KLF2 in Regulation of NF-B-Mediated Immune Cell Function And
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Screening and Identification of Key Biomarkers in Clear Cell Renal Cell Carcinoma Based on Bioinformatics Analysis
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Screening and identification of key biomarkers in clear cell renal cell carcinoma based on bioinformatics analysis Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Clear cell renal cell carcinoma (ccRCC) is one of the most common types of malignancy of the urinary system. The pathogenesis and effective diagnosis of ccRCC have become popular topics for research in the previous decade. In the current study, an integrated bioinformatics analysis was performed to identify core genes associated in ccRCC. An expression dataset (GSE105261) was downloaded from the Gene Expression Omnibus database, and included 26 ccRCC and 9 normal kideny samples. Assessment of the microarray dataset led to the recognition of differentially expressed genes (DEGs), which was subsequently used for pathway and gene ontology (GO) enrichment analysis. -
Activated Peripheral-Blood-Derived Mononuclear Cells
Transcription factor expression in lipopolysaccharide- activated peripheral-blood-derived mononuclear cells Jared C. Roach*†, Kelly D. Smith*‡, Katie L. Strobe*, Stephanie M. Nissen*, Christian D. Haudenschild§, Daixing Zhou§, Thomas J. Vasicek¶, G. A. Heldʈ, Gustavo A. Stolovitzkyʈ, Leroy E. Hood*†, and Alan Aderem* *Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103; ‡Department of Pathology, University of Washington, Seattle, WA 98195; §Illumina, 25861 Industrial Boulevard, Hayward, CA 94545; ¶Medtronic, 710 Medtronic Parkway, Minneapolis, MN 55432; and ʈIBM Computational Biology Center, P.O. Box 218, Yorktown Heights, NY 10598 Contributed by Leroy E. Hood, August 21, 2007 (sent for review January 7, 2007) Transcription factors play a key role in integrating and modulating system. In this model system, we activated peripheral-blood-derived biological information. In this study, we comprehensively measured mononuclear cells, which can be loosely termed ‘‘macrophages,’’ the changing abundances of mRNAs over a time course of activation with lipopolysaccharide (LPS). We focused on the precise mea- of human peripheral-blood-derived mononuclear cells (‘‘macro- surement of mRNA concentrations. There is currently no high- phages’’) with lipopolysaccharide. Global and dynamic analysis of throughput technology that can precisely and sensitively measure all transcription factors in response to a physiological stimulus has yet to mRNAs in a system, although such technologies are likely to be be achieved in a human system, and our efforts significantly available in the near future. To demonstrate the potential utility of advanced this goal. We used multiple global high-throughput tech- such technologies, and to motivate their development and encour- nologies for measuring mRNA levels, including massively parallel age their use, we produced data from a combination of two distinct signature sequencing and GeneChip microarrays. -
Angiogenic Patterning by STEEL, an Endothelial-Enriched Long
Angiogenic patterning by STEEL, an endothelial- enriched long noncoding RNA H. S. Jeffrey Mana,b, Aravin N. Sukumara,b, Gabrielle C. Lamc,d, Paul J. Turgeonb,e, Matthew S. Yanb,f, Kyung Ha Kub,e, Michelle K. Dubinskya,b, J. J. David Hob,f, Jenny Jing Wangb,e, Sunit Dasg,h, Nora Mitchelli, Peter Oettgeni, Michael V. Seftonc,d,j, and Philip A. Marsdena,b,e,f,1 aInstitute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada; bKeenan Research Centre for Biomedical Science in the Li Ka Shing Knowledge Institute, St. Michael’s Hospital, University of Toronto, Toronto, ON M5B 1T8, Canada; cDonnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E2, Canada; dInstitute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada; eDepartment of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada; fDepartment of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; gArthur and Sonia Labatt Brain Tumour Research Institute, Hospital for SickKids, University of Toronto, Toronto, ON M5G 1X8, Canada; hDivision of Neurosurgery and Keenan Research Centre for Biomedical Science, St. Michael’s Hospital, University of Toronto, Toronto, ON M5B 1W8, Canada; iDepartment of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115; and jDepartment of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada Edited by Napoleone Ferrara, University of California, San Diego, La Jolla, CA, and approved January 24, 2018 (received for review August 28, 2017) Endothelial cell (EC)-enriched protein coding genes, such as endothelial formation in vitro and blood vessel formation in vivo. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Expression and Regulation of Sex Determining Genes in the Mouse
