Tumor Suppressor Role of Sfrp‑4 in Hepatocellular Carcinoma Via the Wnt/Β‑Catenin Signaling Pathway
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Chromatin State Signatures Associated with Tissue-Specific Gene Expression and Enhancer Activity in the Embryonic Limb. Justin C
Downloaded from genome.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb. Justin Cotney1, Jing Leng2, Sunghee Oh1+, Laura E. DeMare1, Steven K. Reilly1, Mark B. Gerstein2,3,4 and James P. Noonan1,2,5* 1. Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA 2. Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA. 3. Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA. 4. Department of Computer Science, Yale University, New Haven, CT 06511, USA. 5. Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA + Current address: Division of Human Genetics, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 *Corresponding author Running title: Chromatin states identify developmental enhancers Keywords: chromatin, enhancers, development, limb, ChIP-seq Downloaded from genome.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press Abstract The regulatory elements that direct tissue-specific gene expression in the developing mammalian embryo remain largely unknown. Although chromatin profiling has proven to be a powerful method for mapping regulatory sequences in cultured cells, chromatin states characteristic of active developmental enhancers have not been directly identified in embryonic tissues. Here we use whole transcriptome analysis coupled with genome-wide profiling of H3K27ac and H3K27me3 to map chromatin states and enhancers in mouse embryonic forelimb and hindlimb. We show that gene expression differences between forelimb and hindlimb, and between limb and other embryonic cell types, are correlated with tissue-specific H3K27ac signatures at promoters and distal sites. -
Increased Liver Carcinogenesis and Enrichment of Stem Cell Properties in Livers of Dickkopf 2 (Dkk2) Deleted Mice
www.impactjournals.com/oncotarget/ Oncotarget, Vol. 7, No. 20 Increased liver carcinogenesis and enrichment of stem cell properties in livers of Dickkopf 2 (Dkk2) deleted mice Thorsten Maass1, Jens Marquardt2, Ju-Seog Lee3, Markus Krupp4, Peter Scholz-Kreisel2, Carolin Mogler5, Peter Schirmacher5, Martina Müller1, Heiner Westphal6, Peter R. Galle2, Andreas Teufel1 1Department of Internal Medicine I, University of Regensburg, Regensburg, Germany 2I. Department of Medicine, University Medical Center Mainz, Mainz, Germany 3Cancer Biology Program, MD Anderson Cancer Center, Houston, TX, USA 4Department of Informatics, Johannes Gutenberg University Mainz, Mainz, Germany 5Institute of Pathology, University of Heidelberg, Heidelberg, Germany 6 Laboratory of Mammalian Genes and Development, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA Correspondence to: Andreas Teufel, email: [email protected] Keywords: transcriptomics profiling, prognostic signature, genetic signature, Dkk2, stem cells Received: January 13, 2015 Accepted: February 08, 2015 Published: March 16, 2015 ABSTRACT Dkk2 a antagonist of the Wnt/β-catenin-signaling pathway was shown to be silenced in diverse cancers. More recent data indicate that Dkk family members may also possess functions independent of Wnt-signaling during carcinogenesis. The detailed biological function of Dkks and its relevance for liver cancer is unknown. We analyzed the effects of a genetic deletion of Dkk2 (Dkk2−/−) in a hepatocarcinogenesis model using DEN/Phenobarbital. Untreated Dkk2−/− animals, showed considerable atypia with variation of hepatocyte size and chromatin density. In livers of Dkk2−/− mice nodule formation was seen at 9 months of age with focal loss of trabecular architecture and atypical hepatocytes and after DEN induction Dkk2−/− mice developed significantly more liver tumors compared to controls. -
Aneuploidy: Using Genetic Instability to Preserve a Haploid Genome?
