CREB3L2-Pparg Fusion Mutation Identifies a Thyroid Signaling Pathway Regulated by Intramembrane Proteolysis
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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 -
Downloaded Uniformly Processed RNA-Seq Datasets from 3,764,506 High-Throughput Sequencing Samples from Skymap in Raw Count Format19
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 April 2020 doi:10.20944/preprints202003.0360.v2 TMPRSS2 transcriptional inhibition as a therapeutic strategy for COVID-19 Xinchen Wang, Ph.D.1*, Ryan S. Dhindsa, Ph.D.1,2, Gundula Povysil, M.D., Ph.D.1, Anthony Zoghbi, M.D.1,3,4, Joshua E. Motelow, M.D., Ph.D.1,5, Joseph A. Hostyk, B.Sc.1, Nicholas Nickols, M.D. Ph.D.6,7, Matthew Rettig, M.D.8,9, David B. Goldstein, Ph.D.1,2* 1Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, 2Department of Genetics & Development, Columbia University Irving Medical Center, New York, 3Department of Psychiatry, Columbia University Irving Medical Center, New York 4New York State Psychiatric Institute, New York 5Division of Pediatric Critical Care, Department of Pediatrics, New York-Presbyterian Morgan Stanley Children’s Hospital, Columbia University Irving Medical Center, New York 6Department of Radiation Oncology, University of California, Los Angeles, Los Angeles 7Department of Radiation Oncology, Veteran Affairs Greater Los Angeles Healthcare System, Los Angeles, California 8Division of Hematology and Oncology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles 9Division of Hematology and Oncology, VA Greater Los Angeles Healthcare System, Los Angeles, Los Angeles, California *To whom correspondence should be addressed: [email protected] (X.W.), [email protected] (D.B.G.) Abstract There is an urgent need to identify effective therapies for COVID-19. The SARS-CoV-2 host factor protease TMPRSS2 is required for viral entry and thus an attractive target for therapeutic intervention. -
Self-Organized Amniogenesis by Human Pluripotent Stem Cells in a Biomimetic Implantation-Like Niche
LETTERS PUBLISHED ONLINE: 12 DECEMBER 2016 | DOI: 10.1038/NMAT4829 Self-organized amniogenesis by human pluripotent stem cells in a biomimetic implantation-like niche Yue Shao1†, Kenichiro Taniguchi2†, Katherine Gurdziel3, Ryan F. Townshend2, Xufeng Xue1, Koh Meng Aw Yong1, Jianming Sang1, Jason R. Spence2, Deborah L. Gumucio2* and Jianping Fu1,2,4* Amniogenesis—the development of amnion—is a critical factors seen in the in vivo amniogenic niche: a three-dimensional developmental milestone for early human embryogenesis (3D) extracellular matrix (ECM) that is provided by the basement and successful pregnancy1,2. However, human amniogenesis membrane surrounding the epiblast during implantation11; and a is poorly understood due to limited accessibility to peri- soft tissue bed provided by the uterine wall and trophoblast to implantation embryos and a lack of in vitro models. Here support the developing amnion (Fig. 1a,b). Since amniogenesis ini- we report an ecient biomaterial system to generate human tiates from the expanding pluripotent epiblast, we utilized mTeSR1 amnion-like tissue in vitro through self-organized development medium and basement membrane matrix (Geltrex) to render the of human pluripotent stem cells (hPSCs) in a bioengineered culture permissive for pluripotency maintenance. niche mimicking the in vivo implantation environment. We In this culture system, H9 human embryonic stem cells (hESCs) show that biophysical niche factors act as a switch to toggle were plated as single cells at 30,000 cells cm−2 onto a thick, hPSC self-renewal versus amniogenesis under self-renewal- soft gel bed of Geltrex (with thickness ≥100 µm, bulk Young's permissive biochemical conditions. We identify a unique modulus ∼900 Pa, coated on a glass coverslip), in mTeSR1 medium molecular signature of hPSC-derived amnion-like cells and supplemented with the ROCK inhibitor Y27632 (Fig. -
Transcriptional Regulation of Tenascin Genes