Expression and regulation of sex determining genes in the mouse. Veronica Mercedes Narvaez Padilla A thesis submitted for the Degree of Doctor of Philosophy 1996 Department of Developmental Genetics Department of Biology National Institute for Medical Research, University College London The Ridgeway, Mill Hill, Gower Street, London, NW7 lAA London, WCIE GET ProQuest Number: 10016705 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. uest. ProQuest 10016705 Published by ProQuest LLC(2016). Copyright of the Dissertation is held by the Author. All rights reserved. This work is protected against unauthorized copying under Title 17, United States Code. Microform Edition © ProQuest LLC. ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 In memory of Pepe and Arturo. ...Many times Fve been alone and many times Fve cried. Anyway you’ll never know the many ways Fve tried... (Lennon & M cC artney) Little darling, it’s being a long cold lonely winter. Little darling, it feels like years since it’s been here. Here comes the sun, here comes the sun and I say It’s alright! (G. Harrison) Contents Contents ...................................................................................................................................................4 -
Prognostic Impact of Concurrent MYC and BCL6 Rearrangements and Expression in De Novo Diffuse Large B-Cell Lymphoma
www.impactjournals.com/oncotarget/ Oncotarget, Vol. 7, No. 3 Prognostic impact of concurrent MYC and BCL6 rearrangements and expression in de novo diffuse large B-cell lymphoma Qing Ye1,*, Zijun Y. Xu-Monette1,*, Alexandar Tzankov2,*, Lijuan Deng1, Xiaoxiao Wang1, Ganiraju C. Manyam3, Carlo Visco4, Santiago Montes-Moreno5, Li Zhang3, Karen Dybkær6, April Chiu7, Attilio Orazi8, Youli Zu9, Govind Bhagat10, Kristy L. Richards11, Eric D. Hsi12, William W.L. Choi13, J. Han van Krieken14, Jooryung Huh15, Maurilio Ponzoni16, Andrés J.M. Ferreri16, Ben M. Parsons17, Michael B. Møller18, Miguel A. Piris5, Jane N. Winter19, L. Jeffrey Medeiros1 Shimin Hu1 and Ken H. Young1,20 1 Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA 2 University Hospital, Basel, Switzerland 3 Department of Computational Biology and Bioinformatics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA 4 San Bortolo Hospital, Vicenza, Italy 5 Hospital Universitario Marques de Valdecilla, Santander, Spain 6 Aalborg University Hospital, Aalborg, Denmark 7 Memorial Sloan-Kettering Cancer Center, New York, New York, USA 8 Weill Medical College of Cornell University, New York, New York, USA 9 Houston Methodist Hospital, Houston, Texas, USA 10 Columbia University Medical Center and New York Presbyterian Hospital, New York, New York, USA 11 University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA 12 Cleveland Clinic, Cleveland, Ohio, USA 13 University of Hong Kong Li Ka Shing Faculty of Medicine, Hong Kong, China 14 Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands 15 Asan Medical Center, Ulsan University College of Medicine, Seoul, Korea 16 San Raffaele H. -
Directing an Artificial Zinc Finger Protein to New Targets by Fusion to a Non-DNA Binding Domain
Directing an artificial zinc finger protein to new targets by fusion to a non-DNA binding domain Wooi Fang (Catheryn) Lim A thesis in fulfilment of the requirements for the degree of Doctor of Philosophy School of Biotechnology and Biomolecular Sciences Faculty of Science March 2016 Page | 0 THESIS/ DISSERTATION SHEET Page | i ORIGINALITY STATEMENT ‘I hereby declare that this submission is my own work and to the best of my knowledge it contains no materials previously published or written by another person, or substantial proportions of material which have been accepted for the award of any other degree or diploma at UNSW or any other educational institution, except where due acknowledgement is made in the thesis. Any contribution made to the research by others, with whom I have worked at UNSW or elsewhere, is explicitly acknowledged in the thesis. I also declare that the intellectual content of this thesis is the product of my own work, except to the extent that assistance from others in the project's design and conception or in style, presentation and linguistic expression is acknowledged.’ WOOI FANG LIM Signed …………………………………………….............. 31-03-2016 Date …………………………………………….............. Page | i COPYRIGHT STATEMENT ‘I hereby grant the University of New South Wales or its agents the right to archive and to make available my thesis or dissertation in whole or part in the University libraries in all forms of media, now or here after known, subject to the provisions of the Copyright Act 1968. I retain all proprietary rights, such as patent rights. I also retain the right to use in future works (such as articles or books) all or part of this thesis or dissertation. -
