Next-Generation Sequencing Gene List
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Functions of the Mineralocorticoid Receptor in the Hippocampus By
Functions of the Mineralocorticoid Receptor in the Hippocampus by Aaron M. Rozeboom A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Cellular and Molecular Biology) in The University of Michigan 2008 Doctoral Committee: Professor Audrey F. Seasholtz, Chair Professor Elizabeth A. Young Professor Ronald Jay Koenig Associate Professor Gary D. Hammer Assistant Professor Jorge A. Iniguez-Lluhi Acknowledgements There are more people than I can possibly name here that I need to thank who have helped me throughout the process of writing this thesis. The first and foremost person on this list is my mentor, Audrey Seasholtz. Between working in her laboratory as a research assistant and continuing my training as a graduate student, I spent 9 years in Audrey’s laboratory and it would be no exaggeration to say that almost everything I have learned regarding scientific research has come from her. Audrey’s boundless enthusiasm, great patience, and eager desire to teach students has made my time in her laboratory a richly rewarding experience. I cannot speak of Audrey’s laboratory without also including all the past and present members, many of whom were/are not just lab-mates but also good friends. I also need to thank all the members of my committee, an amazing group of people whose scientific prowess combined with their open-mindedness allowed me to explore a wide variety of interests while maintaining intense scientific rigor. Outside of Audrey’s laboratory, there have been many people in Ann Arbor without whom I would most assuredly have gone crazy. -
KAT6A Syndrome: Genotype-Phenotype Correlation in 76 Patients with Pathogenic KAT6A Variants
KAT6A Syndrome: genotype-phenotype correlation in 76 patients with pathogenic KAT6A variants. Item Type Article Authors Kennedy, Joanna;Goudie, David;Blair, Edward;Chandler, Kate;Joss, Shelagh;McKay, Victoria;Green, Andrew;Armstrong, Ruth;Lees, Melissa;Kamien, Benjamin;Hopper, Bruce;Tan, Tiong Yang;Yap, Patrick;Stark, Zornitza;Okamoto, Nobuhiko;Miyake, Noriko;Matsumoto, Naomichi;Macnamara, Ellen;Murphy, Jennifer L;McCormick, Elizabeth;Hakonarson, Hakon;Falk, Marni J;Li, Dong;Blackburn, Patrick;Klee, Eric;Babovic- Vuksanovic, Dusica;Schelley, Susan;Hudgins, Louanne;Kant, Sarina;Isidor, Bertrand;Cogne, Benjamin;Bradbury, Kimberley;Williams, Mark;Patel, Chirag;Heussler, Helen;Duff- Farrier, Celia;Lakeman, Phillis;Scurr, Ingrid;Kini, Usha;Elting, Mariet;Reijnders, Margot;Schuurs-Hoeijmakers, Janneke;Wafik, Mohamed;Blomhoff, Anne;Ruivenkamp, Claudia A L;Nibbeling, Esther;Dingemans, Alexander J M;Douine, Emilie D;Nelson, Stanley F;Arboleda, Valerie A;Newbury-Ecob, Ruth DOI 10.1038/s41436-018-0259-2 Journal Genetics in medicine : official journal of the American College of Medical Genetics Download date 30/09/2021 21:53:13 Link to Item http://hdl.handle.net/10147/627191 Find this and similar works at - http://www.lenus.ie/hse HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Genet Med Manuscript Author . Author manuscript; Manuscript Author available in PMC 2019 October 01. Published in final edited form as: Genet Med. 2019 April ; 21(4): 850–860. doi:10.1038/s41436-018-0259-2. KAT6A Syndrome: Genotype-phenotype correlation in 76 patients with pathogenic KAT6A variants A full list of authors and affiliations appears at the end of the article. Abstract Purpose: Mutations in KAT6A have recently been identified as a cause of syndromic developmental delay. -
Molecular and Physiological Basis for Hair Loss in Near Naked Hairless and Oak Ridge Rhino-Like Mouse Models: Tracking the Role of the Hairless Gene