View metadata, citation and similar papers at core.ac.uk brought to you by CORE REVIEW provided by Bern Open Repository and Information System (BORIS) Cell Adhesion & Migration 9:1-2, 34--47; January–April 2015; © 2015 Taylor & Francis Group, LLC Transcriptional regulation of tenascin genes Francesca Chiovaro1,2, Ruth Chiquet-Ehrismann1,2,*, and Matthias Chiquet3 1Friedrich Miescher Institute for Biomedical Research; Basel, Switzerland; 2Faculty of Science; University of Basel; Basel, Switzerland; 3Department of Orthodontics and Dentofacial Orthopedics; School of Dental Medicine; University of Bern; Bern, Switzerland Keywords: cytokine, cancer, development, extracellular matrix, glucocorticoid, growth factor, gene regulation, gene promoter, homeobox gene, matricellular, mechanical stress, tenascin, transcription factor Abbreviations: AKT, v-akt murine thymoma viral oncogene homolog; ALK, anaplastic lymphoma kinase; ATF, activating transcrip- tion factor; AP-1, activator protein-1; BMP, bone morphogenetic protein; CBP, CREB binding protein; ChIP, chromatin immuno- precipitation; CREB, cAMP response element-binding protein; CREB-RP, CREB-related protein; CYP21A2, cytochrome P450 family 21 subfamily A polypeptide 2; EBS, Ets binding site; ECM, extracellular matrix; EGF, epidermal growth factor; ERK1/2, extracellular signal-regulated kinase 1/2; ETS, E26 transformation-specific; Evx1, even skipped homeobox 1; EWS-ETS, Ewing sar- coma-Ets fusion protein; FGF, fibroblast growth factor; HBS, homeodomain binding sequence; IL, interleukin; ILK, -
The Rationale for Angiotensin Receptor Neprilysin Inhibitors in a Multi-Targeted Therapeutic Approach to COVID-19
International Journal of Molecular Sciences Review The Rationale for Angiotensin Receptor Neprilysin Inhibitors in a Multi-Targeted Therapeutic Approach to COVID-19 Alessandro Bellis 1 , Ciro Mauro 1, Emanuele Barbato 2, Bruno Trimarco 2 and Carmine Morisco 2,* 1 Unità Operativa Complessa Cardiologia con UTIC ed Emodinamica-Dipartimento Emergenza Accettazione, Azienda Ospedaliera “Antonio Cardarelli”, 80131 Napoli, Italy; [email protected] (A.B.); [email protected] (C.M.) 2 Dipartimento di Scienze Biomediche Avanzate, Università FEDERICO II, 80131 Napoli, Italy; [email protected] (E.B.); [email protected] (B.T.) * Correspondence: [email protected]; Tel.: +39-081-746-2253; Fax: +39-081-746-2256 Received: 12 October 2020; Accepted: 11 November 2020; Published: 15 November 2020 Abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease (COVID-19) determines the angiotensin converting enzyme 2 (ACE2) down-regulation and related decrease in angiotensin II degradation. Both these events trigger “cytokine storm” leading to acute lung and cardiovascular injury. A selective therapy for COVID-19 has not yet been identified. Clinical trials with remdesivir gave discordant results. Thus, healthcare systems have focused on “multi-targeted” therapeutic strategies aiming at relieving systemic inflammation and thrombotic complications. No randomized clinical trial has demonstrated the efficacy of renin angiotensin system antagonists in reducing inflammation related to COVID-19. Dexamethasone and tocilizumab showed encouraging data, but their use needs to be further validated. The still-controversial efficacy of these treatments highlighted the importance of organ injury prevention in COVID-19. Neprilysin (NEP) might be an interesting target for this purpose. NEP expression is increased by cytokines on lung fibroblasts surface. -
Markers for Detection of Prostate Cancer
Cancers 2010, 2, 1125-1154; doi:10.3390/cancers2021125 OPEN ACCESS cancers ISSN 2072-6694 www.mdpi.com/journal/cancers Review Markers for Detection of Prostate Cancer Raymond A. Clarke 1, Horst J. Schirra 2, James W. Catto 3, Martin F. Lavin 4,5 and Robert A. Gardiner 5,* 1 Prostate Cancer Institute, Cancer Care Centre, St George Hospital Clinical School of Medicine, University of New South Wales, Kogarah, NSW 2217, Australia; E-Mail: [email protected] 2 School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane QLD, 4072, Australia; E-Mail: [email protected] 3 Academic Urology Unit and Institute for Cancer Studies, University of Sheffield, Royal Hallamshire Hospital, Sheffield S10 2JF, UK; E-Mail: [email protected] 4 Queensland Institute of Medical Research, Radiation Biology and Oncology, Brisbane, QLD 4029, Australia; E-Mail: [email