Genetic Variations of ISL1 Associated with Human Congenital Heart Disease in Chinese Han People
Genetic variations of ISL1 associated with human congenital heart disease in Chinese Han people Z.L. Luo1, H. Sun2, Z.Q. Yang2, Y.H. Ma3, Y. Gu1, Y.Q. He2, D. Wei4, L.B. Xia4, B.H. Yang1 and T. Guo1 1Department of Cardiology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China 2Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, Yunnan, China 3Department of Obstetrics and Gynecology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China 4Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China Corresponding author: T. Guo E-mail: [email protected] Genet. Mol. Res. 13 (1): 1329-1338 (2014) Received January 2, 2013 Accepted May 23, 2013 Published February 28, 2014 DOI http://dx.doi.org/10.4238/2014.February.28.5 ABSTRACT. Congenital heart disease (CHD) is the most common birth abnormality, but the etiology of CHD is unknown. ISL1 may play a fundamental role in cardiac morphogenesis, and mutations of this gene could cause CHD. To evaluate whether genetic variations of ISL1 are associated with CHD in Chinese Han people, polymerase chain reaction restriction fragment-length polymorphism and SNaPshot were used to examine 9 polymorphisms of ISL1 in 233 patients with CHD Genetics and Molecular Research 13 (1): 1329-1338 (2014) ©FUNPEC-RP www.funpecrp.com.br Z.L. Luo et al. 1330 as well as 288 healthy controls. We found that one SNP (rs1017) in ISL1 was significantly associated with simple CHD. Genetic variation of ISL1 was confirmed to be associated with the risk of CHD. -
Estrogen Receptor Β Sustains Epithelial Differentiation by Regulating Prolyl Hydroxylase 2 Transcription
Estrogen receptor β sustains epithelial differentiation by regulating prolyl hydroxylase 2 transcription Paul Mak, Cheng Chang, Bryan Pursell, and Arthur M. Mercurio1 Department of Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605 Edited* by Jan-Åke Gustafsson, University of Houston, Houston, TX, and approved February 5, 2013 (received for review December 12, 2012) Estrogen receptor β (ERβ) promotes the degradation of hypoxia target genes, including VEGF, lysyl oxidase, and TWIST, have the inducible factor 1α (HIF-1α), which contributes to the ability of this ability to promote epithelial dedifferentiation (9, 18–20). A chal- hormone receptor to sustain the differentiation of epithelial and lenging problem that emerges from these findings is how a nuclear carcinoma cells. Although the loss of ERβ and consequent HIF-1 hormone receptor induces the degradation of HIF-1α (21). HIF- activation occur in prostate cancer with profound consequences, 1α is degraded in normoxia by a well-established mechanism that the mechanism by which ERβ promotes the degradation of HIF-1α involves its hydroxylation on specific prolines by prolyl hydrox- is unknown. We report that ERβ regulates the ligand (3β-adiol)- ylases (PHDs), which target HIF-1α for recognition by the E3 li- dependent transcription of prolyl hydroxylase 2 (PHD2) also gase von Hippel-Lindau (VHL) and consequent degradation in – fi α known as Egl nine homolog 1 (EGLN1), a 2-oxoglutarate-depen- the proteosome (22 24). More speci cally, HIF-1 is hydroxylated dent dioxygenase that hydroxylates HIF-1α and targets it for rec- on two conserved proline residues (p402 and p564), which allows ognition by the von Hippel-Lindau tumor suppressor and consequent for its interaction with VHL E3 ubiquitin ligase for subsequent β PHD2 polyubiquitination and proteasomal degradation (22). -
Krüppel-Like Factor 17 Upregulates Uterine Corin Expression and Promotes Spiral Artery Remodeling in Pregnancy
