A Database of Transcription Factors Involved in Lymphocyte Development
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Integrase Interactor 1 (INI-1) Deficient Renal Cell Carcinoma
Open Access Case Report DOI: 10.7759/cureus.13082 Integrase Interactor 1 (INI-1) Deficient Renal Cell Carcinoma Manpreet Singh 1 , Harkirat Singh 1 , Benjamin Hambro 1 , Jasleen Kaur 1 , Ravi Rao 2 1. Internal Medicine, St Agnes Medical Center, Fresno, USA 2. Hematology and Oncology, St Agnes Medical Center, Fresno, USA Corresponding author: Manpreet Singh, [email protected] Abstract Members of the SWItch/sucrose nonfermentable (SWI-SNF) family, including SWI/SNF related, matrix- associated, actin-dependent regulator of chromatin, subfamily A, member 4 (SMARCA4), SWI/SNF related, matrix‐associated, actin‐dependent regulator of chromatin, subfamily B member 1 (SMARCB1)/integrase interactor 1 (INI-1) are known tumor suppressor genes. Interactions between SMARCB1/INI-1 and key protein components in various cellular pathways are related to tumor progression and proliferation. SMARCB1/INI-1 protein was undetectable in rhabdoid tumor cells, whereas non-tumorous cells express the SMARCB1/INI-1 genes. Germline and sporadic mutations of several genes encoding for proteins in this complex are known to cause a spectrum of cancers, usually with sarcomatoid features which include a very aggressive renal medullary carcinoma. We report a case of a 29-year-old male who presented with SMARCA4 deficient renal tumor with a very aggressive clinical behavior which ultimately led to his death. Categories: Nephrology, Oncology Keywords: renal medullary carcinoma, ini-1, renal cell carcinoma, swi/snf, smarcb1, integrase interactor 1 Introduction Renal medullary carcinoma is a rare and very aggressive malignancy affecting young adults with rare cases in patients with sickle cell disease or trait [1]. The tumor arises predominantly in the renal medulla and exhibits a variety of growth patterns including reticular, solid, tubular, trabecular, cribriform, sarcomatoid, and micropapillary [1]. -
Bioinformatics Applications Through Visualization of Variations on Protein
1 Bioinformatics applications through visualization of variations on protein structures, comparative functional genomics, and comparative modeling for protein structure studies A dissertation presented by Alper Uzun to The Department of Biology In partial fulfillment of the requirements for the degree of Doctor of Philosophy in the field of Biology Northeastern University Boston, Massachusetts July 2009 2 ©2009 Alper Uzun ALL RIGHTS RESERVED 3 Bioinformatics applications through visualization of variations on protein structures, comparative functional genomics, and comparative modeling for protein structure studies by Alper Uzun ABSTRACT OF DISSERTATION Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biology in the Graduate School of Arts and Sciences of Northeastern University, July, 2009 4 Abstract The three-dimensional structure of a protein provides important information for understanding and answering many biological questions in molecular detail. The rapidly growing number of sequenced genes and related genomic information is intensively accumulating in the biological databases. It is significantly important to combine biological data and developing bioinformatics tools while information of protein sequences, structures and DNA sequences are exponentially growing. On the other hand, especially the number of known protein sequences is much larger than the number of experimentally solved protein structures. However the experimental methods cannot always be applied or protein structures -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Loss of Integrase Interactor 1 (INI1) Expression in a Subset of Differentiated Thyroid Cancer
