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Loss of Fam60a, a Sin3a Subunit, Results in Embryonic Lethality and Is Associated with Aberrant Methylation at a Subset of Gene
RESEARCH ARTICLE Loss of Fam60a, a Sin3a subunit, results in embryonic lethality and is associated with aberrant methylation at a subset of gene promoters Ryo Nabeshima1,2, Osamu Nishimura3,4, Takako Maeda1, Natsumi Shimizu2, Takahiro Ide2, Kenta Yashiro1†, Yasuo Sakai1, Chikara Meno1, Mitsutaka Kadota3,4, Hidetaka Shiratori1†, Shigehiro Kuraku3,4*, Hiroshi Hamada1,2* 1Developmental Genetics Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan; 2Laboratory for Organismal Patterning, RIKEN Center for Developmental Biology, Kobe, Japan; 3Phyloinformatics Unit, RIKEN Center for Life Science Technologies, Kobe, Japan; 4Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan Abstract We have examined the role of Fam60a, a gene highly expressed in embryonic stem cells, in mouse development. Fam60a interacts with components of the Sin3a-Hdac transcriptional corepressor complex, and most Fam60a–/– embryos manifest hypoplasia of visceral organs and die in utero. Fam60a is recruited to the promoter regions of a subset of genes, with the expression of these genes being either up- or down-regulated in Fam60a–/– embryos. The DNA methylation level of the Fam60a target gene Adhfe1 is maintained at embryonic day (E) 7.5 but markedly reduced at –/– *For correspondence: E9.5 in Fam60a embryos, suggesting that DNA demethylation is enhanced in the mutant. [email protected] (SK); Examination of genome-wide DNA methylation identified several differentially methylated regions, [email protected] (HH) which were preferentially hypomethylated, in Fam60a–/– embryos. Our data suggest that Fam60a is †These authors contributed required for proper embryogenesis, at least in part as a result of its regulation of DNA methylation equally to this work at specific gene promoters. -
Breast Cancer Resource Book Breast Cancer Resource BOOK
TM Breast Cancer Resource Book BREAST CANCER RESOURCE BOOK Table of Contents Introduction ��������������������������������������������������������������������������������������������������������������������������������������������������� 1 Tumor Cell Lines ��������������������������������������������������������������������������������������������������������������������������������������������� 2 Tumor Cell Panels ������������������������������������������������������������������������������������������������������������������������������������������� 3 hTERT immortalized Cells ������������������������������������������������������������������������������������������������������������������������������ 4 Primary Cells ��������������������������������������������������������������������������������������������������������������������������������������������������� 5 Culture and Assay Reagents �������������������������������������������������������������������������������������������������������������������������� 6 Transfection Reagents ����������������������������������������������������������������������������������������������������������������������������������� 8 Appendix ��������������������������������������������������������������������������������������������������������������������������������������������������������� 9 Tumor Cell Lines ................................................................................................................................................................................. 9 Tumor Cell -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Directing an Artificial Zinc Finger Protein to New Targets by Fusion to a Non-DNA Binding Domain
