High-Level Expression of Mastermind-Like 2 Contributes to Aberrant Activation of the NOTCH Signaling Pathway in Human Lymphomas

Total Page:16

File Type:pdf, Size:1020Kb

High-Level Expression of Mastermind-Like 2 Contributes to Aberrant Activation of the NOTCH Signaling Pathway in Human Lymphomas Oncogene (2011) 30, 1831–1840 & 2011 Macmillan Publishers Limited All rights reserved 0950-9232/11 www.nature.com/onc ORIGINAL ARTICLE High-level expression of Mastermind-like 2 contributes to aberrant activation of the NOTCH signaling pathway in human lymphomas KKo¨chert1,2, K Ullrich1,2, S Kreher1,2, JC Aster3, M Kitagawa4,KJo¨hrens5, I Anagnostopoulos5, F Jundt1,2, B Lamprecht1,2, U Zimber-Strobl6, H Stein3, M Janz1,2,BDo¨rken1,2 and S Mathas1,2 1Max-Delbru¨ck-Center for Molecular Medicine, Berlin, Germany; 2Hematology, Oncology and Tumorimmunology, Charite´ University Medical School, CVK, Berlin, Germany; 3Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA; 4Department of Molecular and Tumor Pathology, Chiba University Graduate School of Medicine, Chiba, Japan; 5Institute of Pathology, Charite´ University Medical School, CBF, Berlin, Germany and 6Department of Gene Vectors, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany Inappropriate activation of the NOTCH signaling path- In Mammalia there are four NOTCH receptors that way, for example, by activating mutations, contributes to interact with a still growing list of ligands (Kopan the pathogenesis of various human malignancies. Here, and Ilagan, 2009). Upon ligand binding, cleavage of we demonstrate that aberrant expression of an essential the NOTCH receptor produces a membrane-anchored NOTCH coactivator of the Mastermind-like (MAML) form of NOTCH termed NOTCH transmembrane family provides an alternative mechanism to activate (NOTCHTM). NOTCHTM, in turn is cleaved by the NOTCH signaling in human lymphoma cells. We detected g-secretase membrane protease complex, releasing in- high-level MAML2 expression in several B cell-derived tracellular NOTCH (ICN), which then translocates to lymphoma types, including classical Hodgkin lymphoma the nucleus and activates transcription. (cHL) cells, relative to normal B cells. Inhibition of ICN does not directly bind to DNA, but interacts MAML-protein activity by a dominant negative form of with the enhancer-binding protein member CSL (CBF1, MAML or by small hairpin RNAs targeting MAML2 in Suppressor of Hairless, LAG-1) (Kopan and Ilagan, cHL cells resulted in downregulation of the NOTCH 2009). In the absence of ICN, CSL binds to DNA in target genes HES7 and HEY1, which we identified as a sequence-dependent manner and recruits various overexpressed in cHL cells, and in reduced proliferation. corepressor molecules. Interaction of ICN with CSL Furthermore, a NOTCH gene-expression signature in converts CSL from a transcriptional repressor to an cHL cells confirmed their cell-autonomous NOTCH activator (Lubman et al., 2007) by creating a dual ICN/ activity. Finally, in line with the essential role of MAML CSL binding interface for transcriptional coactivators proteins for assembly and activity of the NOTCH of the Mastermind-like (MAML) family (Fryer et al., transcriptional complex (NTC), we show that MAML- 2002; Jeffries et al., 2002; Del Bianco et al., 2008). derived small-peptide constructs block NOTCH activity Three MAML members exist (MAML1, MAML2 and and disrupt NTC formation in vitro. These data strongly MAML3) (Lin et al., 2002; Wu et al., 2000, 2002), all of suggest direct targeting of the NTC as treatment strategy which contain an N-terminal region of approximately 60 for NOTCH-dependent malignancies. amino acids (AA) that binds an extended groove formed Oncogene (2011) 30, 1831–1840; doi:10.1038/onc.2010.544; by CSL and the ankyrin–domain of ICN (Nam et al., published online 29 November 2010 2006; Wilson and Kovall, 2006). Binding of MAML proteins to the ICN–CSL complex is essential for Keywords: Mastermind-like; NOTCH; lymphoma; Hodgkin NOTCH-mediated transcriptional activation (Fryer et al., 2002; Nam et al., 2003, 2006; Maillard et al., 2004). The mechanisms by which MAML proteins regulate the fine-tuning of NOTCH signaling remain to Introduction be elucidated. However, several lines of evidence, for example, the (11;19)(q21;p13) translocation found in Numerous studies revealed a fundamental role of the mucoepidermoid carcinoma that creates a MAML2 NOTCH signaling pathway for key processes such as fusion protein and activates NOTCH target genes cellular differentiation, growth and apoptosis regulation (Tonon et al., 2003), point to the oncogenic potential of (Koch and Radtke, 2007; Kopan and Ilagan, 2009). MAML dysregulation. Deregulated NOTCH signaling results in pathological disorders, including developmental syndromes and various Correspondence: Dr S Mathas, Max-Delbru¨ck-Center for Molecular malignancies (Grabher et al., 2006; Koch and Radtke, Medicine and Charite´ University Medical School, Hematology/ 2007). Different mechanisms leading to aberrant NOTCH Oncology, Robert-Ro¨ssle-Str. 10, Berlin D-13125, Germany. E-mail: [email protected] activation have been unraveled so far, including activating Received 7 April 2010; revised 28 September 2010; accepted 20 October mutations of the NOTCH1 receptor itself (Weng et al., 2010; published online 29 November 2010 2004; Grabher et al., 2006) as well as alterations in proteins NOTCH activation by high MAML2 expression KKo¨chert et al 1832 that control ICN turnover (O’Neil et al., 2007). Such various cell lines. These data were confirmed at the defects are found in more than 50% of childhood and protein level (Figure 1b). In contrast, MAML2 mRNA adult T-cell acute lymphoblastic leukemia (T-ALLs). was abundant in all HRS cell lines, whereas except for We and others have previously shown that aberrant Reh and BL-60 cells, it was undetectable in the other NOTCH activity is involved in the pathogenesis of non-Hodgkin lymphoma cell lines (Figure 1b, upper human B cell-derived malignancies, including multiple panel). MAML2 protein expression correlated with myeloma, B-cell chronic lymphocytic leukemia, diffuse the mRNA expression data (Figure 1b, lower panel). large B-cell lymphoma and the malignant Hodgkin–/ As only few data regarding MAML expression in Reed–Sternberg (HRS) cells of classical Hodgkin lym- human lymphoid cells were available (Lin et al., 2002; phoma (cHL) (Kapp et al., 1999; Jundt et al., 2002, Wu et al., 2002), we analyzed MAML mRNA and 2004, 2008; Lee et al., 2009; Rosati et al., 2009; Stanelle protein expression in purified CD19 þ B cells and CD3 þ et al., 2010). Given the important function of MAML T cells (Figure 1c). Robust expression of MAML1 and coactivators for NOTCH activation (Wu et al., 2002) MAML3 mRNA was found in all lymphoid samples and for the development of distinct B cell subsets (Figure 1c, upper panel). In contrast, MAML2 was (Oyama et al., 2007; Wu et al., 2007), we analyzed the strongly expressed only in CD3 þ T cells, whereas it contribution of MAML to the deregulated NOTCH was hardly detectable in CD19 þ B cells, which was activity in human B cell-derived lymphomas. confirmed at protein level (Figure 1c, lower panel). We concluded that MAML2 is expressed at an aberrantly high level in several B cell-derived lymphoma cell lines, most commonly in those of cHL origin. Results NOTCH1TM and cleaved ICN1 in human B cell-derived Aberrant MAML2 expression in distinct primary lymphoma cell lines lymphoma entities We first analyzed the expression levels of NOTCH1TM Next, we analyzed MAML2 expression in non-neoplas- and ICN1 in various cell lines by use of antibodies tic lymphoid tissue and 180 B cell-derived primary recognizing these different forms of NOTCH1 human lymphoma cases by immunohistochemistry (Figure 1a). As previously published (Jundt et al., (Figure 1d and Table 1). In contrast to normal tonsillar 2002), HRS cell lines (L428, L1236, KM-H2, L591, B cells, high MAML2 expression was detectable in HDLM-2, L540 and L540Cy) showed a prominent malignant cells of various