DOCSLIB.ORG

Potential Role of WSB1 Isoforms in Growth and Survival of Neuroblastoma Cells

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Potential Role of WSB1 Isoforms in Growth and Survival of Neuroblastoma Cells nature publishing group Articles Basic Science Investigation Potential role of WSB1 isoforms in growth and survival of neuroblastoma cells Keren Shichrur1,2, Galina Feinberg-Gorenshtein1,2, Drorit Luria3, Shifra Ash3, Isaac Yaniv1,2,3 and Smadar Avigad1,2,3 BACKGROUND: WD repeat and SOCS box containing protein inhibition of their expression might be a new way of targeting 1 (WSB1) generates three isoforms that were found to play a NB. WD repeat and SOCS box containing protein 1 (WSB1) role in cancer cell growth and tumor progression. We have was described before as a potential stress-induced gene that studied their expression in neuroblastoma (NB). supports pancreatic tumor progression by modulating the METHODS: The behavior of the expression levels of the WSB1 alternative splicing of three isoforms after exposure to sev- isoforms was analyzed in NB cell lines, in an in vivo NB xenograft eral stress signals (10). Moreover, Chen et al. (11) had already mouse model, and in primary NB tumors using real-time PCR. identified WSB1 to have a gene dosage effect and reported Effective WSB1 small interfering RNAs were transfected into that its high expression is associated with better survival in cultured NB cell lines, and cell viability was analyzed using XTT NB patients. Our main purpose in this study was to examine assay and flow cytometry. the behavior of the expression levels of the WSB1 isoforms in RESULTS: A significant predominance of the WSB1 isoform 3 several NB cell systems and to understand the role of WSB1 (WSB13) expression level was demonstrated in all NB systems isoforms in relation to NB tumors using small interfering RNA examined. Correspondingly, combination of WSB13 silencing (siRNA) technology. In this article, we describe a significant together with WSB1 isoforms 1+2 silencing in NB cells showed predominance of specific WSB1 isoform in all NB cell systems reduced growth, enhanced apoptosis rate, and increased sen- examined and its role in tumor cell growth. We suggest that sitivity to chemotherapeutic agents, specifically related to low modulation of WSB1 isoforms might be a potential option for expression of WSB13. therapy in NB. CONCLUSION: Our results point to a possible differential role of WSB1 isoforms in NB and suggest WSB13 as a target for ther- RESULTS apy in NB. WSB1 Expression in NB Cell Lines, Tumor Xenografts, and Primary NB Tumors The WSB1 gene generates, by alternative splicing, three euroblastoma (NB) is one of the most common pediat- variant transcripts encoding distinct protein isoforms. We Nric solid tumors in children aged ≤5 years and accounts developed a specific primer assay to analyze independently for 15% of all pediatric cancer deaths (1). NB tumors exhibit the expression of WSB1 isoforms 1+2 (WSB11+2) and isoform a remarkable heterogeneity with respect to clinical behavior, 3 (WSB13) by real-time quantitative PCR (RQ-PCR). First, ranging from spontaneous regression or differentiation with the expression levels of WSB1 isoforms were measured in favorable outcome to a rapid progression with poor outcome, four human NB cell lines (SK-N-SH, SH-SY5Y, IMR32, and despite multimodal therapy (2–5). This extreme clinical het- SH-EP). As shown in Figure 1a, the relative expression level erogeneity reflects the complexity of the events associated with of WSB13 was two- to fivefold higher than the expression development and progression of the disease. Analyzing the of WSB11+2 in all cell lines studied. In order to measure the changes in gene expression at diagnosis and during NB tumor expression of WSB1 isoforms in vivo, we developed an NB progression could lead to the understanding of the molecular mouse xenograft