergence of different diseases including cancer. While microRNAs (miRNAs) are small non-coding RNAs and one of the potent regulators of the post-transcriptional 0 gene expression, miRNAs regulate gene expression by targeting the 3 untranslated region and/or coding region of the messenger RNAs (mRNAs), and by interacting with the 50 untranslated region, Citation: Reza, A.M.M.T.; Yuan, Y.-G. -
Fusion Transcripts and Transcribed Retrotransposed Loci Discovered Through Comprehensive Transcriptome Analysis Using Paired-End Ditags (Pets)
Downloaded from genome.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press Letter Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs) Yijun Ruan,1,6 Hong Sain Ooi,2 Siew Woh Choo,2 Kuo Ping Chiu,2 Xiao Dong Zhao,1 K.G. Srinivasan,1 Fei Yao,1 Chiou Yu Choo,1 Jun Liu,1 Pramila Ariyaratne,2 Wilson G.W. Bin,2 Vladimir A. Kuznetsov,2 Atif Shahab,3 Wing-Kin Sung,2,4 Guillaume Bourque,2 Nallasivam Palanisamy,5 and Chia-Lin Wei1,6 1Genome Technology and Biology Group, Genome Institute of Singapore, Singapore 138672, Singapore; 2Information and Mathematical Science Group, Genome Institute of Singapore, Singapore 138672, Singapore; 3Bioinformatics Institute, Singapore 138671, Singapore; 4School of Computing, National University of Singapore, Singapore 117543, Singapore; 5Cancer Biology Group, Genome Institute of Singapore, Singapore 138672, Singapore Identification of unconventional functional features such as fusion transcripts is a challenging task in the effort to annotate all functional DNA elements in the human genome. Paired-End diTag (PET) analysis possesses a unique capability to accurately and efficiently characterize the two ends of DNA fragments, which may have either normal or unusual compositions. This unique nature of PET analysis makes it an ideal tool for uncovering unconventional features residing in the human genome. Using the PET approach for comprehensive transcriptome analysis, we were able to identify fusion transcripts derived from genome rearrangements and actively expressed retrotransposed pseudogenes, which would be difficult to capture by other means. Here, we demonstrate this unique capability through the analysis of 865,000 individual transcripts in two types of cancer cells. -
Oncomir Mir-125B Regulates Hematopoiesis by Targeting the Gene Lin28a
Oncomir miR-125b regulates hematopoiesis by targeting the gene Lin28A Aadel A. Chaudhuria,1, Alex Yick-Lun Soa,1, Arnav Mehtaa, Aarathi Minisandrama, Nikita Sinhaa, Vanessa D. Jonssonb, Dinesh S. Raoc, Ryan M. O’Connelld, and David Baltimorea,2 Departments of aBiology and bComputing and Mathematical Sciences, California Institute of Technology, Pasadena, CA 91125; cDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095; and dDepartment of Pathology, University of Utah, Salt Lake City, UT 84112 Contributed by David Baltimore, January 23, 2012 (sent for review October 29, 2011) MicroRNA-125b (miR-125b) is up-regulated in patients with leukemia. regulation of miR-125b has profound effects on normal hema- Overexpression of miR-125b alone in mice causes a very aggressive, topoiesis, and Lin28A overexpression mimics those effects. transplantable myeloid leukemia. Before leukemia, these mice do not display elevation of white blood cells in the spleen or bone marrow; Results rather, the hematopoietic compartment shows lineage-skewing, with miR-125b Ectopic Expression Favors Myeloid Differentiation and myeloid cell numbers dramatically increased and B-cell numbers Causes a Highly Invasive Myeloid Leukemia. Previously, we showed severely diminished. miR-125b exerts this effect by up-regulating the that overexpression of miR-125b in bone marrow-transplanted number of common myeloid progenitors while inhibiting develop- recipient mice causes a myeloid leukemia 4–6 mo after bone ment of pre-B cells. We applied a miR-125b sponge loss of function marrow reconstitution (5). Here, we found that the neoplastic system in vivo to show that miR-125b physiologically regulates myeloid cells infiltrate nonhematopoietic organs, including the hematopoietic development. -
Sprouty Proteins, Masterminds of Receptor Tyrosine Kinase Signaling
CORE Metadata, citation and similar papers at core.ac.uk Provided by RERO DOC Digital Library Angiogenesis (2008) 11:53–62 DOI 10.1007/s10456-008-9089-1 ORIGINAL PAPER Sprouty proteins, masterminds of receptor tyrosine kinase signaling Miguel A. Cabrita Æ Gerhard Christofori Received: 14 December 2007 / Accepted: 7 January 2008 / Published online: 25 January 2008 Ó Springer Science+Business Media B.V. 2008 Abstract Angiogenesis relies on endothelial cells prop- Abbreviations erly processing signals from growth factors provided in Ang Angiopoietin both an autocrine and a paracrine manner. These mitogens c-Cbl Cellular homologue of Casitas B-lineage bind to their cognate receptor tyrosine kinases (RTKs) on lymphoma proto-oncogene product the cell surface, thereby activating a myriad of complex EGF Epidermal growth factor intracellular signaling pathways whose outputs include cell EGFR EGF receptor growth, migration, and morphogenesis. Understanding how eNOS Endothelial nitric oxide synthase these cascades are precisely controlled will provide insight ERK Extracellular signal-regulated kinase into physiological and pathological angiogenesis. The FGF Fibroblast growth factor Sprouty (Spry) family of proteins is a highly conserved FGFR FGF receptor group of negative feedback loop modulators of growth GDNF Glial-derived neurotrophic factor factor-mediated mitogen-activated protein kinase (MAPK) Grb2 Growth factor receptor-bound protein 2 activation originally described in Drosophila. There are HMVEC Human microvascular endothelial cell four mammalian orthologs (Spry1-4) whose modulation of Hrs Hepatocyte growth factor-regulated tyrosine RTK-induced signaling pathways is growth factor – and kinase substrate cell context – dependant. Endothelial cells are a group of HUVEC Human umbilical vein endothelial cell highly differentiated cell types necessary for defining the MAPK Mitogen-activated protein kinase mammalian vasculature.