primary lymphomas, in parti- expression of NOTCH1TM compared with most other cular, in all analyzed B lymphoblastic leukemias (8/8), non-Hodgkin lymphoma cell lines (Reh, Namalwa, 40% of mantle cell lymphoma cases (4/10), approxi- BL-60, BJAB and SU-DHL-4). However, although mately half of the marginal zone lymphoma cases and in ICN1 was detectable at variable levels in the cell lines the HRS cells of half of the cHL cases (30/61). Overall, (Figure 1a), ICN1 protein levels were not correlated these data revealed MAML2 deregulation as a common with NOTCH1TM protein levels (compare NOTCH1TM defect in B cell-derived lymphomas. Given the robust and ICN1 in, for example, L428, L1236 or BJAB cells). expression of MAML2 in the HRS cell lines (Figure 1), Furthermore, the ICN1 protein level did not predict the we investigated the function of MAML2 in these cell functional activity of the NOTCH transcriptional lines in more detail. complex (NTC), as the NTC was active in L428 cells with a low level of ICN1 but apparently inactive in MAML2 drives NOTCH-mediated transcriptional et al. BJAB cells (see also Figures 2–3; Weng , 2003; activation in lymphoid-derived cells and regulates the Jundt et al., 2002, 2008; Moellering et al., 2009). We NOTCH target genes HES7 and HEY1 in cHL cells hypothesized that altered expression or activity of NTC To study the function of MAML2 in lymphoid cell lines, components other than ICN1 might explain aberrant we first assessed the potential of MAML2 to potentiate activation of the NOTCH signaling pathway in certain NOTCH transcriptional activity in such cells, as cellular contexts. We therefore decided to analyze previous analyses were primarily performed with other expression and activity of NOTCH coactivators of the cell types (Wu et al., 2000, 2002; Lin et al., 2002). To MAML family in the various cell lines in detail. establish the experimental system, we cotransfected HEK293 cells with a NOTCH-dependent promoter High-level expression of MAML2 in human B cell-derived construct, and either ICN1 or MAML2 alone or lymphomas, in particular HRS cell lines in combination (Figure 2a). As previously published To this end, messenger RNA (mRNA) and protein (Wu et al., 2002), ICN1 and MAML2 synergistically expression of the three MAML family members activated the reporter construct.
Recommended publications
  • MAML1 Antibody A
    Revision 1 C 0 2 - t MAML1 Antibody a e r o t S Orders: 877-616-CELL (2355) [email protected] Support: 877-678-TECH (8324) 8 0 Web: [email protected] 6 www.cellsignal.com 4 # 3 Trask Lane Danvers Massachusetts 01923 USA For Research Use Only. Not For Use In Diagnostic Procedures. Applications: Reactivity: Sensitivity: MW (kDa): Source: UniProt ID: Entrez-Gene Id: WB, IP H Endogenous 130 Rabbit Q92585 9794 Product Usage Information Application Dilution Western Blotting 1:1000 Immunoprecipitation 1:50 Storage Supplied in 10 mM sodium HEPES (pH 7.5), 150 mM NaCl, 100 µg/ml BSA and 50% glycerol. Store at –20°C. Do not aliquot the antibody. Specificity / Sensitivity MAML1 Antibody detects endogenous levels of total MAML1 protein. It does not cross- react with MAML2 and MAML3. Species Reactivity: Human Source / Purification Polyclonal antibodies are produced by immunizing animals with a synthetic peptide corresponding to residues surrounding His811 of human MAML1. Antibodies are purified by protein A and peptide affinity chromatography. Background Mastermind-like (MAML) family of proteins are homologs of Drosophila Mastermind. The family is composed of three members in mammals: MAML1, MAML2, and MAML3 (1,2). MAML proteins form complexes with the intracellular domain of Notch (ICN) and the transcription factor CSL (RBP-Jκ) to regulate Notch target gene expression (3-5). MAML1 also interacts with myocyte enhancer factor 2C (MEF2C) to regulate myogenesis (6). MAML2 is frequently found to be fused with Mucoepidermoid carcinoma translocated gene 1 (MECT1, also know as WAMTP1 or TORC1) in patients with mucoepidermoid carcinomas and Warthin's tumors (7).