model. Injection of 107 MNA (MYCN gene characteristics of NB tumor initiation and progression pro- amplified) Nub6 cells subcutaneously resulted in the estab- cesses and, eventually, to improvement in therapy. NB tumor lishment of tumors in 100% of 6- to 8-week-old nonobese progression is accompanied by changes in gene expression diabetic/severe combined immunodeficiency (NOD/SCID) affecting angiogenesis, invasion, proliferation, and apoptosis, mice within a few days after injection. Two weeks after injec- as well as hypoxia and resistance to chemotherapeutic agents tion, all 34 mice showed generation of a tumor. RNA was (6–9). The identification of genes involved in these processes extracted from the tumors, and the expression levels of WSB1 could lead to a significant improvement in understanding isoforms were measured using our RQ-PCR-specific primer the molecular mechanisms of NB tumor development, and assay. The relative expression level of the WSB13 isoform 1Molecular Oncology, Felsenstein Medical Research Center, Petah Tikva, Israel; 2Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; 3Pediatric Hematology Oncology Center, Schneider Children’s Medical Center of Israel, Petah Tikva, Israel. Correspondence: Smadar Avigad ([email protected]) Received 10 October 2012; accepted 1 October 2013; advance online publication 12 February 2014. doi:10.1038/pr.2014.2 482 Pediatric ResearcH Volume 75 | Number 4 | April 2014 Copyright © 2014 International Pediatric Research Foundation, Inc. WSB1 isoforms in neuroblastoma Articles in the xenograft tumor cells was 4.7-fold higher than the WSB1 Enhances Cell Proliferation expression of WSB11+2 (Figure 1b). Interestingly, the same The function of WSB1, particularly of the WSB13 isoform, in cell line grown in vitro showed only 2.1-fold increase, sug- human cancer is mostly unknown. We investigated the role of gesting a possible role of WSB13/WSB11+2 ratio in tumor cell WSB1 isoforms in cell viability and apoptosis by XTT assay and development. flow cytometry (fluorescence-activated cell sorting analysis). Finally, we analyzed the expression pattern of WSB11+2 and We inhibited WSB1 expression by transfecting SK-N-SH and WSB13 isoforms in six primary NB MNA tumor samples. SH-EP NB cell lines with several siRNAs that target the three Average expression level of WSB13 isoform was again 26-fold isoforms. Twenty four to 72 h following transfection, siRNA1 higher than WSB11+2 expression level, indicating the pre- efficiently caused a reduction of 90–95% of WSB11+2 expres- dominance of the WSB13 isoform also in primary NB samples sion levels and a 60–70% reduction of WSB13, whereas siRNA2 (Figure 1b). reduced mostly WSB11+2 expression (90–95% of WSB11+2 and only 10–20% of WSB13; Figure 2). We were not able to tar- 3 a 0.12 get the WSB1 isoform specifically by siRNAs in a sufficient manner. Our assay enabled us to study the effect of WSB13 downregulation using two silenced cell lines, each represent- 0.1 ing different expression levels of the WSB13 isoform. To assess the effect of WSB1 isoform reduction on cell viabil- els v 0.08 ity, the siRNA1- and siRNA2-silenced cell lines were analyzed using XTT viability assay and compared with untransfected cell line. Results indicate that cells transfected with WSB1 0.06 siRNA1 are less viable than control cells or cells transfected xpression le e with siRNA2. Forty-eight hours after transfection, only 45% 0.04 of the cells were viable in the siRNA1-transfected cells (Figure Relativ 3a). Apoptosis in the siRNA1-transfected cells was two- to threefold higher than that in siRNA2-transfected and con- 0.02 trol cells, indicating that the levels of WSB13 are responsible for this effect (Figure 3b). In fact, siRNA2-silenced cells dis- 0 played similar characteristics when compared with the control SK-N-SH SH-EP SH-SY5Y IMR32 cells, suggesting that WSB11+2 silencing alone had no effect