diagnostics Article Loss of Integrase Interactor 1 (INI1) Expression in a Subset of Differentiated Thyroid Cancer Kung-Chen Ho 1, Jie-Jen Lee 1, Chi-Hsin Lin 2,3, Ching-Hsiang Leung 4 and Shih-Ping Cheng 1,5,* 1 Department of Surgery, MacKay Memorial Hospital and Mackay Medical College, Taipei 104215, Taiwan; [email protected] (K.-C.H.); [email protected] (J.-J.L.) 2 Department of Medical Research, MacKay Memorial Hospital, Taipei 104215, Taiwan; [email protected] 3 Department of Bioscience Technology, Chung Yuan Christian University, Taoyuan City 320314, Taiwan 4 Division of Endocrinology and Metabolism, Department of Internal Medicine, MacKay Memorial Hospital and Mackay Medical College, Taipei 104215, Taiwan; [email protected] 5 Department of Pharmacology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan * Correspondence: [email protected]; Tel.: +886-2-2543-3535 Received: 19 April 2020; Accepted: 2 May 2020; Published: 5 May 2020 Abstract: Alterations in the switching defective/sucrose non-fermenting (SWI/SNF) chromatin-remodeling complex are enriched in advanced thyroid cancer. Integrase interactor 1 (INI1), encoded by the SMARCB1 gene on the long arm of chromosome 22, is one of the core subunits of the SWI/SNF complex. INI1 immunohistochemistry is frequently used for the diagnosis of malignant rhabdoid neoplasms. In the present study, we found normal and benign thyroid tissues generally had diffusely intense nuclear immunostaining. Loss of INI1 immunohistochemical expression was observed in 8% of papillary thyroid cancer and 30% of follicular thyroid cancer. Furthermore, loss of INI1 expression was associated with extrathyroidal extension (p < 0.001) and lymph node metastasis (p = 0.038). -
Renal Medullary Carcinomas Depend Upon SMARCB1 Loss And
RESEARCH ARTICLE Renal medullary carcinomas depend upon SMARCB1 loss and are sensitive to proteasome inhibition Andrew L Hong1,2,3, Yuen-Yi Tseng3, Jeremiah A Wala3, Won-Jun Kim2, Bryan D Kynnap2, Mihir B Doshi3, Guillaume Kugener3, Gabriel J Sandoval2,3, Thomas P Howard2, Ji Li2, Xiaoping Yang3, Michelle Tillgren2, Mahmhoud Ghandi3, Abeer Sayeed3, Rebecca Deasy3, Abigail Ward1,2, Brian McSteen4, Katherine M Labella2, Paula Keskula3, Adam Tracy3, Cora Connor5, Catherine M Clinton1,2, Alanna J Church1, Brian D Crompton1,2,3, Katherine A Janeway1,2, Barbara Van Hare4, David Sandak4, Ole Gjoerup2, Pratiti Bandopadhayay1,2,3, Paul A Clemons3, Stuart L Schreiber3, David E Root3, Prafulla C Gokhale2, Susan N Chi1,2, Elizabeth A Mullen1,2, Charles WM Roberts6, Cigall Kadoch2,3, Rameen Beroukhim2,3,7, Keith L Ligon2,3,7, Jesse S Boehm3, William C Hahn2,3,7* 1Boston Children’s Hospital, Boston, United States; 2Dana-Farber Cancer Institute, Boston, United States; 3Broad Institute of Harvard and MIT, Cambridge, United States; 4Rare Cancer Research Foundation, Durham, United States; 5RMC Support, North Charleston, United States; 6St. Jude Children’s Research Hospital, Memphis, United States; 7Brigham and Women’s Hospital, Boston, United States Abstract Renal medullary carcinoma (RMC) is a rare and deadly kidney cancer in patients of African descent with sickle cell trait. We have developed faithful patient-derived RMC models and using whole-genome sequencing, we identified loss-of-function intronic fusion events in one SMARCB1 allele with concurrent loss of the other allele. Biochemical and functional characterization of these models revealed that RMC requires the loss of SMARCB1 for survival. -
Identification of a Core Member of the SWI/SNF Complex, BAF155/SMARCC1, As a Human Tumor Suppressor Gene
