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      Transformation of the intestinal epithelium by the MSI2 RNA binding protein

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          Abstract

          The MSI2 RNA binding protein is a potent oncogene playing key roles in hematopoietic stem cell homeostasis and malignant hematopoiesis. Here we demonstrate that MSI2 is expressed in the intestinal stem cell compartment, that its expression is elevated in colorectal adenocarcinomas, and that MSI2 loss of function abrogates colorectal cancer cell growth. MSI2 gain of function in the intestinal epithelium in a drug inducible mouse model is sufficient to phenocopy many of the morphological and molecular consequences of acute loss of the APC tumor suppressor in the intestinal epithelium in a Wnt-independent manner. Transcriptome-wide RNA-binding analysis indicates that MSI2 acts as a pleiotropic inhibitor of known intestinal tumor suppressors including Lrig1, Bmpr1a, Cdkn1a, and Pten. Finally, we demonstrate that inhibition of the PDK-AKT-mTORC1 axis rescues oncogenic consequences of MSI2 induction. Taken together, our findings identify MSI2 as a central component in an unappreciated oncogenic pathway promoting intestinal transformation.

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          Ago HITS-CLIP decodes miRNA-mRNA interaction maps

          Summary MicroRNAs (miRNAs) play critical roles in the regulation of gene expression. However, since miRNA activity requires base pairing with only 6-8 nucleotides of mRNA, predicting target mRNAs is a major challenge. Recently, high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) has identified functional protein-RNA interaction sites. Here we use HITS-CLIP to covalently crosslink native Argonaute (Ago) protein-RNA complexes in mouse brain. This produced two simultaneous datasets—Ago-miRNA and Ago-mRNA binding sites—that were combined with bioinformatic analysis to identify miRNA-target mRNA interaction sites. We validated genome-wide interaction maps for miR-124, and generated additional maps for the 20 most abundant miRNAs present in P13 mouse brain. Ago HITS-CLIP provides a general platform for exploring the specificity and range of miRNA action in vivo, and identifies precise sequences for targeting clinically relevant miRNA-mRNA interactions.
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            Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles.

            DNA microarrays have been widely applied to cancer transcriptome analysis; however, the majority of such data are not easily accessible or comparable. Furthermore, several important analytic approaches have been applied to microarray analysis; however, their application is often limited. To overcome these limitations, we have developed Oncomine, a bioinformatics initiative aimed at collecting, standardizing, analyzing, and delivering cancer transcriptome data to the biomedical research community. Our analysis has identified the genes, pathways, and networks deregulated across 18,000 cancer gene expression microarrays, spanning the majority of cancer types and subtypes. Here, we provide an update on the initiative, describe the database and analysis modules, and highlight several notable observations. Results from this comprehensive analysis are available at http://www.oncomine.org.
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              The beta-catenin/TCF-4 complex imposes a crypt progenitor phenotype on colorectal cancer cells.

              The transactivation of TCF target genes induced by Wnt pathway mutations constitutes the primary transforming event in colorectal cancer (CRC). We show that disruption of beta-catenin/TCF-4 activity in CRC cells induces a rapid G1 arrest and blocks a genetic program that is physiologically active in the proliferative compartment of colon crypts. Coincidently, an intestinal differentiation program is induced. The TCF-4 target gene c-MYC plays a central role in this switch by direct repression of the p21(CIP1/WAF1) promoter. Following disruption of beta-catenin/TCF-4 activity, the decreased expression of c-MYC releases p21(CIP1/WAF1) transcription, which in turn mediates G1 arrest and differentiation. Thus, the beta-catenin/TCF-4 complex constitutes the master switch that controls proliferation versus differentiation in healthy and malignant intestinal epithelial cells.
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                Author and article information

                Journal
                101528555
                37539
                Nat Commun
                Nat Commun
                Nature communications
                2041-1723
                3 February 2015
                16 March 2015
                2015
                13 November 2015
                : 6
                : 6517
                Affiliations
                [1 ]State Key Laboratories for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
                [2 ]Molecular Pharmacology and Chemistry Program, Experimental Therapeutics Center and Center for Stem Cell Biology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
                [3 ]The Broad Institute of Harvard and MIT, 415 Main St, Cambridge, MA 02142
                [4 ]Center for Molecular Studies in Digestive and Liver Diseases, University of Pennsylvania, Philadelphia, PA 19104
                [5 ]Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104
                [6 ]PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, PA 19104
                [7 ]PENN Molecular Profiling Facility, University of Pennsylvania, Philadelphia, PA 19104
                [8 ]Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, PA 19104
                [9 ]Cell and Molecular Biology Graduate Program, University of Pennsylvania, Philadelphia, PA 19104
                [10 ]Department of Cell and Developmental Biology, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
                [11 ]Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104
                [12 ]Department of Animal Biology, School of Veterinary Medicine University of Pennsylvania, Philadelphia, PA 19104
                Author notes
                [* ]To whom correspondence should be addressed: Zhengquan Yu ( Zyu@ 123456cau.edu.cn ) or Christopher Lengner ( Lengner@ 123456vet.upenn.edu )
                [13]

                These authors contributed equally to this work

                Article
                NIHMS660360
                10.1038/ncomms7517
                4643281
                25774828
                ab717958-ab62-4df8-a427-4e961dd5294a
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