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 5-2006 Molecular and Physiological Basis for Hair Loss in Near Naked Hairless and Oak Ridge Rhino-like Mouse Models: Tracking the Role of the Hairless Gene Yutao Liu University of Tennessee - Knoxville Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Part of the Life Sciences Commons Recommended Citation Liu, Yutao, "Molecular and Physiological Basis for Hair Loss in Near Naked Hairless and Oak Ridge Rhino- like Mouse Models: Tracking the Role of the Hairless Gene. " PhD diss., University of Tennessee, 2006. https://trace.tennessee.edu/utk_graddiss/1824 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Yutao Liu entitled "Molecular and Physiological Basis for Hair Loss in Near Naked Hairless and Oak Ridge Rhino-like Mouse Models: Tracking the Role of the Hairless Gene." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the requirements for the degree of Doctor of Philosophy, with a major in Life Sciences. Brynn H. Voy, Major Professor We have read this dissertation and recommend its acceptance: Naima Moustaid-Moussa, Yisong Wang, Rogert Hettich Accepted for the Council: Carolyn R. -
Cells RI-Dependent Signal Transduction in Mast Ε Rhoh Plays
RhoH Plays Critical Roles in Fcε RI-Dependent Signal Transduction in Mast Cells This information is current as Hiroyo Oda, Manabu Fujimoto, Michael S. Patrick, Dai of October 2, 2021. Chida, Yoshinori Sato, Yoshinao Azuma, Hiroki Aoki, Takaya Abe, Harumi Suzuki and Mutsunori Shirai J Immunol 2009; 182:957-962; ; doi: 10.4049/jimmunol.182.2.957 http://www.jimmunol.org/content/182/2/957 Downloaded from References This article cites 45 articles, 13 of which you can access for free at: http://www.jimmunol.org/content/182/2/957.full#ref-list-1 http://www.jimmunol.org/ Why The JI? Submit online. • 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 by guest on October 2, 2021 *average 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 © 2009 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology RhoH Plays Critical Roles in FcRI-Dependent Signal Transduction in Mast Cells1 Hiroyo Oda,* Manabu Fujimoto,† Michael S. Patrick,*‡ Dai Chida,* Yoshinori Sato,* Yoshinao Azuma,‡ Hiroki Aoki,§ Takaya Abe,¶ Harumi Suzuki,2* and Mutsunori Shirai‡ RhoH is an atypical small G protein with defective GTPase activity that is specifically expressed in hematopoietic lineage cells. -
ONCOPANEL (Popv3)
ONCOPANEL (POPv3) TEST INFORMATION BACKGROUND: Somatic genetic alterations in oncogenes and tumor-suppressor genes contribute to the pathogenesis and evolution of human cancers. These alterations can provide prognostic and predictive information and stratify cancers for targeted therapeutic information. We classify these alterations into five tiers using the following guidelines: Tier 1: The alteration has well-established published evidence confirming clinical utility in this tumor type, in at least one of the following contexts: predicting response to treatment with an FDA-approved therapy; assessing prognosis; establishing a definitive diagnosis; or conferring an inherited increased risk of cancer to this patient and family. Tier 2: The alteration may have clinical utility in at least one of the following contexts: selection of an investigational therapy in clinical trials for this cancer type; limited evidence of prognostic association; supportive of a specific diagnosis; proven association of response to treatment with an FDA-approved therapy in a different type of cancer; or similar to a different mutation with a proven association with response to treatment with an FDA-approved