Health Science Campus FINAL APPROVAL OF DISSERTATION Doctor of Philosophy in Biomedical Science (Cancer Biology) Aneuploidy: Using genetic instability to preserve a haploid genome? Submitted by: Ramona Ramdath In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical Science Examination Committee Signature/Date Major Advisor: David Allison, M.D., Ph.D. Academic James Trempe, Ph.D. Advisory Committee: David Giovanucci, Ph.D. Randall Ruch, Ph.D. Ronald Mellgren, Ph.D. Senior Associate Dean College of Graduate Studies Michael S. Bisesi, Ph.D. Date of Defense: April 10, 2009 Aneuploidy: Using genetic instability to preserve a haploid genome? Ramona Ramdath University of Toledo, Health Science Campus 2009 Dedication I dedicate this dissertation to my grandfather who died of lung cancer two years ago, but who always instilled in us the value and importance of education. And to my mom and sister, both of whom have been pillars of support and stimulating conversations. To my sister, Rehanna, especially- I hope this inspires you to achieve all that you want to in life, academically and otherwise. ii Acknowledgements As we go through these academic journeys, there are so many along the way that make an impact not only on our work, but on our lives as well, and I would like to say a heartfelt thank you to all of those people: My Committee members- Dr. James Trempe, Dr. David Giovanucchi, Dr. Ronald Mellgren and Dr. Randall Ruch for their guidance, suggestions, support and confidence in me. My major advisor- Dr. David Allison, for his constructive criticism and positive reinforcement. -
Dysregulation of Spliceosome Gene Expression in Advanced Prostate Cancer by RNA-Binding Protein PSF
Dysregulation of spliceosome gene expression in advanced prostate cancer by RNA-binding protein PSF Ken-ichi Takayamaa, Takashi Suzukib, Tetsuya Fujimurac, Yuta Yamadac, Satoru Takahashid, Yukio Hommac, Yutaka Suzukie, and Satoshi Inouea,f,1 aDepartment of Functional Biogerontology, Tokyo Metropolitan Institute of Gerontology, Tokyo 173-0015, Japan; bDepartment of Pathology and Histotechnology, Tohoku University Graduate School of Medicine, Miyagi 980-8575, Japan; cDepartment of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; dDepartment of Urology, Nihon University School of Medicine, Tokyo 173-0032, Japan; eDepartment of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8652, Japan; and fDivision of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Saitama 350-1241, Japan Edited by Hsing-Jien Kung, National Health Research Institutes, Miaoli, Taiwan, and accepted by Editorial Board Member Peter K. Vogt July 26, 2017 (received for review April 13, 2017) Developing therapeutic approaches are necessary for treating PSF is a ubiquitous nuclear protein essential for neural de- hormone-refractory prostate cancer. Activation of androgen re- velopment by regulating axon viability (12, 13). PSF has a unique ceptor (AR) and its variants’ expression along with the down- structure possessing both DNA- and RNA-binding domains, stream signals are mostly important for disease progression. implicated in transcription and nuclear RNA processing (14–16). However, the mechanism for marked increases of AR signals and However, the transcriptional and posttranscriptional specific its expression is still unclear. Here, we revealed that various spli- targets and the clinical significance of these proteins in prostate ceosome genes are aberrantly induced by RNA-binding protein cancer progression still remain to be elucidated. -
Externalized Glycolytic Enzymes Are Novel, Conserved, and Early Biomarkers of Apoptosis*DS