    [Show full text]
  • Cystatin-B Negatively Regulates the Malignant Characteristics of Oral Squamous Cell Carcinoma Possibly Via the Epithelium Proliferation/ Differentiation Program
    ORIGINAL RESEARCH published: 24 August 2021 doi: 10.3389/fonc.2021.707066 Cystatin-B Negatively Regulates the Malignant Characteristics of Oral Squamous Cell Carcinoma Possibly Via the Epithelium Proliferation/ Differentiation Program Tian-Tian Xu 1, Xiao-Wen Zeng 1, Xin-Hong Wang 2, Lu-Xi Yang 1, Gang Luo 1* and Ting Yu 1* 1 Department of Periodontics, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China, 2 Department of Oral Pathology and Medicine, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China Disturbance in the proteolytic process is one of the malignant signs of tumors. Proteolysis Edited by: Eva Csosz, is highly orchestrated by cysteine cathepsin and its inhibitors. Cystatin-B (CSTB) is a University of Debrecen, Hungary general cysteine cathepsin inhibitor that prevents cysteine cathepsin from leaking from Reviewed by: lysosomes and causing inappropriate proteolysis. Our study found that CSTB was Csongor Kiss, downregulated in both oral squamous cell carcinoma (OSCC) tissues and cells University of Debrecen, Hungary Gergely Nagy, compared with normal controls. Immunohistochemical analysis showed that CSTB was University of Debrecen, Hungary mainly distributed in the epithelial structure of OSCC tissues, and its expression intensity *Correspondence: was related to the grade classification. A correlation analysis between CSTB and clinical Gang Luo [email protected] prognosis was performed using gene expression data and clinical information acquired Ting Yu from The Cancer Genome Atlas (TCGA) database. Patients with lower expression levels of [email protected] CSTB had shorter disease-free survival times and poorer clinicopathological features Specialty section: (e.g., lymph node metastases, perineural invasion, low degree of differentiation, and This article was submitted to advanced tumor stage).
    [Show full text]
  • Selenite Inhibits Notch Signaling in Cells and Mice
    International Journal of Molecular Sciences Article Selenite Inhibits Notch Signaling in Cells and Mice Michael Powers 1, Liu Liu 1, Dane Deemer 1, Selina Chen 1, Aaron Scholl 1, Masafumi Yoshinaga 2 and Zijuan Liu 1,* 1 Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA; [email protected] (M.P.); [email protected] (L.L.); [email protected] (D.D.); [email protected] (S.C.); [email protected] (A.S.) 2 Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA; myoshina@fiu.edu * Correspondence: [email protected]; Tel.: +1-248-370-3554 Abstract: Selenium is an essential micronutrient with a wide range of biological effects in mammals. The inorganic form of selenium, selenite, is supplemented to relieve individuals with selenium deficiency and to alleviate associated symptoms. Additionally, physiological and supranutritional selenite have shown selectively higher affinity and toxicity towards cancer cells, highlighting their potential to serve as chemotherapeutic agents or adjuvants. At varying doses, selenite extensively regulates cellular signaling and modulates many cellular processes. In this study, we report the identification of Delta–Notch signaling as a previously uncharacterized selenite inhibited target. Our transcriptomic results in selenite treated primary mouse hepatocytes revealed that the tran- scription of Notch1, Notch2, Hes1, Maml1, Furin and c-Myc were all decreased following selenite treatment. We further showed that selenite can inhibit Notch1 expression in cultured MCF7 breast adenocarcinoma cells and HEPG2 liver carcinoma cells. In mice acutely treated with 2.5 mg/kg Citation: Powers, M.; Liu, L.; selenite via intraperitoneal injection, we found that Notch1 expression was drastically lowered in Deemer, D.; Chen, S.; Scholl, A.; liver and kidney tissues by 90% and 70%, respectively.