Directing an artificial zinc finger protein to new targets by fusion to a non-DNA binding domain Wooi Fang (Catheryn) Lim A thesis in fulfilment of the requirements for the degree of Doctor of Philosophy School of Biotechnology and Biomolecular Sciences Faculty of Science March 2016 Page | 0 THESIS/ DISSERTATION SHEET Page | i ORIGINALITY STATEMENT ‘I hereby declare that this submission is my own work and to the best of my knowledge it contains no materials previously published or written by another person, or substantial proportions of material which have been accepted for the award of any other degree or diploma at UNSW or any other educational institution, except where due acknowledgement is made in the thesis. Any contribution made to the research by others, with whom I have worked at UNSW or elsewhere, is explicitly acknowledged in the thesis. I also declare that the intellectual content of this thesis is the product of my own work, except to the extent that assistance from others in the project's design and conception or in style, presentation and linguistic expression is acknowledged.’ WOOI FANG LIM Signed …………………………………………….............. 31-03-2016 Date …………………………………………….............. Page | i COPYRIGHT STATEMENT ‘I hereby grant the University of New South Wales or its agents the right to archive and to make available my thesis or dissertation in whole or part in the University libraries in all forms of media, now or here after known, subject to the provisions of the Copyright Act 1968. I retain all proprietary rights, such as patent rights. I also retain the right to use in future works (such as articles or books) all or part of this thesis or dissertation. -
Role and Regulation of the P53-Homolog P73 in the Transformation of Normal Human Fibroblasts
Role and regulation of the p53-homolog p73 in the transformation of normal human fibroblasts Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades der Bayerischen Julius-Maximilians-Universität Würzburg vorgelegt von Lars Hofmann aus Aschaffenburg Würzburg 2007 Eingereicht am Mitglieder der Promotionskommission: Vorsitzender: Prof. Dr. Dr. Martin J. Müller Gutachter: Prof. Dr. Michael P. Schön Gutachter : Prof. Dr. Georg Krohne Tag des Promotionskolloquiums: Doktorurkunde ausgehändigt am Erklärung Hiermit erkläre ich, dass ich die vorliegende Arbeit selbständig angefertigt und keine anderen als die angegebenen Hilfsmittel und Quellen verwendet habe. Diese Arbeit wurde weder in gleicher noch in ähnlicher Form in einem anderen Prüfungsverfahren vorgelegt. Ich habe früher, außer den mit dem Zulassungsgesuch urkundlichen Graden, keine weiteren akademischen Grade erworben und zu erwerben gesucht. Würzburg, Lars Hofmann Content SUMMARY ................................................................................................................ IV ZUSAMMENFASSUNG ............................................................................................. V 1. INTRODUCTION ................................................................................................. 1 1.1. Molecular basics of cancer .......................................................................................... 1 1.2. Early research on tumorigenesis ................................................................................. 3 1.3. Developing -
Breast Cancer Metastasis Suppressor 1 Inhibits Gene Expression by Targeting Nuclear Factor-KB Activity
Research Article Breast Cancer Metastasis Suppressor 1 Inhibits Gene Expression by Targeting Nuclear Factor-KB Activity Muzaffer Cicek,1 Ryuichi Fukuyama,1 Danny R. Welch,2 Nywana Sizemore,1 and Graham Casey1 1Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic Lerner School of Medicine, Cleveland, Ohio and 2Department of Pathology, Comprehensive Cancer Center, and National Foundation for Cancer Research Center for Metastasis Research, University of Alabama at Birmingham, Birmingham, Alabama Abstract An important component of metastatic dissemination is the Breast cancer metastasis suppressor 1 (BRMS1) functions as a proteolysis and degradation of the extracellular matrix (ECM), and metastasis suppressor gene in breast cancer and melanoma among the key mediators of ECM remodeling is the urokinase-type cell lines, but the mechanism of BRMS1 suppression remains