Supplemental Material can be found at: http://www.jbc.org/content/suppl/2012/01/18/M111.314971.DC1.html THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 287, NO. 13, pp. 10325–10343, March 23, 2012 © 2012 by The American Society for Biochemistry and Molecular Biology, Inc. Published in the U.S.A. Externalized Glycolytic Enzymes Are Novel, Conserved, and Early Biomarkers of Apoptosis*□S Received for publication, October 19, 2011, and in revised form, December 23, 2011 Published, JBC Papers in Press, January 18, 2012, DOI 10.1074/jbc.M111.314971 David S. Ucker‡1, Mohit Raja Jain§¶, Goutham Pattabiraman‡, Karol Palasiewicz‡, Raymond B. Birge¶, and Hong Li§¶2 From the ‡Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, Illinois 60612 and the §Center for Advanced Proteomics Research and ¶Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School Cancer Center, Newark, New Jersey 07214 Background: Apoptotic cell recognition triggers profound immunosuppressive responses; relevant recognition determi- nants are uncharacterized. Results: Surface exposure of glycolytic enzymes is a common early apoptotic event. Conclusion: Externalized glycolytic enzyme molecules are novel apoptotic biomarkers and candidate immunomodulatory/ recognition determinants. Significance: Apoptotic glycolytic enzyme externalization explicates plasminogen binding to mammalian cells and potential Downloaded from mechanisms of immune privilege by commensal bacteria and pathogens. The intriguing cell biology of apoptotic -
Alternative Splicing Is Frequent During Early Embryonic Development in Mouse BMC Genomics 2010, 11:399
Revil et al. BMC Genomics 2010, 11:399 http://www.biomedcentral.com/1471-2164/11/399 RESEARCH ARTICLE Open Access AlternativeResearch article splicing is frequent during early embryonic development in mouse Timothée Revil*1, Daniel Gaffney*1, Christel Dias1,2, Jacek Majewski1,2 and Loydie A Jerome-Majewska†1,3 Abstract Background: Alternative splicing is known to increase the complexity of mammalian transcriptomes since nearly all mammalian genes express multiple pre-mRNA isoforms. However, our knowledge of the extent and function of alternative splicing in early embryonic development is based mainly on a few isolated examples. High throughput technologies now allow us to study genome-wide alternative splicing during mouse development. Results: A genome-wide analysis of alternative isoform expression in embryonic day 8.5, 9.5 and 11.5 mouse embryos and placenta was carried out using a splicing-sensitive exon microarray. We show that alternative splicing and isoform expression is frequent across developmental stages and tissues, and is comparable in frequency to the variation in whole-transcript expression. The genes that are alternatively spliced across our samples are disproportionately involved in important developmental processes. Finally, we find that a number of RNA binding proteins, including putative splicing factors, are differentially expressed and spliced across our samples suggesting that such proteins may be involved in regulating tissue and temporal variation in isoform expression. Using an example of a well characterized splicing factor, Fox2, we demonstrate that changes in Fox2 expression levels can be used to predict changes in inclusion levels of alternative exons that are flanked by Fox2 binding sites. -
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. -
DKK2 Rabbit Pab
Leader in Biomolecular Solutions for Life Science DKK2 Rabbit pAb Catalog No.: A14874 Basic Information Background Catalog No. This gene encodes a protein that is a member of the dickkopf family. The secreted A14874 protein contains two cysteine rich regions and is involved in embryonic development through its interactions with the Wnt signaling pathway. It can act as either an agonist or Observed MW antagonist of Wnt/beta-catenin signaling, depending on the cellular context and the 30kDa presence of the co-factor kremen 2. Activity of this protein is also modulated by binding to the Wnt co-receptor LDL-receptor related protein 6 (LRP6). Calculated MW 28kDa Category Primary antibody Applications WB, IF Cross-Reactivity Human Recommended Dilutions Immunogen