Krüppel-like factor 17 upregulates uterine corin expression and promotes spiral artery remodeling in pregnancy Can Wanga, Zhiting Wanga, Meiling Hea, Tiantian Zhoua, Yayan Niua,b, Shengxuan Sunc, Hui Lia, Ce Zhanga, Shengnan Zhanga, Meng Liua, Ying Xud, Ningzheng Donga,b,1, and Qingyu Wua,e,1 aCyrus Tang Hematology Center, Ministry of Education Engineering Center of Hematological Diseases, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Prevention, Soochow University, 215123 Suzhou, China; bMinistry of Health Key Laboratory of Thrombosis and Hemostasis, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, 215006 Suzhou, China; cDepartment of Orthopedics, The Second Affiliated Hospital of Soochow University, 215004 Suzhou, China; dCambridge-Soochow University Genomic Resource Center, Soochow University, 215123 Suzhou, China; and eCardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 Edited by R. Michael Roberts, University of Missouri, Columbia, MO, and approved June 25, 2020 (received for review February 29, 2020) Spiral artery remodeling is an important physiological process in the In the heart, natriuretic peptide expression is controlled by pregnant uterus which increases blood flow to the fetus. Impaired GATA-4, a zinc finger transcription factor (21, 22). A similar spiral artery remodeling contributes to preeclampsia, a major disease GATA-4–dependent mechanism is critical for cardiac corin ex- in pregnancy. Corin, a transmembrane serine protease, is up- pression. We have shown that human and mouse corin gene pro- regulated in the pregnant uterus to promote spiral artery remodeling. moters contain a conserved sequence that is essential for GATA-4 To date, the mechanism underlying uterine corin up-regulation re- binding and corin expression in cardiomyocytes (23). -
Engineered Type 1 Regulatory T Cells Designed for Clinical Use Kill Primary
ARTICLE Acute Myeloid Leukemia Engineered type 1 regulatory T cells designed Ferrata Storti Foundation for clinical use kill primary pediatric acute myeloid leukemia cells Brandon Cieniewicz,1* Molly Javier Uyeda,1,2* Ping (Pauline) Chen,1 Ece Canan Sayitoglu,1 Jeffrey Mao-Hwa Liu,1 Grazia Andolfi,3 Katharine Greenthal,1 Alice Bertaina,1,4 Silvia Gregori,3 Rosa Bacchetta,1,4 Norman James Lacayo,1 Alma-Martina Cepika1,4# and Maria Grazia Roncarolo1,2,4# Haematologica 2021 Volume 106(10):2588-2597 1Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA; 2Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA; 3San Raffaele Telethon Institute for Gene Therapy, Milan, Italy and 4Center for Definitive and Curative Medicine, Stanford School of Medicine, Stanford, CA, USA *BC and MJU contributed equally as co-first authors #AMC and MGR contributed equally as co-senior authors ABSTRACT ype 1 regulatory (Tr1) T cells induced by enforced expression of interleukin-10 (LV-10) are being developed as a novel treatment for Tchemotherapy-resistant myeloid leukemias. In vivo, LV-10 cells do not cause graft-versus-host disease while mediating graft-versus-leukemia effect against adult acute myeloid leukemia (AML). Since pediatric AML (pAML) and adult AML are different on a genetic and epigenetic level, we investigate herein whether LV-10 cells also efficiently kill pAML cells. We show that the majority of primary pAML are killed by LV-10 cells, with different levels of sensitivity to killing. Transcriptionally, pAML sensitive to LV-10 killing expressed a myeloid maturation signature. -
Bach1 Is Critical for the Transformation of Mouse Embryonic Fibroblasts by Rasv12 and Maintains ERK Signaling
Oncogene (2013) 32, 3231–3245 & 2013 Macmillan Publishers Limited All rights reserved 0950-9232/13 www.nature.com/onc ORIGINAL ARTICLE Bach1 is critical for the transformation of mouse embryonic fibroblasts by RasV12 and maintains ERK signaling A Nakanome1,2, A Brydun1,3, M Matsumoto1,4,KOta1, R Funayama5,6, K Nakayama5, M Ono7, K Shiga2, T Kobayashi2 and K Igarashi1,3,6 Reactive oxygen species (ROS), by-products of aerobic respiration, promote genetic instability and contribute to the malignant transformation of cells. Among the genes related to ROS metabolism, Bach1 is a repressor of the oxidative stress response, and a negative regulator of ROS-induced cellular senescence directed by p53 in higher eukaryotes. While ROS are intimately involved in carcinogenesis, it is not clear whether Bach1 is involved in this process. We found that senescent Bach1-deficient mouse embryonic fibroblasts (MEFs) underwent spontaneous immortalization the same as did the wild-type cells. When transduced with constitutively active Ras (H-RasV12), the proliferation and colony formation of these cells in vitro were markedly reduced. When transplanted into athymic nude mice, the growth and vascularization of tumors derived from Bach1-deficient cells were also decreased. Gene expression profiling of the MEFs revealed a new H-RasV12 signature, which was distinct from the previously reported signatures in epithelial tumors, and was partly dependent on Bach1. The Bach1-deficient cells showed diminished phosphorylation of MEK and ERK1/2 in response to H-RasV12, which was consistent with the alterations in the gene expression profile, including phosphatase genes. Finally, Bach1-deficient mice were less susceptible to 4-nitroquinoline-1-oxidide (4-NQO)- induced tongue carcinoma than wild-type mice.