plasminogen activator (uPA), a serine protease that stimulates the conversion of inactive plasminogen to the broad-spectrum unclear. We determined that BRMS1 expression was inversely correlated with that of urokinase-type plasminogen activator protease plasmin (4, 5). Plasmin mediates cellular invasion directly (uPA), a prometastatic gene that is regulated at least in part by by degrading members of the matrix proteins (6, 7) and indirectly nuclear factor-KB (NF-KB). To further investigate the role of by activating matrix metalloproteinases (MMP; ref. 8). Several NF-KB in BRMS1-regulated gene expression, we examined NF- groups have shown that uPA plays a critical role in tumor KB binding activity and found an inverse correlation between metastasis (9) and that elevated levels of uPA as well as its inhibitor BRMS1 expression and NF-KB binding activity in MDA-MB-231 plasminogen activator inhibitor-1 (PAI-1) are strong indicators of poor prognosis in breast cancers (10–14). -
BRMS1 Expression in Resected Lung Adenocarcinoma
366 Editorial BRMS1 expression in resected lung adenocarcinoma Domenico Galetta, Pamela Pizzutilo, Vito Longo Medical Thoracic Oncology Unit, IRCCS Istituto Tumori “Giovanni Paolo II”, Bari, Italy Correspondence to: Vito Longo, MD, PhD. Medical Thoracic Oncology Unit, IRCCS Istituto Tumori “Giovanni Paolo II”, Viale Orazio Flacco 65 - 70124, Bari, Italy. Email: [email protected]. Comment on: Bucciarelli PR, Tan KS, Chudgar NP, et al. BRMS1 Expression in Surgically Resected Lung Adenocarcinoma Predicts Future Metastases and Is Associated with a Poor Prognosis. J Thorac Oncol 2018;13:73-84. Submitted Sep 16, 2018. Accepted for publication Sep 25, 2018. doi: 10.21037/tlcr.2018.09.20 View this article at: http://dx.doi.org/10.21037/tlcr.2018.09.20 The identification of prognostic markers for surgical that it may be part of a transcription complex (11). BRMS1 resected cancers is a current issue for several malignancies has been shown to function as a corepressor to inhibit NF- (1,2). As regard lung adenocarcinoma (LUAD), despite kB transactivation by deacetylation of the RelA/p65 subunit curative-intent surgical resection, tumor recurrence and at K310. It also regulates angiogenesis, phosphoinositide spread remain the primary causes of cancer-related death signalling, expression of microRNA, and p300 histone among patients with early stage. A precise prediction of the acetyltransferase levels. Moreover, the loss of endogenous risk of tumor recurrence at the time of surgery could spare BRMS1 significantly promotes basal and TGF-Beta-induced patients the toxicity of adjuvant chemotherapy, and target epithelial to mesenchymal transition (EMT) in lung cancer other patients for increased therapy and surveillance (3). -
BRMS1 Gene Expression May Be Associated with Clinico-Pathological Features of Breast Cancer
Bioscience Reports (2017) 37 BSR20170672 DOI: 10.1042/BSR20170672 Research Article BRMS1 gene expression may be associated with clinico-pathological features of breast cancer Li-Zhong Lin1, Miao-Guo Cai2, Yue-Chu Dai1, Zhi-Bao Zheng1, Fang-Fang Jiang1, Li-Li Shi3,YinPan1 and Han-Bing Song3 1Department of Oncology, Taizhou Central Hospital, Taizhou 318000, P.R. China; 2Department of Oncology, Luqiao Branch of Taizhou Hospital, Taizhou 318000, P.R. China; Downloaded from http://portlandpress.com/bioscirep/article-pdf/37/4/BSR20170672/480548/bsr-2017-0672.pdf by guest on 30 September 2021 3Department of Infection, Luqiao Branch of Taizhou Hospital, Taizhou 318000, P.R. China Correspondence: Yin Pan ([email protected]) Our aim is to investigate whether or not the breast cancer metastasis suppressor 1 (BRMS1) gene expression is directly linked to clinico-pathological features of breast cancer. Following a stringent inclusion and exclusion criteria, case–control studies with associations between BRMS1 and breast cancer were selected from articles obtained by way of searches con- ducted through an electronic database. All statistical analyses were performed