    [Show full text]
  • Anti-MAML1 (Aa 655-754) Polyclonal Antibody (DPAB-DC3896) This Product Is for Research Use Only and Is Not Intended for Diagnostic Use
    Anti-MAML1 (aa 655-754) polyclonal antibody (DPAB-DC3896) This product is for research use only and is not intended for diagnostic use. PRODUCT INFORMATION Antigen Description This protein is the human homolog of mastermind, a Drosophila protein that plays a role in the Notch signaling pathway involved in cell-fate determination. There is in vitro evidence that the human homolog forms a complex with the intracellular portion of human Notch receptors and can increase expression of a Notch-induced gene. This evidence supports its proposed function as a transcriptional co-activator in the Notch signaling pathway. Immunogen MAML1 (NP_055572, 655 a.a. ~ 754 a.a) partial recombinant protein with GST tag. The sequence is AEQEKQQFQRHLTRPPPQYQDPTQGSFPQQVGQFTGSSAAVPGMNTLGPSNSSCPRVFPQA GNLMPMGPGHASVSSLPTNSGQQDRGVAQFPGSQNMPQS Source/Host Mouse Species Reactivity Human Conjugate Unconjugated Applications WB (Recombinant protein), ELISA, Size 50 μl Buffer 50 % glycerol Preservative None Storage Store at -20°C or lower. Aliquot to avoid repeated freezing and thawing. GENE INFORMATION Gene Name MAML1 mastermind-like 1 (Drosophila) [ Homo sapiens (human) ] Official Symbol MAML1 Synonyms MAML1; mastermind-like 1 (Drosophila); Mam1; Mam-1; mastermind-like protein 1; mastermind homolog; 45-1 Ramsey Road, Shirley, NY 11967, USA Email: [email protected] Tel: 1-631-624-4882 Fax: 1-631-938-8221 1 © Creative Diagnostics All Rights Reserved Entrez Gene ID 9794 Protein Refseq NP_055572 UniProt ID Q92585 Chromosome Location 5q35 Pathway Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants; Delta-Notch Signaling Pathway; FBXW7 Mutants and NOTCH1 in Cancer; Generic Transcription Pathway Function peptide antigen binding; protein binding; protein kinase binding; transcription coactivator activity 45-1 Ramsey Road, Shirley, NY 11967, USA Email: [email protected] Tel: 1-631-624-4882 Fax: 1-631-938-8221 2 © Creative Diagnostics All Rights Reserved.
    [Show full text]
  • Computational Approach to Identify Mutations in Genes of Notch Signaling Pathway and Its Association with OSCC
    Journal of Pharmaceutical Research International 32(20): 84-92, 2020; Article no.JPRI.59681 ISSN: 2456-9119 (Past name: British Journal of Pharmaceutical Research, Past ISSN: 2231-2919, NLM ID: 101631759) Computational Approach to Identify Mutations in Genes of Notch Signaling Pathway and Its Association with OSCC Madhumithaa Sivarajan1, A. S. Smiline Girija2, A. Paramasivam3 and J. Vijayashree Priyadharsini3* 1Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, India. 2Department of Microbiology, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, 162 , Poonamallee High Road, Chennai 600077, Tamil Nadu, India. 3Biomedical Research Unit and Laboratory Animal Centre-Dental Research Cell, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai 600077, India. Authors’ contributions This work was carried out in collaboration among all authors. Author JVP designed the study, performed the statistical analysis, wrote the protocol and wrote the first draft of the manuscript. Authors ASSG and AP managed the analyses of the study. Author MS managed the literature searches and certain computational analysis. All authors read and approved the final manuscript. Article Information DOI: 10.9734/JPRI/2020/v32i2030732 Editor(s): (1) Dr. Mohamed Fawzy Ramadan Hassanien, Zagazig University, Egypt. Reviewers: (1) Mustika Tuwo, Hasanuddin University, Indonesia. (2) Maysaa
    [Show full text]
  • Interpreting Cancer Genomes Using Systematic Host Perturbations by Tumour Virus Proteins