on cell viability. Similar results were obtained with SK-N-SH b 3 cells (data not shown). Taken together, these results strongly 100 2.5 ** 90 els v 2 80 70 1.5 xpression le e 60 1 xpression * 50 Relativ e 40 0.5 % Relativ 30 0 NB cell lines Mouse NB primary 20 xenograft tumors tumors 10 Figure 1. WD repeat and SOCS box containing protein 1 isoform 3 0 (WSB13) is highly expressed in mice neuroblastoma (NB) xenografts and Control siRNAi1 siRNAi2 human NB cell lines. (a) Relative expression of WSB11+2 (black bars) and WSB13 (white bars) mRNAs was assessed by real-time quantitative PCR Figure 2. WD repeat and SOCS box-containing protein 1 (WSB1) (RQ-PCR) in four NB cell lines (SK-N-SH, SH-EP, SH-SY5Y, and IMR32). (b) downregulation in neuroblastoma (NB)-silenced cell line. Expression of Average expression of WSB11+2 (black bars) and WSB13 (white bars) mRNAs WSB11+2 (black bars) and WSB13 (white bars) mRNAs is shown in SH-EP was assessed by RQ-PCR of 5 NB cell lines (SK-N-SH, SH-EP, SH-SY5Y, IMR32, cells transfected with small interfering RNA (siRNA) 1 and siRNA2 directed and Nub6), 34 xenografted tumors, and 6 primary NB MNA tumor samples. against WSB1. Values are expressed as the mean ± SE of results performed Values are expressed as the mean ± SE (*P < 0.05; **P < 0.0001). in duplicates. Copyright © 2014 International Pediatric Research Foundation, Inc. Volume 75 | Number 4 | April 2014 Pediatric ResearcH 483 Articles Shichrur et al. a a 1.6 1.4 1.4 1.2 1.2 1 1 0.8 * 0.8 0.6 ** 0.4 0.6 Absorbance (A570 nm/A630 nm) 0.2 0.4 0 Absorbance (A570 nm/A630 nm) 024 48 Time after transfection (h) 0.2 b 35 0 * 0 150 200 30 Doxorubicin (µmol/l) b 25 1.4 20 1.2 15 1 % Apoptotic cells 10 0.8 5 * 0 0.6 Control siRNAi1 siRNAi2 Figure 3. WD repeat and SOCS box containing protein 1 (WSB1) down- 0.4 regulation decreases cell growth. (a) Cell viability measured by XTT assay Absorbance (A570 nm/A630 nm) * in WSB1 siRNA1–transfected SH-EP cells (black circles), siRNA2-transfected 0.2 SH-EP cells (black squares), and untransfected SH-EP cells (white triangle) 24 and 48 h after transfection.
Load more

Recommended publications
  • 1 Supporting Information for a Microrna Network Regulates
    Supporting Information for A microRNA Network Regulates Expression and Biosynthesis of CFTR and CFTR-ΔF508 Shyam Ramachandrana,b, Philip H. Karpc, Peng Jiangc, Lynda S. Ostedgaardc, Amy E. Walza, John T. Fishere, Shaf Keshavjeeh, Kim A. Lennoxi, Ashley M. Jacobii, Scott D. Rosei, Mark A. Behlkei, Michael J. Welshb,c,d,g, Yi Xingb,c,f, Paul B. McCray Jr.a,b,c Author Affiliations: Department of Pediatricsa, Interdisciplinary Program in Geneticsb, Departments of Internal Medicinec, Molecular Physiology and Biophysicsd, Anatomy and Cell Biologye, Biomedical Engineeringf, Howard Hughes Medical Instituteg, Carver College of Medicine, University of Iowa, Iowa City, IA-52242 Division of Thoracic Surgeryh, Toronto General Hospital, University Health Network, University of Toronto, Toronto, Canada-M5G 2C4 Integrated DNA Technologiesi, Coralville, IA-52241 To whom correspondence should be addressed: Email: [email protected] (M.J.W.); yi- [email protected] (Y.X.); Email: [email protected] (P.B.M.) This PDF file includes: Materials and Methods References Fig. S1. miR-138 regulates SIN3A in a dose-dependent and site-specific manner. Fig. S2. miR-138 regulates endogenous SIN3A protein expression. Fig. S3. miR-138 regulates endogenous CFTR protein expression in Calu-3 cells. Fig. S4. miR-138 regulates endogenous CFTR protein expression in primary human airway epithelia. Fig. S5. miR-138 regulates CFTR expression in HeLa cells. Fig. S6. miR-138 regulates CFTR expression in HEK293T cells. Fig. S7. HeLa cells exhibit CFTR channel activity. Fig. S8. miR-138 improves CFTR processing. Fig. S9. miR-138 improves CFTR-ΔF508 processing. Fig. S10. SIN3A inhibition yields partial rescue of Cl- transport in CF epithelia.