RESEARCH PAPER Epigenetics 6:12, 1444-1453; December 2011; © 2011 Landes Bioscience Identification of a core member of the SWI/SNF complex, BAF155/SMARCC1, as a human tumor suppressor gene Jessica DelBove,1,6 Gary Rosson,2,7 Matthew Strobeck,3 Jianguang Chen,4 Trevor K. Archer,4 Weidong Wang,5 Erik S. Knudsen3 and Bernard E. Weissman1,2,* 1Department of Pathology and Laboratory Medicine; 2University of North Carolina-Lineberger Comprehensive Cancer Center; 7Department of Genetics; University of North Carolina; Chapel Hill, NC USA; 3Department of Cancer Biology and the Kimmel Cancer Center; Thomas Jefferson University; Philadelphia, PA USA; 4Chromatin and Gene Expression Section; Laboratory of Molecular Carcinogenesis; National Institute of Environmental Health Sciences; National Institutes of Health; Research Triangle Park, NC USA; 5Laboratory of Genetics; National Institute on Aging; National Institutes of Health; Baltimore, MD USA; 6Department of Hematology; University of Utah School of Medicine; Salt Lake City, UT USA Key words: SWI/SNF, BAF155, SMARCC1, tumor suppressor gene, cancer epigenetics Recent studies have established that two core members of the SWI/SNF chromatin remodeling complex, BRG1 and SNF5/ INI1, possess tumor-suppressor activity in human and mouse cancers. While the third core member, BAF155, has been implicated by several studies as having a potential role in tumor development, direct evidence for its tumor suppressor activity has remained lacking. Therefore, we screened for BAF155 deficiency in a large number of human tumor cell lines. We identified two cell lines, the SNUC2B colon carcinoma and the SKOV3 ovarian carcinoma, displaying a complete loss of protein expression while maintaining normal levels of mRNA expression. -
Leukocyte-Specific Adaptor Protein Grap2 Interacts with Hematopoietic
Oncogene (2001) 20, 1703 ± 1714 ã 2001 Nature Publishing Group All rights reserved 0950 ± 9232/01 $15.00 www.nature.com/onc Leukocyte-speci®c adaptor protein Grap2 interacts with hematopoietic progenitor kinase 1 (HPK1) to activate JNK signaling pathway in T lymphocytes Wenbin Ma1, Chunzhi Xia1, Pin Ling2, Mengsheng Qiu3, Ying Luo4, Tse-Hua Tan2 and Mingyao Liu*,1 1Department of Medical Biochemistry and Genetics, Center for Cancer Biology and Nutrition, Institute of Biosciences and Technology, Texas A&M University System Health Science Center, 2121 W. Holcombe Blvd., Houston, Texas, TX 77030, USA; 2Department of Immunology, Baylor College of Medicine, Houston, Texas, TX 77030, USA; 3Department of Anatomical Sciences and Neurobiology, School of Medicine, University of Louisville, Louisville, Kentucky, KY 40202, USA; 4Shanghai Genomics, Inc., Zhangjiang Hi-Tech Park, Pudong, Shangai 201204, P.R.C. Immune cell-speci®c adaptor proteins create various Introduction combinations of multiprotein complexes and integrate signals from cell surface receptors to the nucleus, Activation of resting T cells through the T-cell antigen modulating the speci®city and selectivity of intracellular receptor triggers a cascade of intracellular signaling signal transduction. Grap2 is a newly identi®ed adaptor events that lead to enhanced gene transcription, protein speci®cally expressed in lymphoid tissues. This cellular dierentiation and proliferation (Cantrell, protein shares 40 ± 50% sequence homology in the SH3 1996; Weiss and Littman, 1994; Chan and Shaw, and the SH2 domain with Grb2 and Grap. However, the 1996; Crabtree and Clipstone, 1994; Wange and Grap2 protein has a unique 120-amino acid glutamine- Samelson, 1996). Although components of the T-cell and proline-rich domain between the SH2 and C- receptor complex have no intrinsic kinase activity, the terminal SH3 domains. -
MALE Protein Name Accession Number Molecular Weight CP1 CP2 H1 H2 PDAC1 PDAC2 CP Mean H Mean PDAC Mean T-Test PDAC Vs. H T-Test
