Identification of Novel TMPRSS2:ERG Mechanisms in Prostate Cancer Metastasis: Involvement of MMP9 and PLXNA2
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Prioritization and Evaluation of Depression Candidate Genes by Combining Multidimensional Data Resources
Prioritization and Evaluation of Depression Candidate Genes by Combining Multidimensional Data Resources Chung-Feng Kao1, Yu-Sheng Fang2, Zhongming Zhao3, Po-Hsiu Kuo1,2,4* 1 Department of Public Health and Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan, 2 Institute of Clinical Medicine, School of Medicine, National Cheng-Kung University, Tainan, Taiwan, 3 Departments of Biomedical Informatics and Psychiatry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America, 4 Research Center for Genes, Environment and Human Health, National Taiwan University, Taipei, Taiwan Abstract Background: Large scale and individual genetic studies have suggested numerous susceptible genes for depression in the past decade without conclusive results. There is a strong need to review and integrate multi-dimensional data for follow up validation. The present study aimed to apply prioritization procedures to build-up an evidence-based candidate genes dataset for depression. Methods: Depression candidate genes were collected in human and animal studies across various data resources. Each gene was scored according to its magnitude of evidence related to depression and was multiplied by a source-specific weight to form a combined score measure. All genes were evaluated through a prioritization system to obtain an optimal weight matrix to rank their relative importance with depression using the combined scores. The resulting candidate gene list for depression (DEPgenes) was further evaluated by a genome-wide association (GWA) dataset and microarray gene expression in human tissues. Results: A total of 5,055 candidate genes (4,850 genes from human and 387 genes from animal studies with 182 being overlapped) were included from seven data sources. -
Supplemental Table 1. Complete Gene Lists and GO Terms from Figure 3C
Supplemental Table 1. Complete gene lists and GO terms from Figure 3C. Path 1 Genes: RP11-34P13.15, RP4-758J18.10, VWA1, CHD5, AZIN2, FOXO6, RP11-403I13.8, ARHGAP30, RGS4, LRRN2, RASSF5, SERTAD4, GJC2, RHOU, REEP1, FOXI3, SH3RF3, COL4A4, ZDHHC23, FGFR3, PPP2R2C, CTD-2031P19.4, RNF182, GRM4, PRR15, DGKI, CHMP4C, CALB1, SPAG1, KLF4, ENG, RET, GDF10, ADAMTS14, SPOCK2, MBL1P, ADAM8, LRP4-AS1, CARNS1, DGAT2, CRYAB, AP000783.1, OPCML, PLEKHG6, GDF3, EMP1, RASSF9, FAM101A, STON2, GREM1, ACTC1, CORO2B, FURIN, WFIKKN1, BAIAP3, TMC5, HS3ST4, ZFHX3, NLRP1, RASD1, CACNG4, EMILIN2, L3MBTL4, KLHL14, HMSD, RP11-849I19.1, SALL3, GADD45B, KANK3, CTC- 526N19.1, ZNF888, MMP9, BMP7, PIK3IP1, MCHR1, SYTL5, CAMK2N1, PINK1, ID3, PTPRU, MANEAL, MCOLN3, LRRC8C, NTNG1, KCNC4, RP11, 430C7.5, C1orf95, ID2-AS1, ID2, GDF7, KCNG3, RGPD8, PSD4, CCDC74B, BMPR2, KAT2B, LINC00693, ZNF654, FILIP1L, SH3TC1, CPEB2, NPFFR2, TRPC3, RP11-752L20.3, FAM198B, TLL1, CDH9, PDZD2, CHSY3, GALNT10, FOXQ1, ATXN1, ID4, COL11A2, CNR1, GTF2IP4, FZD1, PAX5, RP11-35N6.1, UNC5B, NKX1-2, FAM196A, EBF3, PRRG4, LRP4, SYT7, PLBD1, GRASP, ALX1, HIP1R, LPAR6, SLITRK6, C16orf89, RP11-491F9.1, MMP2, B3GNT9, NXPH3, TNRC6C-AS1, LDLRAD4, NOL4, SMAD7, HCN2, PDE4A, KANK2, SAMD1, EXOC3L2, IL11, EMILIN3, KCNB1, DOK5, EEF1A2, A4GALT, ADGRG2, ELF4, ABCD1 Term Count % PValue Genes regulation of pathway-restricted GDF3, SMAD7, GDF7, BMPR2, GDF10, GREM1, BMP7, LDLRAD4, SMAD protein phosphorylation 9 6.34 1.31E-08 ENG pathway-restricted SMAD protein GDF3, SMAD7, GDF7, BMPR2, GDF10, GREM1, BMP7, LDLRAD4, phosphorylation -
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. -
CREB3L2-Pparg Fusion Mutation Identifies a Thyroid Signaling Pathway Regulated by Intramembrane Proteolysis
Research Article CREB3L2-PPARg Fusion Mutation Identifies a Thyroid Signaling Pathway Regulated by Intramembrane Proteolysis Weng-Onn Lui,3 Lingchun Zeng,1 Victoria Rehrmann,1 Seema Deshpande,5 Maria Tretiakova,1 Edwin L. Kaplan,2 Ingo Leibiger,3 Barbara Leibiger,3 Ulla Enberg,3 Anders Ho¨o¨g,4 Catharina Larsson,3 and Todd G. Kroll1 Departments of 1Pathology and 2Surgery, University of Chicago Medical Center, Chicago, Illinois; Departments of 3Molecular Medicine and Surgery and 4Oncology-Pathology, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden; and 5Department of Pathology, Emory University School of Medicine, Atlanta, Georgia Abstract cancer in patients; and (c) the implementation of effective molecular-targeted chemotherapies that have relatively few side The discovery of gene fusion mutations, particularly in effects. The discovery of fusion mutations is therefore important, leukemia, has consistently identified new cancer pathways particularly in carcinoma, the most common cancer group in and led to molecular diagnostic assays and molecular-targeted which few gene fusions have been identified (1). The recent chemotherapies for cancer patients. Here, we report our discoveries of ERG (2) and ALK (3) gene fusions in prostate and discovery of a novel CREB3L2-PPARg fusion mutation in lung carcinoma, respectively, increase the prospect that new thyroid carcinoma with t(3;7)(p25;q34), showing that a family diagnostic and therapeutic strategies based on gene fusions will of somatic PPARg fusion mutations exist in thyroid cancer. The be applicable to common epithelial cancers. CREB3L2-PPARg fusion encodes a CREB3L2-PPAR; fusion Families of gene fusions tend to characterize specific cancer protein that is composed of the transactivation domain of types. -