    [Show full text]
  • Molecular Effects of Isoflavone Supplementation Human Intervention Studies and Quantitative Models for Risk Assessment
    Molecular effects of isoflavone supplementation Human intervention studies and quantitative models for risk assessment Vera van der Velpen Thesis committee Promotors Prof. Dr Pieter van ‘t Veer Professor of Nutritional Epidemiology Wageningen University Prof. Dr Evert G. Schouten Emeritus Professor of Epidemiology and Prevention Wageningen University Co-promotors Dr Anouk Geelen Assistant professor, Division of Human Nutrition Wageningen University Dr Lydia A. Afman Assistant professor, Division of Human Nutrition Wageningen University Other members Prof. Dr Jaap Keijer, Wageningen University Dr Hubert P.J.M. Noteborn, Netherlands Food en Consumer Product Safety Authority Prof. Dr Yvonne T. van der Schouw, UMC Utrecht Dr Wendy L. Hall, King’s College London This research was conducted under the auspices of the Graduate School VLAG (Advanced studies in Food Technology, Agrobiotechnology, Nutrition and Health Sciences). Molecular effects of isoflavone supplementation Human intervention studies and quantitative models for risk assessment Vera van der Velpen Thesis submitted in fulfilment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof. Dr M.J. Kropff, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Friday 20 June 2014 at 13.30 p.m. in the Aula. Vera van der Velpen Molecular effects of isoflavone supplementation: Human intervention studies and quantitative models for risk assessment 154 pages PhD thesis, Wageningen University, Wageningen, NL (2014) With references, with summaries in Dutch and English ISBN: 978-94-6173-952-0 ABSTRact Background: Risk assessment can potentially be improved by closely linked experiments in the disciplines of epidemiology and toxicology.
    [Show full text]
  • Nuclear PTEN Safeguards Pre-Mrna Splicing to Link Golgi Apparatus for Its Tumor Suppressive Role
    ARTICLE DOI: 10.1038/s41467-018-04760-1 OPEN Nuclear PTEN safeguards pre-mRNA splicing to link Golgi apparatus for its tumor suppressive role Shao-Ming Shen1, Yan Ji2, Cheng Zhang1, Shuang-Shu Dong2, Shuo Yang1, Zhong Xiong1, Meng-Kai Ge1, Yun Yu1, Li Xia1, Meng Guo1, Jin-Ke Cheng3, Jun-Ling Liu1,3, Jian-Xiu Yu1,3 & Guo-Qiang Chen1 Dysregulation of pre-mRNA alternative splicing (AS) is closely associated with cancers. However, the relationships between the AS and classic oncogenes/tumor suppressors are 1234567890():,; largely unknown. Here we show that the deletion of tumor suppressor PTEN alters pre-mRNA splicing in a phosphatase-independent manner, and identify 262 PTEN-regulated AS events in 293T cells by RNA sequencing, which are associated with significant worse outcome of cancer patients. Based on these findings, we report that nuclear PTEN interacts with the splicing machinery, spliceosome, to regulate its assembly and pre-mRNA splicing. We also identify a new exon 2b in GOLGA2 transcript and the exon exclusion contributes to PTEN knockdown-induced tumorigenesis by promoting dramatic Golgi extension and secretion, and PTEN depletion significantly sensitizes cancer cells to secretion inhibitors brefeldin A and golgicide A. Our results suggest that Golgi secretion inhibitors alone or in combination with PI3K/Akt kinase inhibitors may be therapeutically useful for PTEN-deficient cancers. 1 Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200025, China. 2 Institute of Health Sciences, Shanghai Institutes for Biological Sciences of Chinese Academy of Sciences and SJTU-SM, Shanghai 200025, China.