MALE t-test t-test Accession Molecular H PDAC PDAC vs. PDAC vs. Protein Name Number Weight CP1 CP2 H1 H2 PDAC1 PDAC2 CP Mean Mean Mean H CP PDAC/H PDAC/CP - 22 kDa protein IPI00219910 22 kDa 7 5 4 8 1 0 6 6 1 0.1126 0.0456 0.1 0.1 - Cold agglutinin FS-1 L-chain (Fragment) IPI00827773 12 kDa 32 39 34 26 53 57 36 30 55 0.0309 0.0388 1.8 1.5 - HRV Fab 027-VL (Fragment) IPI00827643 12 kDa 4 6 0 0 0 0 5 0 0 - 0.0574 - 0.0 - REV25-2 (Fragment) IPI00816794 15 kDa 8 12 5 7 8 9 10 6 8 0.2225 0.3844 1.3 0.8 A1BG Alpha-1B-glycoprotein precursor IPI00022895 54 kDa 115 109 106 112 111 100 112 109 105 0.6497 0.4138 1.0 0.9 A2M Alpha-2-macroglobulin precursor IPI00478003 163 kDa 62 63 86 72 14 18 63 79 16 0.0120 0.0019 0.2 0.3 ABCB1 Multidrug resistance protein 1 IPI00027481 141 kDa 41 46 23 26 52 64 43 25 58 0.0355 0.1660 2.4 1.3 ABHD14B Isoform 1 of Abhydrolase domain-containing proteinIPI00063827 14B 22 kDa 19 15 19 17 15 9 17 18 12 0.2502 0.3306 0.7 0.7 ABP1 Isoform 1 of Amiloride-sensitive amine oxidase [copper-containing]IPI00020982 precursor85 kDa 1 5 8 8 0 0 3 8 0 0.0001 0.2445 0.0 0.0 ACAN aggrecan isoform 2 precursor IPI00027377 250 kDa 38 30 17 28 34 24 34 22 29 0.4877 0.5109 1.3 0.8 ACE Isoform Somatic-1 of Angiotensin-converting enzyme, somaticIPI00437751 isoform precursor150 kDa 48 34 67 56 28 38 41 61 33 0.0600 0.4301 0.5 0.8 ACE2 Isoform 1 of Angiotensin-converting enzyme 2 precursorIPI00465187 92 kDa 11 16 20 30 4 5 13 25 5 0.0557 0.0847 0.2 0.4 ACO1 Cytoplasmic aconitate hydratase IPI00008485 98 kDa 2 2 0 0 0 0 2 0 0 - 0.0081 - 0.0 -
CD28 Costimulation in Jurkat Cells Signaling Networks Triggered By
Quantitative Analysis of Phosphotyrosine Signaling Networks Triggered by CD3 and CD28 Costimulation in Jurkat Cells This information is current as Ji-Eun Kim and Forest M. White of September 26, 2021. J Immunol 2006; 176:2833-2843; ; doi: 10.4049/jimmunol.176.5.2833 http://www.jimmunol.org/content/176/5/2833 Downloaded from References This article cites 47 articles, 22 of which you can access for free at: http://www.jimmunol.org/content/176/5/2833.full#ref-list-1 Why The JI? Submit online. http://www.jimmunol.org/ • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average by guest on September 26, 2021 Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2006 by The American Association of Immunologists All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Quantitative Analysis of Phosphotyrosine Signaling Networks Triggered by CD3 and CD28 Costimulation in Jurkat Cells1 Ji-Eun Kim and Forest M. White2 The mechanism by which stimulation of coreceptors such as CD28 contributes to full activation of TCR signaling pathways has been intensively studied, yet quantitative measurement of costimulation effects on functional TCR signaling networks has been lacking. -
Epidyne®-FRET for Nucleosome Remodeling Assays
Nucleosome Remodeling Assay by EpiDyne®-FRET EpiDyne®-FRET allows unprecedented access to disease-relevant ATP-dependent chromatin remodeling complexes FIGURE 3 SMARCA 2 SMARCA 4 EpiDyne®-FRET nucleosomes (20 nM) were incubated with Figure 3A Figure 3B chromatin remodeling enzyme (Panel 3A, SMARCA2; panel 3B, SMARCA4) at the indicated concentration in 4.0 3.5 the presence of ATP (2 mM). 3.5 Upon ATP addition, reactions 3.0 were immediately read in 3.0 an Envision Multi-label plate 2.5 reader. Data are presented as 2.5 the mean of the Cy3-Cy5 ratio 2.0 (N=2). 2.0 1.5 Cy3/Cy5 Ratio Cy3/Cy5 1.5 Ratio Cy3/Cy5 1.0 1.0 0 1 2 3 4 5 6 7 8 9 10 0 10 20 30 40 Time, Min Time, Min nM Enzyme nM Enzyme 28 14 7 3.5 0.0 12.50 6.25 3.13 1.56 0 ORDERING INFO Chromatin Remodeling Substrate, Fluorescent Readout Enzymes EpiDyne®-FRET Nucleosome Remodeling Assay Substrate SMARCA2 Chromatin Remodeling Enzyme Catalog No. 16-4201 (Human BRM) Pack Size: 50 μg Catalog No. 15-1015 Pack Size: 100 remodeling rxns Chromatin Remodeling Substrates, Non-Fluorescent Readout SMARCA4 Chromatin Remodeling Enzyme (Human BRG1) ST601-GATC1 ST601-GATC1, 50-N-66, Biotinylated Catalog No. 15-1014 Cat. No. 16-4101 Cat. No.: 16-4114 Pack Size: 100 remodeling rxns Pack Size: 50 μg Pack Size: 50 μg ACF Chromatin Remodeling Enzyme Complex ST601-GATC1, Biotinylated ST601-GATC1,2, 50-N-66, Biotinylated Catalog No. 15-1013 Cat. -