protected] 5 University of Queensland Centre for Clinical Research, Brisbane, Australia * Author to whom correspondence should be addressed; E-Mail: [email protected]. Received: 22 March 2010; in revised form: 2 June 2010 / Accepted: 3 June 2010 / Published: 4 June 2010 Abstract: Early detection of prostate cancer is problematic, not just because of uncertainly whether a diagnosis will benefit an individual patient, but also as a result of the imprecise and invasive nature of establishing a diagnosis by biopsy. Despite its low sensitivity and specificity for identifying patients harbouring prostate cancer, serum prostate specific antigen (PSA) has become established as the most reliable and widely-used diagnostic marker for this condition. In its wake, many other markers have been described and evaluated. -
Transcription of Nrdp1 by the Androgen Receptor Is Regulated by Nuclear filamin a in Prostate Cancer
R M Savoy et al. Nrdp1 is an AR target regulated 22:3 369–386 Research by FLNA Transcription of Nrdp1 by the androgen receptor is regulated by nuclear filamin A in prostate cancer Rosalinda M Savoy1,2, Liqun Chen2, Salma Siddiqui1, Frank U Melgoza1, Blythe Durbin- Johnson3, Christiana Drake4, Maitreyee K Jathal1,2, Swagata Bose1,2, Thomas M Steele1, Benjamin A Mooso1, Leandro S D’Abronzo1,2, William H Fry5, Kermit L Carraway III5, Maria Mudryj1,6 and Paramita M Ghosh1,2,5 1VA Northern California Health Care System, Mather, California, USA 2Department of Urology, School of Medicine, University of California Davis, 4860 Y Street, Suite 3500, Correspondence Sacramento, California 95817, USA should be addressed 3Division of Biostatistics, Department of Public Health Sciences, University of California Davis, Davis, California, USA to P M Ghosh 4Department of Statistics, University of California Davis, Davis, California, USA Email 5Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, California, USA paramita.ghosh@ucdmc. 6Department of Medical Microbiology and Immunology, University of California Davis, Davis, California, USA ucdavis.edu Abstract Prostate cancer (PCa) progression is regulated by the androgen receptor (AR); however, Key Words patients undergoing androgen-deprivation therapy (ADT) for disseminated PCa eventually " castration-resistant prostate develop castration-resistant PCa (CRPC). Results of previous studies indicated that AR,a cancer transcription factor, occupies distinct genomic loci in CRPC compared with hormone-naı¨ve " AR/androgen receptor " Endocrine-Related Cancer PCa; however, the cause of this distinction was unknown. The E3 ubiquitin ligase Nrdp1 is a FLRF/RNF41/Nrdp1 model AR target modulated by androgens in hormone-naı¨ve PCa but not in CRPC. -
Molecular Mechanism of L-Proline Induced EPL-Cell Formation
MOLECULAR MECHANISM OF L.PROLINE INDUCED EPL.CELL FORMATION A thesis submitted to the,University of Adelaide for the Degree of Doctor of PhilosoPhY By Ana Lonic, Bachelor of Science (Honours) Department of Biochem istrY School of Molecular and Biomedical Science University of Adelaide Adelaide, South Australia December, 2006 TABLE OF GONTENTS Summary Statement....,. Acknowledgements GHAPTER 1: GENERAL INTRODUCTION 11 1.1 MOUSE EMBRYOLOGY 11 1.1.1 Pre-implantation development .......... ....... 11 1.1.2 Peri-and Post-implantationdevelopment.......... ........14 1 .1 .2.1 Blastocyst implantation .......... 14 1.1.2.2 Cavitation and primitive ectoderm formation..................... 15 1.1.2.3 Signalling involved in pluripotent cell progression in vivo . 17 1.1.2.4 Role of visceral endoderm in induction of primitive ectoderm t9 1 1 2 s ,,,",,*"i",,;,;, ,;;: ,: :r,;r:",,",;;'*io, o, the primitive ectoderm. 20 1.1.2.6 Gastrulation of the mouse embryo 21 1.1.2.7 Establishment of polarity during mouse development....... 23 1.2 EMBRYONIC STEM CELLS AND THE]R DERIVATIVES ....25 1.2.1 Mouse ES-cell derivation and properties........ .........25 1.2.2 Human ES cells .............27 1.2.3 ln vitro differentiation of mES cells .........28 1.2.4 ln vitro model of early embryogenesis - Homogeneous formation of early primitive ectoderm-like cells from ES cells .. 32 1.2.4.1 EPL-cell morphology....... '.. 