    [Show full text]
  • Viewed and Published Immediately Upon Acceptance Cited in Pubmed and Archived on Pubmed Central Yours — You Keep the Copyright
    BMC Genomics BioMed Central Research article Open Access Differential gene expression in ADAM10 and mutant ADAM10 transgenic mice Claudia Prinzen1, Dietrich Trümbach2, Wolfgang Wurst2, Kristina Endres1, Rolf Postina1 and Falk Fahrenholz*1 Address: 1Johannes Gutenberg-University, Institute of Biochemistry, Mainz, Johann-Joachim-Becherweg 30, 55128 Mainz, Germany and 2Helmholtz Zentrum München – German Research Center for Environmental Health, Institute for Developmental Genetics, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany Email: Claudia Prinzen - [email protected]; Dietrich Trümbach - [email protected]; Wolfgang Wurst - [email protected]; Kristina Endres - [email protected]; Rolf Postina - [email protected]; Falk Fahrenholz* - [email protected] * Corresponding author Published: 5 February 2009 Received: 19 June 2008 Accepted: 5 February 2009 BMC Genomics 2009, 10:66 doi:10.1186/1471-2164-10-66 This article is available from: http://www.biomedcentral.com/1471-2164/10/66 © 2009 Prinzen et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: In a transgenic mouse model of Alzheimer disease (AD), cleavage of the amyloid precursor protein (APP) by the α-secretase ADAM10 prevented amyloid plaque formation, and alleviated cognitive deficits. Furthermore, ADAM10 overexpression increased the cortical synaptogenesis. These results suggest that upregulation of ADAM10 in the brain has beneficial effects on AD pathology. Results: To assess the influence of ADAM10 on the gene expression profile in the brain, we performed a microarray analysis using RNA isolated from brains of five months old mice overexpressing either the α-secretase ADAM10, or a dominant-negative mutant (dn) of this enzyme.
    [Show full text]
  • 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
    [Show full text]
  • WSB1: from Homeostasis to Hypoxia Moinul Haque1,2,3, Joseph Keith Kendal1,2,3, Ryan Matthew Macisaac1,2,3 and Douglas James Demetrick1,2,3,4*
    Haque et al. Journal of Biomedical Science (2016) 23:61 DOI 10.1186/s12929-016-0270-3 REVIEW Open Access WSB1: from homeostasis to hypoxia Moinul Haque1,2,3, Joseph Keith Kendal1,2,3, Ryan Matthew MacIsaac1,2,3 and Douglas James Demetrick1,2,3,4* Abstract The wsb1 gene has been identified to be important in developmental biology and cancer. A complex transcriptional regulation of wsb1 yields at least three functional transcripts. The major expressed isoform, WSB1 protein, is a substrate recognition protein within an E3 ubiquitin ligase, with the capability to bind diverse targets and mediate ubiquitinylation and proteolytic degradation. Recent data suggests a new role for WSB1 as a component of a neuroprotective pathway which results in modification and aggregation of neurotoxic proteins such as LRRK2 in Parkinson’s Disease, via an unusual mode of protein ubiquitinylation. WSB1 is also involved in thyroid hormone homeostasis, immune regulation and cellular metabolism, particularly glucose metabolism and hypoxia. In hypoxia, wsb1 is a HIF-1 target, and is a regulator of the degradation of diverse proteins associated with the cellular response to hypoxia, including HIPK2, RhoGDI2 and VHL. Major roles are to both protect HIF-1 function through degradation of VHL, and decrease apoptosis through degradation of HIPK2. These activities suggest a role for wsb1 in cancer cell proliferation and metastasis. As well, recent work has identified a role for WSB1 in glucose metabolism, and perhaps in mediating the Warburg effect in cancer cells by maintaining the function of HIF1. Furthermore, studies of cancer specimens have identified dysregulation of wsb1 associated with several types of cancer, suggesting a biologically relevant role in cancer development and/or progression.