therapyin this type of cancer. Tier 3: The alteration is of uncertain clinical utility, but may have a role as suggested by at least one of the following: demonstration of association with response to treatment in this cancer type in preclinical studies (e.g., in vitro studies or animal models); alteration in a biochemical pathway that has other known, therapeutically-targetable alterations; alteration in a highly conserved region of the protein predicted, in silico, to alter protein function; or selection of an investigational therapy for a different cancer type. -
Table S1 the Four Gene Sets Derived from Gene Expression Profiles of Escs and Differentiated Cells
Table S1 The four gene sets derived from gene expression profiles of ESCs and differentiated cells Uniform High Uniform Low ES Up ES Down EntrezID GeneSymbol EntrezID GeneSymbol EntrezID GeneSymbol EntrezID GeneSymbol 269261 Rpl12 11354 Abpa 68239 Krt42 15132 Hbb-bh1 67891 Rpl4 11537 Cfd 26380 Esrrb 15126 Hba-x 55949 Eef1b2 11698 Ambn 73703 Dppa2 15111 Hand2 18148 Npm1 11730 Ang3 67374 Jam2 65255 Asb4 67427 Rps20 11731 Ang2 22702 Zfp42 17292 Mesp1 15481 Hspa8 11807 Apoa2 58865 Tdh 19737 Rgs5 100041686 LOC100041686 11814 Apoc3 26388 Ifi202b 225518 Prdm6 11983 Atpif1 11945 Atp4b 11614 Nr0b1 20378 Frzb 19241 Tmsb4x 12007 Azgp1 76815 Calcoco2 12767 Cxcr4 20116 Rps8 12044 Bcl2a1a 219132 D14Ertd668e 103889 Hoxb2 20103 Rps5 12047 Bcl2a1d 381411 Gm1967 17701 Msx1 14694 Gnb2l1 12049 Bcl2l10 20899 Stra8 23796 Aplnr 19941 Rpl26 12096 Bglap1 78625 1700061G19Rik 12627 Cfc1 12070 Ngfrap1 12097 Bglap2 21816 Tgm1 12622 Cer1 19989 Rpl7 12267 C3ar1 67405 Nts 21385 Tbx2 19896 Rpl10a 12279 C9 435337 EG435337 56720 Tdo2 20044 Rps14 12391 Cav3 545913 Zscan4d 16869 Lhx1 19175 Psmb6 12409 Cbr2 244448 Triml1 22253 Unc5c 22627 Ywhae 12477 Ctla4 69134 2200001I15Rik 14174 Fgf3 19951 Rpl32 12523 Cd84 66065 Hsd17b14 16542 Kdr 66152 1110020P15Rik 12524 Cd86 81879 Tcfcp2l1 15122 Hba-a1 66489 Rpl35 12640 Cga 17907 Mylpf 15414 Hoxb6 15519 Hsp90aa1 12642 Ch25h 26424 Nr5a2 210530 Leprel1 66483 Rpl36al 12655 Chi3l3 83560 Tex14 12338 Capn6 27370 Rps26 12796 Camp 17450 Morc1 20671 Sox17 66576 Uqcrh 12869 Cox8b 79455 Pdcl2 20613 Snai1 22154 Tubb5 12959 Cryba4 231821 Centa1 17897 -
Expression of Rho Gtpases Family in Melanoma Cells and Its Influence on Cytoskeleton and Migration
www.impactjournals.com/oncotarget/ Oncotarget, 2017, Vol. 8, (No. 18), pp: 30112-30122 Research Paper Expression of Rho GTPases family in melanoma cells and its influence on cytoskeleton and migration Si-Jian Wen1,2, Wei Zhang2, Na-Na Ni3, Qiong Wu2, Xiao-Po Wang2, You-Kun Lin1 Jian-Fang Sun2 1Department of Dermatology and Venerology, First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China 2Department of Pathology, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China 3Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing 210042, China Correspondence to: You-Kun Lin, email: [email protected] Jian-Fang Sun, email: [email protected] Keywords: Rho GTPase, melanoma, cytoskeleton, cell migration Received: November 01, 2016 Accepted: January 11, 2017 Published: February 22, 2017 Copyright: Wen et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC-BY), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT Rho GTPases family members influenced the filopodia, lamellipodia, stress fiber and adhesion plaque of melanoma cells through regulating cytoskeleton recombination. The role of Rho GTPases family in the migration and invasion of melanoma and its molecular mechanism were explored. The morphological difference between three types of melanoma cells (M14, A375 and MV3) and human melanocyte (MC) was observed by the Hoffman microscope. Cells were stained by phalloidin labeled by rhodamine. The differences between 4 types of cells in filopodia, lamellipodia, stress fiber and adhesion plaque (microfilament is the main constituent) were observed under the super-high resolution microscope. -