33 I 1.2.4.2 EPL-cell gene expression.............. ... 34 1.2.4.3 EPL-cell differentiation potential ........... ............ 35 1.2.4.4 Cytokine responsiveness of EPL cells .............. 38 1.2.5 ldentification of MEDII derived factors involved in EPL-cell formation ........39 1.2.6 Remodelling of basement membranes - a potential source of t- proline/short t--proline-containing peptides ........42 1.3 SIGNALLING PATHWAYS INVOLVED IN ES-CELL SELF-RENEWAL, PLURIPOTENCE AND DIFFERENTIATION ..............43 1.3.1 Signalling mechanisms involved in self-renewal and differentiation of ES cells .........43 1 .3.1 .1 STAT3 signalling,n ES cells........ -
S01-01 Therapeutic Targeting of TMPRSS2 and ACE2 As a Potential Strategy to Combat COVID-19. Qu Deng1, Reyaz Ur Rasool1, Ramakrishnan Natesan1, Irfan A
S01-01 Therapeutic targeting of TMPRSS2 and ACE2 as a potential strategy to combat COVID-19. Qu Deng1, Reyaz Ur Rasool1, Ramakrishnan Natesan1, Irfan A. Asangani2. 1Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 2Department of Cancer Biology, Abramson Family Cancer Research Institute, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA. The novel SARS-CoV-2 infection responsible for the COVID-19 pandemic is expected to have an adverse effect on the progression of multiple cancers, including prostate cancer, due to the ensuing cytokine storm associated oncogenic signaling. A better understanding of the host cell factors and their regulators will help identify potential therapies to block SARS-CoV-2 infection at an early stage and thereby prevent cancer progression. Host cell infection by SARS-CoV-2 requires the binding of the viral spike S protein to ACE2 receptor and priming by the serine protease TMPRSS2—encoded by a well-known androgen response gene and highly expressed in patients diagnosed with prostate cancer. Epidemiologic data showing increased severity and mortality of SARS-CoV-2 disease in men suggest a possible role for androgen in the transcriptional activation of ACE2 and TMPRSS2 in the lungs and other primary infection sites. Here, by performing in vivo castration in mice, RT-PCR, immunoblotting, Co-IP, and pseudovirus infection assays in multiple cell lines, we present evidence for the transcriptional regulation of TMPRSS2 and ACE2 by androgen, their endogenous interaction, as well as a novel combination of drugs in blocking viral infection. In adult male mice, castration led to a significant loss in the expression of ACE2 and TMPRSS2 at the transcript and protein levels in the lung, heart, and small intestine. -
Molecular Pathways: Targeting ETS Gene Fusions in Cancer
Published OnlineFirst June 23, 2014; DOI: 10.1158/1078-0432.CCR-13-0275 Clinical Cancer Molecular Pathways Research Molecular Pathways: Targeting ETS Gene Fusions in Cancer Felix Y. Feng1,2,3, J. Chad Brenner2,3,4,5, Maha Hussain3,6,7, and Arul M. Chinnaiyan2,3,4,7,8 Abstract Rearrangements, or gene fusions, involving the ETS family of transcription factors are common driving events in both prostate cancer and Ewing sarcoma. These rearrangements result in pathogenic expression of the ETS genes and trigger activation of transcriptional programs enriched for invasion and other oncogenic features. Although ETS gene fusions represent intriguing therapeutic targets, transcription factors, such as those comprising the ETS family, have been notoriously difficult to target. Recently, preclinical studies have demonstrated an association between ETS gene fusions and components of the DNA damage response pathway, such as PARP1, the catalytic subunit of DNA protein kinase (DNAPK), and histone deactylase 1 (HDAC1), and have suggested that ETS fusions may confer sensitivity to inhibitors of these DNA repair proteins. In this review, we discuss the role of ETS fusions in cancer, the preclinical rationale for targeting ETS fusions with inhibitors of PARP1, DNAPK, and HDAC1, as well as ongoing clinical trials targeting ETS gene fusions. Clin Cancer Res; 20(17); 4442–8. Ó2014 AACR. Background tion domain (from the EWS gene) to the ETS fusion and ETS transcription factors are aberrantly expressed in (ii) replacement of the N-terminus of the ETS protein by several cancers, including prostate cancer (1), the Ewing an RNA-binding domain from the EWS protein that sarcoma family of tumors (2), melanoma (3), secretory enhances posttranscriptional splicing of ETS target genes breast carcinoma (4), acute lymphoblastic leukemia (5), (10; Fig. -