    [Show full text]
  • Hypoxia-Induced WSB1 Promotes the Metastatic Potential Of
    Published OnlineFirst September 30, 2015; DOI: 10.1158/0008-5472.CAN-15-0711 Cancer Molecular and Cellular Pathobiology Research Hypoxia-Induced WSB1 Promotes the Metastatic Potential of Osteosarcoma Cells Ji Cao1, Yijie Wang1, Rong Dong1, Guanyu Lin1, Ning Zhang2, Jing Wang3, Nengming Lin4, Yongchuan Gu5, Ling Ding1, Meidan Ying1, Qiaojun He1, and Bo Yang1 Abstract Intratumoral hypoxia occurs in many solid tumors, where it is titative proteomic and functional analyses revealed that WSB1 associated with the development of metastatic character. How- ubiquitylates the Rho-binding protein RhoGDI2 and promotes its ever, the connections between these phenomena are not fully proteasomal degradation, thereby activating Rac1 to stimulate understood. In this study, we define an integrative role for the E3 tumor cell motility and invasion. Our findings show how WSB1 ubiquitin ligase subunit WSB1. In primary osteosarcomas, regulates key steps of the metastatic cascade in hypoxia-driven increased levels of WSB1 correlated with pulmonary metastatic osteosarcoma, and they highlight a candidate therapeutic target potential. RNAi-mediated attenuation of WSB1 or disruption of to potentially improve the survival of patients with metastatic its E3 ligase activity potently suppressed tumor metastasis. Quan- disease. Cancer Res; 75(22); 1–13. Ó2015 AACR. Introduction most types of solid tumors, including osteosarcoma (7-10). Hypoxia-inducible factor-1 alpha (HIF1a), a transcription factor Osteosarcomaisthemostcommontypeofbonecancerthat that is stabilized in hypoxia, regulates the expression of multiple usually occurs in juvenile groups (1,2). Despite remarkable target genes to help tumor cells adapt to and survive in hypoxic advances in the combined used of chemotherapy, radiotherapy conditions, contributing to poor chemotherapy responses, as well and surgical ablation of the primary tumor, survival rates have as decreased overall survival and disease-free survival in osteo- yet to improve over those of the 1970s (3).
    [Show full text]
  • Association of Cnvs with Methylation Variation
    www.nature.com/npjgenmed ARTICLE OPEN Association of CNVs with methylation variation Xinghua Shi1,8, Saranya Radhakrishnan2, Jia Wen1, Jin Yun Chen2, Junjie Chen1,8, Brianna Ashlyn Lam1, Ryan E. Mills 3, ✉ ✉ Barbara E. Stranger4, Charles Lee5,6,7 and Sunita R. Setlur 2 Germline copy number variants (CNVs) and single-nucleotide polymorphisms (SNPs) form the basis of inter-individual genetic variation. Although the phenotypic effects of SNPs have been extensively investigated, the effects of CNVs is relatively less understood. To better characterize mechanisms by which CNVs affect cellular phenotype, we tested their association with variable CpG methylation in a genome-wide manner. Using paired CNV and methylation data from the 1000 genomes and HapMap projects, we identified genome-wide associations by methylation quantitative trait locus (mQTL) analysis. We found individual CNVs being associated with methylation of multiple CpGs and vice versa. CNV-associated methylation changes were correlated with gene expression. CNV-mQTLs were enriched for regulatory regions, transcription factor-binding sites (TFBSs), and were involved in long- range physical interactions with associated CpGs. Some CNV-mQTLs were associated with methylation of imprinted genes. Several CNV-mQTLs and/or associated genes were among those previously reported by genome-wide association studies (GWASs). We demonstrate that germline CNVs in the genome are associated with CpG methylation. Our findings suggest that structural variation together with methylation may affect cellular phenotype. npj Genomic Medicine (2020) 5:41 ; https://doi.org/10.1038/s41525-020-00145-w 1234567890():,; INTRODUCTION influence transcript regulation is DNA methylation, which involves The extent of genetic variation that exists in the human addition of a methyl group to cytosine residues within a CpG population is continually being characterized in efforts to identify dinucleotide.