    Interpreting Cancer Genomes Using Systematic Host Perturbations by Tumour Virus Proteins The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Rozenblatt-Rosen, Orit, Rahul C. Deo, Megha Padi, Guillaume Adelmant, Michael A. Calderwood, Thomas Rolland, Miranda Grace, et al. 2012. Interpreting cancer genomes using systematic host perturbations by tumour virus proteins. Nature 487(7408): 491-495. Published Version doi:10.1038/nature11288 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:10612841 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA NIH Public Access Author Manuscript Nature. Author manuscript; available in PMC 2013 January 26. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Nature. 2012 July 26; 487(7408): 491–495. doi:10.1038/nature11288. Interpreting cancer genomes using systematic host perturbations by tumour virus proteins Orit Rozenblatt-Rosen1,2,*,#, Rahul C. Deo3,4,*,#, Megha Padi5,6,*,#, Guillaume Adelmant3,7,*,#, Michael A. Calderwood8,9,10,*,^, Thomas Rolland8,9,*,^, Miranda Grace11,*,^, Amélie Dricot8,9,*,^, Manor Askenazi3,7,*,^, Maria Tavares1,2,7,*,^, Sam Pevzner8,9,12,^, Fieda Abderazzaq5,*, Danielle Byrdsong8,9,*, Anne-Ruxandra Carvunis8,9, Alyce A. Chen11,*, Jingwei Cheng1,2, Mick Correll5, Melissa Duarte8,10,*, Changyu Fan8,9,*, Mariet C. Feltkamp13, Scott B. Ficarro3,7,*, Rachel Franchi8,14,*, Brijesh K. Garg3,7,*, Natali Gulbahce8,15,16,*, Tong Hao8,9,*, Amy M.
    [Show full text]
  • A Single Cell but Many Different Transcripts
    International Journal of Molecular Sciences Review A Single Cell but Many Different Transcripts: A Journey into the World of Long Non-Coding RNAs Enrico Alessio 1, Raphael Severino Bonadio 1, Lisa Buson 1, Francesco Chemello 1 and Stefano Cagnin 1,2,3,* 1 Department of Biology, University of Padova, 35131 Padova, Italy; [email protected] (E.A.); [email protected] (R.S.B.); [email protected] (L.B.), [email protected] (F.C.) 2 CRIBI Biotechnology Center, University of Padova, 35131 Padova, Italy 3 CIR-Myo Myology Center, University of Padova, 35131 Padova, Italy * Correspondence: [email protected]; Tel.: +39-049-827-6162 Received: 22 November 2019; Accepted: 23 December 2019; Published: 1 January 2020 Abstract: In late 2012 it was evidenced that most of the human genome is transcribed but only a small percentage of the transcripts are translated. This observation supported the importance of non-coding RNAs and it was confirmed in several organisms. The most abundant non-translated transcripts are long non-coding RNAs (lncRNAs). In contrast to protein-coding RNAs, they show a more cell-specific expression. To understand the function of lncRNAs, it is fundamental to investigate in which cells they are preferentially expressed and to detect their subcellular localization. Recent improvements of techniques that localize single RNA molecules in tissues like single-cell RNA sequencing and fluorescence amplification methods have given a considerable boost in the knowledge of the lncRNA functions. In recent years, single-cell transcription variability was associated with non-coding RNA expression, revealing this class of RNAs as important transcripts in the cell lineage specification.
    [Show full text]
  • Data-Driven and Knowledge-Driven Computational Models of Angiogenesis in Application to Peripheral Arterial Disease
    DATA-DRIVEN AND KNOWLEDGE-DRIVEN COMPUTATIONAL MODELS OF ANGIOGENESIS IN APPLICATION TO PERIPHERAL ARTERIAL DISEASE by Liang-Hui Chu A dissertation submitted to Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland March, 2015 © 2015 Liang-Hui Chu All Rights Reserved Abstract Angiogenesis, the formation of new blood vessels from pre-existing vessels, is involved in both physiological conditions (e.g. development, wound healing and exercise) and diseases (e.g. cancer, age-related macular degeneration, and ischemic diseases such as coronary artery disease and peripheral arterial disease). Peripheral arterial disease (PAD) affects approximately 8 to 12 million people in United States, especially those over the age of 50 and its prevalence is now comparable to that of coronary artery disease. To date, all clinical trials that includes stimulation of VEGF (vascular endothelial growth factor) and FGF (fibroblast growth factor) have failed. There is an unmet need to find novel genes and drug targets and predict potential therapeutics in PAD. We use the data-driven bioinformatic approach to identify angiogenesis-associated genes and predict new targets and repositioned drugs in PAD. We also formulate a mechanistic three- compartment model that includes the anti-angiogenic isoform VEGF165b. The thesis can serve as a framework for computational and experimental validations of novel drug targets and drugs in PAD. ii Acknowledgements I appreciate my advisor Dr. Aleksander S. Popel to guide my PhD studies for the five years at Johns Hopkins University. I also appreciate several professors on my thesis committee, Dr. Joel S. Bader, Dr.