Missense Mutations in the Human Nanophthalmos Gene TMEM98 Cause Retinal Defects in the Mouse
Genetics Missense Mutations in the Human Nanophthalmos Gene TMEM98 Cause Retinal Defects in the Mouse Sally H. Cross,1 Lisa Mckie,1 Margaret Keighren,1 Katrine West,1 Caroline Thaung,2,3 Tracey Davey,4 Dinesh C. Soares,*,1 Luis Sanchez-Pulido,1 and Ian J. Jackson1 1MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom 2Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom 3University College London Institute of Ophthalmology, London, United Kingdom 4Electron Microscopy Research Services, Newcastle University, Newcastle, United Kingdom Correspondence: Sally H. Cross, PURPOSE. We previously found a dominant mutation, Rwhs, causing white spots on the retina MRC Human Genetics Unit, MRC accompanied by retinal folds. Here we identify the mutant gene to be Tmem98. In humans, Institute of Genetics and Molecular mutations in the orthologous gene cause nanophthalmos. We modeled these mutations in Medicine, University of Edinburgh, mice and characterized the mutant eye phenotypes of these and Rwhs. Crewe Road, Edinburgh EH4 2XU, UK; METHODS. The Rwhs mutation was identified to be a missense mutation in Tmem98 by genetic [email protected]. mapping and sequencing. The human TMEM98 nanophthalmos missense mutations were Current affiliation: *ACS International made in the mouse gene by CRISPR-Cas9. Eyes were examined by indirect ophthalmoscopy Ltd., Oxford, United Kingdom and the retinas imaged using a retinal camera. Electroretinography was used to study retinal function. Histology, immunohistochemistry, and electron microscopy techniques were used Submitted: October 10, 2018 Accepted: May 28, 2019 to study adult eyes. Citation: Cross SH, Mckie L, Keighren RESULTS. -
Recurrent Activating Mutations of CD28 in Peripheral T-Cell Lymphomas
Leukemia (2016), 1–9 © 2016 Macmillan Publishers Limited All rights reserved 0887-6924/16 www.nature.com/leu ORIGINAL ARTICLE Recurrent activating mutations of CD28 in peripheral T-cell lymphomas J Rohr1,2,14, S Guo3,14, J Huo4, A Bouska1, C Lachel1,YLi2, PD Simone5, W Zhang1, Q Gong2, C Wang1,2,6, A Cannon1, T Heavican1, A Mottok7,8, S Hung7,8, A Rosenwald9, R Gascoyne7,8,KFu1, TC Greiner1, DD Weisenburger2, JM Vose10, LM Staudt11, W Xiao12, GEO Borgstahl13, S Davis4, C Steidl7,8, T McKeithan2, J Iqbal1 and WC Chan2 Peripheral T-cell lymphomas (PTCLs) comprise a heterogeneous group of mature T-cell neoplasms with a poor prognosis. Recently, mutations in TET2 and other epigenetic modifiers as well as RHOA have been identified in these diseases, particularly in angioimmunoblastic T-cell lymphoma (AITL). CD28 is the major co-stimulatory receptor in T cells which, upon binding ligand, induces sustained T-cell proliferation and cytokine production when combined with T-cell receptor stimulation. We have identified recurrent mutations in CD28 in PTCLs. Two residues—D124 and T195—were recurrently mutated in 11.3% of cases of AITL and in one case of PTCL, not otherwise specified (PTCL-NOS). Surface plasmon resonance analysis of mutations at these residues with predicted differential partner interactions showed increased affinity for ligand CD86 (residue D124) and increased affinity for intracellular adaptor proteins GRB2 and GADS/GRAP2 (residue T195). Molecular modeling studies on each of these mutations suggested how these mutants result in increased affinities. We found increased transcription of the CD28-responsive genes CD226 and TNFA in cells expressing the T195P mutant in response to CD3 and CD86 co-stimulation and increased downstream activation of NF-κB by both D124V and T195P mutants, suggesting a potential therapeutic target in CD28-mutated PTCLs.