    [Show full text]
  • WSB1 (Human) Recombinant Protein (P01)
    WSB1 (Human) Recombinant Protein (P01) Catalog # : H00026118-P01 規格 : [ 10 ug ] [ 25 ug ] List All Specification Application Image Product Human WSB1 full-length ORF ( AAH21110, 1 a.a. - 421 a.a.) Enzyme-linked Immunoabsorbent Assay Description: recombinant protein with GST-tag at N-terminal. Western Blot (Recombinant Sequence: MASFPPRVNEKEIVRLRTIGELLAPAAPFDKKCGRENWTVAFAPDGSYF protein) AWSQGHRTVKLVPWSQCLQNFLLHGTKNVTNSSSLRLPRQNSDGGQK NKPREHIIDCGDIVWSLAFGSSVPEKQSRCVNIEWHRFRFGQDQLLLATG Antibody Production LNNGRIKIWDVYTGKLLLNLVDHTEVVRDLTFAPDGSLILVSASRDKTLRV WDLKDDGNMMKVLRGHQDWVYSCAFSPDSSMLCSVGASKAVFLWNM Protein Array DKYTMIRKLEGHHHDVVACDFSPDGALLATASYDTRVYIWDPHNGDILME FGRLFPPPTPIFAGGANDRWVRSVSFSHDGLHVASLADDKMVRFWRIDE DYPVQVAPLSNGLCCAFSTDGSVLAAGTHDGSVYFWATPRQVPSLQHL CRMSIRRVMPTQEVQELPIPSKLLEFLSYRI Host: Wheat Germ (in vitro) Theoretical MW 72.05 (kDa): Preparation in vitro wheat germ expression system Method: Purification: Glutathione Sepharose 4 Fast Flow Quality Control 12.5% SDS-PAGE Stained with Coomassie Blue. Testing: Storage Buffer: 50 mM Tris-HCI, 10 mM reduced Glutathione, pH=8.0 in the elution buffer. Storage Store at -80°C. Aliquot to avoid repeated freezing and thawing. Instruction: Note: Best use within three months from the date of receipt of this protein. MSDS: Download Datasheet: Download Applications Enzyme-linked Immunoabsorbent Assay Page 1 of 2 2016/5/23 Western Blot (Recombinant protein) Antibody Production Protein Array Gene Information Entrez GeneID: 26118 GeneBank BC021110 Accession#: Protein AAH21110 Accession#: Gene
    [Show full text]
  • UC San Diego Electronic Theses and Dissertations
    UC San Diego UC San Diego Electronic Theses and Dissertations Title Cardiac Stretch-Induced Transcriptomic Changes are Axis-Dependent Permalink https://escholarship.org/uc/item/7m04f0b0 Author Buchholz, Kyle Stephen Publication Date 2016 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, SAN DIEGO Cardiac Stretch-Induced Transcriptomic Changes are Axis-Dependent A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Bioengineering by Kyle Stephen Buchholz Committee in Charge: Professor Jeffrey Omens, Chair Professor Andrew McCulloch, Co-Chair Professor Ju Chen Professor Karen Christman Professor Robert Ross Professor Alexander Zambon 2016 Copyright Kyle Stephen Buchholz, 2016 All rights reserved Signature Page The Dissertation of Kyle Stephen Buchholz is approved and it is acceptable in quality and form for publication on microfilm and electronically: Co-Chair Chair University of California, San Diego 2016 iii Dedication To my beautiful wife, Rhia. iv Table of Contents Signature Page ................................................................................................................... iii Dedication .......................................................................................................................... iv Table of Contents ................................................................................................................ v List of Figures ...................................................................................................................