with Stata 12.0 (Stata Corp, College Station, TX, U.S.A.). Ultimately, 1,263 patients with breast can- cer were found in a meta-analysis retrieved from a total that included 12 studies. Results of our meta-analysis suggested that BRMS1 protein in breast cancer tissues was signifi- cantly lower in comparison with normal breast tissues (odds ratio, OR = 0.08, 95% confi- dence interval (CI) = 0.04–0.15). The BRMS1 protein in metastatic breast cancer tissue was decreased than from that was found in non-metastatic breast cancer tissue (OR = 0.20, 95%CI = 0.13–0.29), and BRMS1 protein in tumor-node-metastasis (TNM) stages 1 and 2 was found to be higher than TNM stages 3 and 4 (OR = 4.62, 95%CI = 2.77–7.70). -
The Breast Cancer Metastasis Suppressor BRMS1 Binds
CORE Metadata, citation and similar papers at core.ac.uk Provided by Digital.CSIC Sorting Nexin 6 interacts with Breast Cancer Metastasis Suppressor-1 and promotes transcriptional repression 1* 2 3* José Rivera , Diego Megías and Jerónimo Bravo 1Centro Nacional de Investigaciones Cardiovasculares Carlos III, C/ Melchor Fernández Almagro 3, E-28029 Madrid, Spain. Email: [email protected]. Phone: (+34) 91 4531200; Fax:+ (34) 91 4531245. 2Confocal Microscopy Unit, Centro Nacional de Investigaciones Oncológicas, C/ Melchor Fernández Almagro 3, E-28029 Madrid, Spain. Email: [email protected] 3 Instituto de Biomedicina de Valencia (IBV-CSIC), Jaime Roig 11, 46010 Valencia, Spain. Email: [email protected] *Corresponding author Running title: SNX6 interacts with BRMS1and repress transcription KEY WORDS: Protein-protein interaction, Yeast two-hybrid assay, Binding domain, FRET, BRMS1, SNX6. Grant sponsor: MCyT; Grant number: SAF2006-10269. Grant sponsor: MICINN; Grant number: SAF2008-04048-E, SAF2009-10667. Grant sponsor: CSIC; Grant number: 200820I020. Grant sponsor: Fundación-Mutua-Madrileña. Grant sponsor: Conselleria de Sanitat, Generalitat valenciana; Grant number: AP001/10. Total Number of text figures and tables: 4 Figures, 1 Table and 2 Supplemental Figures. 1 ABSTRACT Sorting nexin 6 (SNX6), a predominantly cytoplasmic protein involved in intracellular trafficking of membrane receptors, was identified as a TGFβ family interactor. However, apart from being a component of the Retromer, little is known about SNX6 cellular functions. Pim1-dependent SNX6 nuclear translocation has been reported suggesting a putative nuclear role for SNX6. Here we describe a previously non- reported association of SNX6 with Breast Cancer Metastasis Suppressor 1 (BRMS1) protein detected by a yeast two-hybrid screening. -
Protein Annotation of Breast-Cancer-Related Proteins with Machine-Learning Tools
Makara Journal of Science Volume 24 Issue 2 June Article 6 6-26-2020 Protein Annotation of Breast-cancer-related Proteins with Machine-learning Tools Arli Aditya Parikesit Department of Bioinformatics, School of Life Sciences, Indonesia International Institute for Life Sciences, Jakarta 13210, Indonesia, [email protected] David Agustriawan Department of Bioinformatics, School of Life Sciences, Indonesia International Institute for Life Sciences, Jakarta 13210, Indonesia Rizky Nurdiansyah Department of Bioinformatics, School of Life Sciences, Indonesia International Institute for Life Sciences, Jakarta 13210, Indonesia Follow this and additional works at: https://scholarhub.ui.ac.id/science Recommended Citation Parikesit, Arli Aditya; Agustriawan, David; and Nurdiansyah, Rizky (2020) "Protein Annotation of Breast- cancer-related Proteins with Machine-learning Tools," Makara Journal of Science: Vol. 24 : Iss. 2 , Article 6. DOI: 10.7454/mss.v24i1.12106 Available at: https://scholarhub.ui.ac.id/science/vol24/iss2/6 This Article is brought to you for free and open access by the Universitas Indonesia at UI Scholars Hub. It has been accepted for inclusion in Makara Journal of Science by an authorized editor of UI Scholars Hub. Protein Annotation of Breast-cancer-related Proteins with Machine-learning Tools Cover Page Footnote The authors would like to thank the Institute for Research and Community Services of the Indonesia International Institute for Life Sciences (i3l) for their heartfelt support. Thanks also goes to Direktorat Riset dan Pengabdian Masyarakat, Direktorat Jenderal Penguatan Riset dan Pengembangan Kementerian Riset, Teknologi dan Pendidikan Tinggi Republik Indonesia for providing Hibah Penelitian Dasar DIKTI/ LLDIKTI III 2019 No. 1/AKM/PNT/2019. -