    [Show full text]
  • Bioinformatics to Integrate Protein and Gene Information in a Relational Context, Application to Human Proteomic and Transcriptomic Data
    TESIS DOCTORAL BIOINFORMATICS TO INTEGRATE PROTEIN AND GENE INFORMATION IN A RELATIONAL CONTEXT, APPLICATION TO HUMAN PROTEOMIC AND TRANSCRIPTOMIC DATA CONRAD FRIEDRICH DROSTE DIRECTOR DR. JAVIER DE LAS RIVAS SANZ SALAMANCA, JULIO DE 2017 El Dr. Javier De Las Rivas Sanz, con D.N.I. 15949000H, Investigador Científico del Consejo Superior de Investigaciones Científicas (CSIC), director del grupo de Bioinformática y Genómica Funcional en el Instituto de Biología Molecular y Celular del Cáncer (CiC-IBMCC), y profesor del Programa de Doctorado y del Máster de Biología y Clínica del Cáncer de dicho Instituto y la Universidad de Salamanca (USAL). CERTIFICA Que ha dirigido esta Tesis Doctoral titulada "BIOINFORMATICS TO INTEGRATE PROTEIN AND GENE INFORMATION IN A RELATIONAL CONTEXT, APPLICATION TO HUMAN PROTEOMIC AND TRANSCRIPTOMIC DATA" realizada por D. Conrad Friedrich Droste, alumno del Programa de Doctorado de 2012/2013 de la Universidad de Salamanca. y AUTORIZA La presentación de la misma, considerando que reúne las condiciones de originalidad y contenidos requeridos para optar al grado de Doctor por la Universidad de Salamanca. En Salamanca, a 7 de julio de 2017 Dr. Javier De Las Rivas Sanz To my parents, Heike and Friedel and my loved ones. I have to apologize to Pigena for all the time I missed to enjoy with her. ACKNOWLEDGEMENTS & APPRECIATIONS I am deeply grateful to my Ph.D. director Dr. Javier De Las Rivas for the opportunity to realize this work in his research group. His guidance, encouragement and support during these time were always appreciated and needed. I owe a very important debt to Dr.
    [Show full text]
  • Interpreting Cancer Genomes Using Systematic Host Perturbations By
    LETTER doi:10.1038/nature11288 Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins Orit Rozenblatt-Rosen1,2,3*, Rahul C. Deo1,4,5*,MeghaPadi1,6,7*, Guillaume Adelmant1,4,8*, Michael A. Calderwood1,9,10,11, Thomas Rolland1,9,10, Miranda Grace1,12,Ame´lie Dricot1,9,10, Manor Askenazi1,4,8, Maria Tavares1,2,3,8,SamuelJ.Pevzner9,10,13, Fieda Abderazzaq1,6, Danielle Byrdsong1,9,10, Anne-Ruxandra Carvunis9,10, Alyce A. Chen1,12, Jingwei Cheng2,3,MickCorrell6, Melissa Duarte1,9,11,ChangyuFan1,9,10, Mariet C. Feltkamp14, Scott B. Ficarro1,4,8, Rachel Franchi1,9,15, Brijesh K. Garg1,4,8, Natali Gulbahce1,9,16,17,TongHao1,9,10, Amy M. Holthaus1,11,RobertJames1,9,10, Anna Korkhin1,2,3, Larisa Litovchick1,2,3, Jessica C. Mar1,6,7,TheodoreR.Pak18, Sabrina Rabello1,3,9,16, Renee Rubio1,6,YunShen1,9,10, Saurav Singh4,8, Jennifer M. Spangle1,12, Murat Tasan1,4,18, Shelly Wanamaker9,10,15, James T. Webber4,8, Jennifer Roecklein-Canfield9,15,EricJohannsen1,11, Albert-La´szlo´ Baraba´si1,3,9,16,RameenBeroukhim3,19,20, Elliott Kieff1,11, Michael E. Cusick1,9,10, David E. Hill1,9,10, Karl Mu¨nger1,12, Jarrod A. Marto1,4,8,JohnQuackenbush1,6,7, Frederick P. Roth1,4,9,18, James A. DeCaprio1,2,3 & Marc Vidal1,9,10 Genotypic differences greatly influence susceptibility and resist- which DNA tumour virus proteins physically target the products of ance to disease. Understanding genotype–phenotype relationships RB1 or TP53, two well-established germline-inherited and somatically requires that phenotypes be viewed as manifestations of network inactivated tumour-suppressor genes6.