    [Show full text]
  • Content Based Search in Gene Expression Databases and a Meta-Analysis of Host Responses to Infection
    Content Based Search in Gene Expression Databases and a Meta-analysis of Host Responses to Infection A Thesis Submitted to the Faculty of Drexel University by Francis X. Bell in partial fulfillment of the requirements for the degree of Doctor of Philosophy November 2015 c Copyright 2015 Francis X. Bell. All Rights Reserved. ii Acknowledgments I would like to acknowledge and thank my advisor, Dr. Ahmet Sacan. Without his advice, support, and patience I would not have been able to accomplish all that I have. I would also like to thank my committee members and the Biomed Faculty that have guided me. I would like to give a special thanks for the members of the bioinformatics lab, in particular the members of the Sacan lab: Rehman Qureshi, Daisy Heng Yang, April Chunyu Zhao, and Yiqian Zhou. Thank you for creating a pleasant and friendly environment in the lab. I give the members of my family my sincerest gratitude for all that they have done for me. I cannot begin to repay my parents for their sacrifices. I am eternally grateful for everything they have done. The support of my sisters and their encouragement gave me the strength to persevere to the end. iii Table of Contents LIST OF TABLES.......................................................................... vii LIST OF FIGURES ........................................................................ xiv ABSTRACT ................................................................................ xvii 1. A BRIEF INTRODUCTION TO GENE EXPRESSION............................. 1 1.1 Central Dogma of Molecular Biology........................................... 1 1.1.1 Basic Transfers .......................................................... 1 1.1.2 Uncommon Transfers ................................................... 3 1.2 Gene Expression ................................................................. 4 1.2.1 Estimating Gene Expression ............................................ 4 1.2.2 DNA Microarrays ......................................................
    [Show full text]
  • (NF1) As a Breast Cancer Driver
    INVESTIGATION Comparative Oncogenomics Implicates the Neurofibromin 1 Gene (NF1) as a Breast Cancer Driver Marsha D. Wallace,*,† Adam D. Pfefferle,‡,§,1 Lishuang Shen,*,1 Adrian J. McNairn,* Ethan G. Cerami,** Barbara L. Fallon,* Vera D. Rinaldi,* Teresa L. Southard,*,†† Charles M. Perou,‡,§,‡‡ and John C. Schimenti*,†,§§,2 *Department of Biomedical Sciences, †Department of Molecular Biology and Genetics, ††Section of Anatomic Pathology, and §§Center for Vertebrate Genomics, Cornell University, Ithaca, New York 14853, ‡Department of Pathology and Laboratory Medicine, §Lineberger Comprehensive Cancer Center, and ‡‡Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27514, and **Memorial Sloan-Kettering Cancer Center, New York, New York 10065 ABSTRACT Identifying genomic alterations driving breast cancer is complicated by tumor diversity and genetic heterogeneity. Relevant mouse models are powerful for untangling this problem because such heterogeneity can be controlled. Inbred Chaos3 mice exhibit high levels of genomic instability leading to mammary tumors that have tumor gene expression profiles closely resembling mature human mammary luminal cell signatures. We genomically characterized mammary adenocarcinomas from these mice to identify cancer-causing genomic events that overlap common alterations in human breast cancer. Chaos3 tumors underwent recurrent copy number alterations (CNAs), particularly deletion of the RAS inhibitor Neurofibromin 1 (Nf1) in nearly all cases. These overlap with human CNAs including NF1, which is deleted or mutated in 27.7% of all breast carcinomas. Chaos3 mammary tumor cells exhibit RAS hyperactivation and increased sensitivity to RAS pathway inhibitors. These results indicate that spontaneous NF1 loss can drive breast cancer. This should be informative for treatment of the significant fraction of patients whose tumors bear NF1 mutations.
    [Show full text]