The New Therapeutic Strategies in Pediatric T-Cell Acute Lymphoblastic Leukemia
International Journal of Molecular Sciences Review The New Therapeutic Strategies in Pediatric T-Cell Acute Lymphoblastic Leukemia Marta Weronika Lato 1 , Anna Przysucha 1, Sylwia Grosman 1, Joanna Zawitkowska 2 and Monika Lejman 3,* 1 Student Scientific Society, Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland; [email protected] (M.W.L.); [email protected] (A.P.); [email protected] (S.G.) 2 Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, 20-093 Lublin, Poland; [email protected] 3 Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland * Correspondence: [email protected] Abstract: Childhood acute lymphoblastic leukemia is a genetically heterogeneous cancer that ac- counts for 10–15% of T-cell acute lymphoblastic leukemia (T-ALL) cases. The T-ALL event-free survival rate (EFS) is 85%. The evaluation of structural and numerical chromosomal changes is important for a comprehensive biological characterization of T-ALL, but there are currently no ge- netic prognostic markers. Despite chemotherapy regimens, steroids, and allogeneic transplantation, relapse is the main problem in children with T-ALL. Due to the development of high-throughput molecular methods, the ability to define subgroups of T-ALL has significantly improved in the last few years. The profiling of the gene expression of T-ALL has led to the identification of T-ALL subgroups, and it is important in determining prognostic factors and choosing an appropriate treatment. Novel therapies targeting molecular aberrations offer promise in achieving better first remission with the Citation: Lato, M.W.; Przysucha, A.; hope of preventing relapse. -
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. -
The Impact of Chromosomal Translocation Locus and Fusion Oncogene Coding Sequence in Synovial Sarcomagenesis
Oncogene (2016) 35, 5021–5032 © 2016 Macmillan Publishers Limited, part of Springer Nature. All rights reserved 0950-9232/16 www.nature.com/onc ORIGINAL ARTICLE The impact of chromosomal translocation locus and fusion oncogene coding sequence in synovial sarcomagenesis KB Jones1,2,3, JJ Barrott1,2,3, M Xie4, M Haldar5, H Jin1,2,3, J-F Zhu1,2,3, MJ Monument1,3, TL Mosbruger3,6, EM Langer5, RL Randall1,3, RK Wilson4,7,8,9, BR Cairns2,3,10, L Ding4,7,8,9 and MR Capecchi5 Synovial sarcomas are aggressive soft-tissue malignancies that express chromosomal translocation-generated fusion genes, SS18-SSX1 or SS18-SSX2 in most cases. Here, we report a mouse sarcoma model expressing SS18-SSX1, complementing our prior model expressing SS18-SSX2. Exome sequencing identified no recurrent secondary mutations in tumors of either genotype. Most of the few mutations identified in single tumors were present in genes that were minimally or not expressed in any of the tumors. Chromosome 6, either entirely or around the fusion gene expression locus, demonstrated a copy number gain in a majority of tumors of both genotypes. Thus, by fusion oncogene coding sequence alone, SS18-SSX1 and SS18-SSX2 can each drive comparable synovial sarcomagenesis, independent from other genetic drivers. SS18-SSX1 and SS18-SSX2 tumor transcriptomes demonstrated very few consistent differences overall. In direct tumorigenesis comparisons, SS18-SSX2 was slightly more sarcomagenic than SS18-SSX1, but equivalent in its generation of biphasic histologic features. Meta-analysis of human synovial sarcoma patient series identified two tumor–gentoype–phenotype correlations that were not modeled by the mice, namely a scarcity of male hosts and biphasic histologic features among SS18-SSX2 tumors. -