    [Show full text]
  • Supporting Information
    Supporting Information Miller et al. 10.1073/pnas.0914257107 SI Materials and Methods files with 20 to 40 samples and 5,629 to 9,731 genes each and 20 Data Set Acquisition and Filtering. All data sets were downloaded mouse expression files with 18 and 44 samples and 5,176 to 6,157 from the GEO database, and consisted of experiments run on genes each. All preprocessed data files (as well as the resulting either mouse or human brain tissue (Fig. 1A). We filtered out all network data and some associated code and support files) are but a core collection of data sets that were similar enough for available at the WGCNA group Web site (www.genetics.ucla.edu/ useful bioinformatic comparison. First, we removed all data sets labs/horvath/CoexpressionNetwork/MouseHumanBrain). that were not run on an Affymetrix platform, leaving three From these preprocessed expression files we created a human platforms in human (HG-U95A, HG-U133A, HG-U133 Plus 2) and a mouse consensus network (method modified from ref. 4). and two in mouse (MG-U74A, MG-U430A). Second, we ex- For each consensus network we first created correlation matrices cluded all samples in each data set that were not taken from from each data set (obtained by calculating the Pearson correla- brain tissue (for example, in one expression atlas study, more tions between all variable probe sets across all subjects in each than 80% of the samples were excluded). Third, to make the data set), and then weighted them based on the number of sam- correlations between genes more comparable across studies, we ples used in that data set.
    [Show full text]
  • Atlas Journal
    Atlas of Genetics and Cytogenetics in Oncology and Haematology Home Genes Leukemias Solid Tumours Cancer-Prone Deep Insight Portal Teaching X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA Atlas Journal Atlas Journal versus Atlas Database: the accumulation of the issues of the Journal constitutes the body of the Database/Text-Book. TABLE OF CONTENTS Volume 12, Number 3, May-Jun 2008 Previous Issue / Next Issue Genes SOCS2 (suppressor of cytokine signaling 2) (12q21.33). Leandro Fernández-Pérez, Amilcar Flores-Morales. Atlas Genet Cytogenet Oncol Haematol 2008; Vol (12): 351-355. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/SOCS2ID44123ch12q21.html PTHLH (parathyroid hormone-like hormone) (12p11.22). Sai-Ching Jim Yeung. Atlas Genet Cytogenet Oncol Haematol 2008; Vol (12): 356-367. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/PTHLHID41897ch12p11.html MUC17 (mucin 17, cell surface associated) (7q22.1). Wade M Junker, Nicolas Moniaux, Surinder K Batra. Atlas Genet Cytogenet Oncol Haematol 2008; Vol (12): 368-378. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/MUC17ID41456ch7q22.html MUC16 (mucin 16, cell surface associated) (19p13.2). Shantibhusan Senapati, Moorthy P Ponnusamy, Ajay P Singh, Maneesh Jain, Surinder K Batra. Atlas Genet Cytogenet Oncol Haematol 2008; Vol (12): 379-384. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/MUC16ID41455ch19q13.html MAML2 (mastermind-like 2) (11q21) - updated. Kazumi Suzukawa, Jean Loup Huret. Atlas Genet Cytogenet Oncol Haematol 2008; Vol (12): 385-390. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/MAML2ID472.html HYAL1 (hyaluronoglucosaminidase 1) (3p21.3).
    [Show full text]