Genome-Wide Screen for Differentially Methylated Long Noncoding Rnas
OPEN Oncogene (2017) 36, 6446–6461 www.nature.com/onc ORIGINAL ARTICLE Genome-wide screen for differentially methylated long noncoding RNAs identifies Esrp2 and lncRNA Esrp2-as regulated by enhancer DNA methylation with prognostic relevance for human breast cancer K Heilmann, R Toth, C Bossmann, K Klimo, C Plass and C Gerhauser The majority of long noncoding RNAs (lncRNAs) is still poorly characterized with respect to function, interactions with protein- coding genes, and mechanisms that regulate their expression. As for protein-coding RNAs, epigenetic deregulation of lncRNA expression by alterations in DNA methylation might contribute to carcinogenesis. To provide genome-wide information on lncRNAs aberrantly methylated in breast cancer we profiled tumors of the C3(1) SV40TAg mouse model by MCIp-seq (Methylated CpG Immunoprecipitation followed by sequencing). This approach detected 69 lncRNAs differentially methylated between tumor tissue and normal mammary glands, with 26 located in antisense orientation of a protein-coding gene. One of the hypomethylated lncRNAs, 1810019D21Rik (now called Esrp2-antisense (as)) was identified in proximity to the epithelial splicing regulatory protein 2 (Esrp2) that is significantly elevated in C3(1) tumors. ESRPs were shown previously to have a dual role in carcinogenesis. Both gain and loss have been associated with poor prognosis in human cancers, but the mechanisms regulating expression are not known. In- depth analyses indicate that coordinate overexpression of Esrp2 and Esrp2-as inversely correlates with DNA methylation. Luciferase reporter gene assays support co-expression of Esrp2 and the major short Esrp2-as variant from a bidirectional promoter, and transcriptional regulation by methylation of a proximal enhancer. -
Camp/PKA Pathway Activation in Human Mesenchymal Stem Cells in Vitro Results in Robust Bone Formation in Vivo
cAMP/PKA pathway activation in human mesenchymal stem cells in vitro results in robust bone formation in vivo Ramakrishnaiah Siddappa*, Anton Martens†, Joyce Doorn*, Anouk Leusink*, Cristina Olivo†, Ruud Licht*, Linda van Rijn*, Claudia Gaspar‡, Riccardo Fodde‡, Frank Janssen*, Clemens van Blitterswijk*, and Jan de Boer*§ *Department of Tissue Regeneration, Institute for Biomedical Technology, University of Twente, 7500 AE, Enschede, The Netherlands; †Department of Immunology, University Medical Center Utrecht, 3584 EA, Utrecht, The Netherlands; and ‡Department of Pathology, Josephine Nefkens Institute, Erasmus Medical Center, 3000 DR, Rotterdam, The Netherlands Edited by Robert Langer, Massachusetts Institute of Technology, Cambridge, MA, and approved March 17, 2008 (received for review November 29, 2007) Tissue engineering of large bone defects is approached through presented (17, 18). Relatively little is known about the role of PKA implantation of autologous osteogenic cells, generally referred to in osteogenic differentiation of hMSCs, but it is anticipated by the as multipotent stromal cells or mesenchymal stem cells (MSCs). anabolic effect of certain PKA-activating hormones on bone min- Animal-derived MSCs successfully bridge large bone defects, but eral density. Intermittent administration of parathyroid hormone models for ectopic bone formation as well as recent clinical trials increases trabecular and cancelleous bone formation in ovariecto- demonstrate that bone formation by human MSCs (hMSCs) is mized mice, although continuous administration results in net bone inadequate. The expansion phase presents an attractive window loss (19). The effect of PKA activation on osteogenesis has been to direct hMSCs by pharmacological manipulation, even though no studied in different cell types with compounds that directly or profound effect on bone formation in vivo has been described so indirectly activate PKA, although the results are contentious.