A Misplaced Lncrna Causes Brachydactyly in Humans
A misplaced lncRNA causes brachydactyly in humans Philipp G. Maass, … , Friedrich C. Luft, Sylvia Bähring J Clin Invest. 2012;122(11):3990-4002. https://doi.org/10.1172/JCI65508. Research Article Translocations are chromosomal rearrangements that are frequently associated with a variety of disease states and developmental disorders. We identified 2 families with brachydactyly type E (BDE) resulting from different translocations affecting chromosome 12p. Both translocations caused downregulation of the parathyroid hormone-like hormone (PTHLH) gene by disrupting the cis-regulatory landscape. Using chromosome conformation capturing, we identified a regulator on chromosome 12q that interacts in cis with PTHLH over a 24.4-megabase distance and in trans with the sex- determining region Y-box 9 (SOX9) gene on chromosome 17q. The element also harbored a long noncoding RNA (lncRNA). Silencing of the lncRNA, PTHLH, or SOX9 revealed a feedback mechanism involving an expression-dependent network in humans. In the BDE patients, the human lncRNA was upregulated by the disrupted chromosomal association. Moreover, the lncRNA occupancy at the PTHLH locus was reduced. Our results document what we believe to be a novel in cis– and in trans–acting DNA and lncRNA regulatory feedback element that is reciprocally regulated by coding genes. Furthermore, our findings provide a systematic and combinatorial view of how enhancers encoding lncRNAs may affect gene expression in normal development. Find the latest version: https://jci.me/65508/pdf Research article Related Commentary, page 3837 A misplaced lncRNA causes brachydactyly in humans Philipp G. Maass,1,2 Andreas Rump,3 Herbert Schulz,2 Sigmar Stricker,4 Lisanne Schulze,1,2 Konrad Platzer,3 Atakan Aydin,1,2 Sigrid Tinschert,3 Mary B. -
FANCL Sirna (H): Sc-45661
SAN TA C RUZ BI OTEC HNOL OG Y, INC . FANCL siRNA (h): sc-45661 BACKGROUND STORAGE AND RESUSPENSION Defects in FANCL are a cause of Fanconi anemia. Fanconi anemia (FA) is an Store lyophilized siRNA duplex at -20° C with desiccant. Stable for at least autosomal recessive disorder characterized by bone marrow failure, birth one year from the date of shipment. Once resuspended, store at -20° C, defects and chromosomal instability. At the cellular level, FA is characterized avoid contact with RNAses and repeated freeze thaw cycles. by spontaneous chromosomal breakage and a unique hypersensitivity to DNA Resuspend lyophilized siRNA duplex in 330 µl of the RNAse-free water cross-linking agents. At least 8 complementation groups have been identified pro vided. Resuspension of the siRNA duplex in 330 µl of RNAse-free water and 6 FA genes (for subtypes A, C, D2, E, F and G) have been cloned. Phospho- makes a 10 µM solution in a 10 µM Tris-HCl, pH 8.0, 20 mM NaCl, 1 mM rylation of FANC (Fanconi anemia complementation group) proteins is thought EDTA buffered solution. to be important for the function of the FA pathway. FA proteins cooperate in a common pathway, culminating in the monoubiquitination of FANCD2 protein APPLICATIONS and colocalization of FANCD2 and BRCA1 proteins in nuclear foci. FANCL is a ligase protein mediating the ubiquitination of FANCD2, a key step in the FANCL shRNA (h) Lentiviral Particles is recommended for the inhibition of DNA damage pathway. FANCL may be required for proper primordial germ cell FANCL expression in human cells.