Information WB 1:500 - 1:2000 Gene ID Swiss Prot 27123 Q9UBU2 IF 1:50 - 1:200 Immunogen A synthetic peptide corresponding to a sequence within amino acids 100 to the C- terminus of human DKK2 (NP_055236.1). Synonyms DKK2;DKK-2 Contact Product Information www.abclonal.com Source Isotype Purification Rabbit IgG Affinity purification Storage Store at -20℃. Avoid freeze / thaw cycles. Buffer: PBS with 0.02% sodium azide,50% glycerol,pH7.3. Validation Data Western blot analysis of extracts of various cell lines, using DKK2 antibody (A14874) at 1:1000 dilution. Secondary antibody: HRP Goat Anti-Rabbit IgG (H+L) (AS014) at 1:10000 dilution. Lysates/proteins: 25ug per lane. Blocking buffer: 3% nonfat dry milk in TBST. Detection: ECL Basic Kit (RM00020). Exposure time: 10s. Immunofluorescence analysis of human skin cancer using DKK2 Rabbit pAb (A14874) at dilution of 1:400 (40x lens). -
ATP Is Required for Interactions Between UAP56 and Two Conserved Mrna Export Proteins, Aly and CIP29, to Assemble the TREX Complex
ATP is required for interactions between UAP56 and two conserved mRNA export proteins, Aly and CIP29, to assemble the TREX complex Kobina Dufu,1 Michaela J. Livingstone,2 Jan Seebacher,1 Steven P. Gygi,1 Stuart A. Wilson,2 and Robin Reed1,3 1Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA; 2Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom The conserved TREX mRNA export complex is known to contain UAP56, Aly, Tex1, and the THO complex. Here, we carried out proteomic analysis of immunopurified human TREX complex and identified the protein CIP29 as the only new component with a clear yeast relative (known as Tho1). Tho1 is known to function in mRNA export, and we provide evidence that CIP29 likewise functions in this process. Like the known TREX components, a portion of CIP29 localizes in nuclear speckle domains, and its efficient recruitment to mRNA is both splicing- and cap-dependent. We show that UAP56 mediates an ATP-dependent interaction between the THO complex and both CIP29 and Aly, indicating that TREX assembly is ATP-dependent. Using recombinant proteins expressed in Escherichia coli, we show that UAP56, Aly, and CIP29 form an ATP-dependent trimeric complex, and UAP56 bridges the interaction between CIP29 and Aly. We conclude that the interaction of two conserved export proteins, CIP29 and Aly, with UAP56 is strictly regulated by ATP during assembly of the TREX complex. [Keywords: CIP29; Aly; UAP56; TREX complex; Tho1; helicase] Supplemental material is available at http://www.genesdev.org. Received December 20, 2009; revised version accepted July 30, 2010. -
Mining Genes in Type 2 Diabetic Islets and Finding Gold
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Cell Metabolism Previews Fischer, C., Mazzone, M., Jonckx, B., and Carme- Same´ n, E., Lu, L., et al. (2012). Nature 490, Takamoto, I., Sasako, T., et al. (2011). Cell Metab. liet, P. (2008). Nat. Rev. Cancer 8, 942–956. 426–430. 13, 294–307. Hagberg, C.E., Falkevall, A., Wang, X., Larsson, E., Karpanen, T., Bry, M., Ollila, H.M., Seppa¨ nen- Poesen, K., Lambrechts, D., Van Damme, P., Huusko, J., Nilsson, I., van Meeteren, L.A., Samen, Laakso, T., Liimatta, E., Leskinen, H., Kivela¨ , R., Dhondt, J., Bender, F., Frank, N., Bogaert, E., E., Lu, L., Vanwildemeersch, M., et al. (2010). Helkamaa, T., Merentie, M., Jeltsch, M., et al. Claes, B., Heylen, L., Verheyen, A., et al. (2008). Nature 464, 917–921. (2008). Circ. Res. 103, 1018–1026. J. Neurosci. 28, 10451–10459. Hagberg, C.E., Mehlem, A., Falkevall, A., Muhl, L., Kubota, T., Kubota, N., Kumagai, H., Yamaguchi, Samuel, V.T., and Shulman, G.I. (2012). Cell 148, Fam, B.C., Ortsa¨ ter, H., Scotney, P., Nyqvist, D., S., Kozono, H., Takahashi, T., Inoue, M., Itoh, S., 852–871. Mining Genes in Type 2 Diabetic Islets and Finding Gold Decio L. Eizirik1,* and Miriam Cnop1,2 1Laboratory of Experimental Medicine, Medical Faculty 2Division of Endocrinology, Erasmus Hospital Universite Libre de Bruxelles (ULB), 1000 Brussels, Belgium *Correspondence: [email protected] http://dx.doi.org/10.1016/j.cmet.2012.10.012 Pancreatic b cell failure is central in the pathogenesis of type 2 diabetes (T2D), but the mechanisms involved remain unclear. -