Krüppel-Like Factor 17 Upregulates Uterine Corin Expression and Promotes Spiral Artery Remodeling in Pregnancy
Krüppel-like factor 17 upregulates uterine corin expression and promotes spiral artery remodeling in pregnancy Can Wanga, Zhiting Wanga, Meiling Hea, Tiantian Zhoua, Yayan Niua,b, Shengxuan Sunc, Hui Lia, Ce Zhanga, Shengnan Zhanga, Meng Liua, Ying Xud, Ningzheng Donga,b,1, and Qingyu Wua,e,1 aCyrus Tang Hematology Center, Ministry of Education Engineering Center of Hematological Diseases, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Prevention, Soochow University, 215123 Suzhou, China; bMinistry of Health Key Laboratory of Thrombosis and Hemostasis, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, 215006 Suzhou, China; cDepartment of Orthopedics, The Second Affiliated Hospital of Soochow University, 215004 Suzhou, China; dCambridge-Soochow University Genomic Resource Center, Soochow University, 215123 Suzhou, China; and eCardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 Edited by R. Michael Roberts, University of Missouri, Columbia, MO, and approved June 25, 2020 (received for review February 29, 2020) Spiral artery remodeling is an important physiological process in the In the heart, natriuretic peptide expression is controlled by pregnant uterus which increases blood flow to the fetus. Impaired GATA-4, a zinc finger transcription factor (21, 22). A similar spiral artery remodeling contributes to preeclampsia, a major disease GATA-4–dependent mechanism is critical for cardiac corin ex- in pregnancy. Corin, a transmembrane serine protease, is up- pression. We have shown that human and mouse corin gene pro- regulated in the pregnant uterus to promote spiral artery remodeling. moters contain a conserved sequence that is essential for GATA-4 To date, the mechanism underlying uterine corin up-regulation re- binding and corin expression in cardiomyocytes (23). -
Engineered Type 1 Regulatory T Cells Designed for Clinical Use Kill Primary
ARTICLE Acute Myeloid Leukemia Engineered type 1 regulatory T cells designed Ferrata Storti Foundation for clinical use kill primary pediatric acute myeloid leukemia cells Brandon Cieniewicz,1* Molly Javier Uyeda,1,2* Ping (Pauline) Chen,1 Ece Canan Sayitoglu,1 Jeffrey Mao-Hwa Liu,1 Grazia Andolfi,3 Katharine Greenthal,1 Alice Bertaina,1,4 Silvia Gregori,3 Rosa Bacchetta,1,4 Norman James Lacayo,1 Alma-Martina Cepika1,4# and Maria Grazia Roncarolo1,2,4# Haematologica 2021 Volume 106(10):2588-2597 1Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA; 2Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA; 3San Raffaele Telethon Institute for Gene Therapy, Milan, Italy and 4Center for Definitive and Curative Medicine, Stanford School of Medicine, Stanford, CA, USA *BC and MJU contributed equally as co-first authors #AMC and MGR contributed equally as co-senior authors ABSTRACT ype 1 regulatory (Tr1) T cells induced by enforced expression of interleukin-10 (LV-10) are being developed as a novel treatment for Tchemotherapy-resistant myeloid leukemias. In vivo, LV-10 cells do not cause graft-versus-host disease while mediating graft-versus-leukemia effect against adult acute myeloid leukemia (AML). Since pediatric AML (pAML) and adult AML are different on a genetic and epigenetic level, we investigate herein whether LV-10 cells also efficiently kill pAML cells. We show that the majority of primary pAML are killed by LV-10 cells, with different levels of sensitivity to killing. Transcriptionally, pAML sensitive to LV-10 killing expressed a myeloid maturation signature.