Transcriptomic and Epigenomic Characterization of the Developing Bat Wing
ARTICLES OPEN Transcriptomic and epigenomic characterization of the developing bat wing Walter L Eckalbar1,2,9, Stephen A Schlebusch3,9, Mandy K Mason3, Zoe Gill3, Ash V Parker3, Betty M Booker1,2, Sierra Nishizaki1,2, Christiane Muswamba-Nday3, Elizabeth Terhune4,5, Kimberly A Nevonen4, Nadja Makki1,2, Tara Friedrich2,6, Julia E VanderMeer1,2, Katherine S Pollard2,6,7, Lucia Carbone4,8, Jeff D Wall2,7, Nicola Illing3 & Nadav Ahituv1,2 Bats are the only mammals capable of powered flight, but little is known about the genetic determinants that shape their wings. Here we generated a genome for Miniopterus natalensis and performed RNA-seq and ChIP-seq (H3K27ac and H3K27me3) analyses on its developing forelimb and hindlimb autopods at sequential embryonic stages to decipher the molecular events that underlie bat wing development. Over 7,000 genes and several long noncoding RNAs, including Tbx5-as1 and Hottip, were differentially expressed between forelimb and hindlimb, and across different stages. ChIP-seq analysis identified thousands of regions that are differentially modified in forelimb and hindlimb. Comparative genomics found 2,796 bat-accelerated regions within H3K27ac peaks, several of which cluster near limb-associated genes. Pathway analyses highlighted multiple ribosomal proteins and known limb patterning signaling pathways as differentially regulated and implicated increased forelimb mesenchymal condensation in differential growth. In combination, our work outlines multiple genetic components that likely contribute to bat wing formation, providing insights into this morphological innovation. The order Chiroptera, commonly known as bats, is the only group of To characterize the genetic differences that underlie divergence in mammals to have evolved the capability of flight. -
Role of TGF-Β and Wnt Antagonist Gene Sfrp4 in Predicting Overall
Role of TGF-β and Wnt antagonist gene sFRP4 in predicting overall survival and clinic-pathological outcomes in lung cancer patients treated with platinum based doublet chemotherapy A Thesis Submitted in the partial fulfillment of the requirement for the award of the degree of MASTER OF TECHNOLOGY IN BIOTECHNOLOGY Under the supervision of: Submitted by: Dr. Siddharth Sharma Sheetal Vats Assistant Professor Roll No. 601504009 DEPARTMENT OF BIOTECHNOLOGY THAPAR UNIVERSITY, PATIALA -147004 Scanned by CamScanner Scanned by CamScanner Scanned by CamScanner ABSTARCT Title: Role of TGF beta and Wnt antagonists gene sFRP4 in predicting overall survival and clinic-pathological outcomes in lung cancer patients treated with platinum based doublet chemotherapy. TGF-β1 gene is located at chromosome no. 19q13.1-13.39. TGF-β1 maintains balance between cell renewal and cell differentiation by inhibiting cell cycle progression through G1 arrest. Depending upon the tumor type and stage, TGF-β has been reported for tumor suppression as well as for tumor activation properties. sFRP4 is 346 amino acid long sequence, 10.99 Kb long and located on 7p14.1. They are extracellular glycoproteins which act as Wnt antagonists as they bind with Wnt proteins and block Wnt signaling pathways. Objectives: To investigate the role of TGF-β1 polymorphism in modulating the survival and clinical outcomes of lung cancer patients and to examine the role of sFRP4 polymorphisms in affecting the overall survival and prognosis of lung cancer patients. Materials and methods: A total of 186 and 340 cases were genotyped in case of TGF beta and sFRP4 respectively using PCR-RFLP.