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. -
Whole Genome Sequencing of Familial Non-Medullary Thyroid Cancer Identifies Germline Alterations in MAPK/ERK and PI3K/AKT Signaling Pathways
biomolecules Article Whole Genome Sequencing of Familial Non-Medullary Thyroid Cancer Identifies Germline Alterations in MAPK/ERK and PI3K/AKT Signaling Pathways Aayushi Srivastava 1,2,3,4 , Abhishek Kumar 1,5,6 , Sara Giangiobbe 1, Elena Bonora 7, Kari Hemminki 1, Asta Försti 1,2,3 and Obul Reddy Bandapalli 1,2,3,* 1 Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany; [email protected] (A.S.); [email protected] (A.K.); [email protected] (S.G.); [email protected] (K.H.); [email protected] (A.F.) 2 Hopp Children’s Cancer Center (KiTZ), D-69120 Heidelberg, Germany 3 Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), D-69120 Heidelberg, Germany 4 Medical Faculty, Heidelberg University, D-69120 Heidelberg, Germany 5 Institute of Bioinformatics, International Technology Park, Bangalore 560066, India 6 Manipal Academy of Higher Education (MAHE), Manipal, Karnataka 576104, India 7 S.Orsola-Malphigi Hospital, Unit of Medical Genetics, 40138 Bologna, Italy; [email protected] * Correspondence: [email protected]; Tel.: +49-6221-42-1709 Received: 29 August 2019; Accepted: 10 October 2019; Published: 13 October 2019 Abstract: Evidence of familial inheritance in non-medullary thyroid cancer (NMTC) has accumulated over the last few decades. However, known variants account for a very small percentage of the genetic burden. Here, we focused on the identification of common pathways and networks enriched in NMTC families to better understand its pathogenesis with the final aim of identifying one novel high/moderate-penetrance germline predisposition variant segregating with the disease in each studied family. -
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. -
Case–Control Association Study of 59 Candidate Genes Reveals the DRD2
Journal of Human Genetics (2009) 54, 98–107 & 2009 The Japan Society of Human Genetics All rights reserved 1434-5161/09 $32.00 www.nature.com/jhg ORIGINAL ARTICLE Case–control association study of 59 candidate genes reveals the DRD2 SNP rs6277 (C957T) as the only susceptibility factor for schizophrenia in the Bulgarian population Elitza T Betcheva1, Taisei Mushiroda2, Atsushi Takahashi3, Michiaki Kubo4, Sena K Karachanak5, Irina T Zaharieva5, Radoslava V Vazharova5, Ivanka I Dimova5, Vihra K Milanova6, Todor Tolev7, George Kirov8, Michael J Owen8, Michael C O’Donovan8, Naoyuki Kamatani3, Yusuke Nakamura1,9 and Draga I Toncheva5 The development of molecular psychiatry in the last few decades identified a number of candidate genes that could be associated with schizophrenia. A great number of studies often result with controversial and non-conclusive outputs. However, it was determined that each of the implicated candidates would independently have a minor effect on the susceptibility to that disease. Herein we report results from our replication study for association using 255 Bulgarian patients with schizophrenia and schizoaffective disorder and 556 Bulgarian healthy controls. We have selected from the literatures 202 single nucleotide polymorphisms (SNPs) in 59 candidate genes, which previously were implicated in disease susceptibility, and we have genotyped them. Of the 183 SNPs successfully genotyped, only 1 SNP, rs6277 (C957T) in the DRD2 gene (P¼0.0010, odds ratio¼1.76), was considered to be significantly associated with schizophrenia after the replication study using independent sample sets. Our findings support one of the most widely considered hypotheses for schizophrenia etiology, the dopaminergic hypothesis. -
Whole Exome Sequencing Reveals NOTCH1 Mutations in Anaplastic Large Cell Lymphoma and Points to Notch Both As a Key Pathway and a Potential Therapeutic Target
Non-Hodgkin Lymphoma SUPPLEMENTARY APPENDIX Whole exome sequencing reveals NOTCH1 mutations in anaplastic large cell lymphoma and points to Notch both as a key pathway and a potential therapeutic target Hugo Larose, 1,2 Nina Prokoph, 1,2 Jamie D. Matthews, 1 Michaela Schlederer, 3 Sandra Högler, 4 Ali F. Alsulami, 5 Stephen P. Ducray, 1,2 Edem Nuglozeh, 6 Mohammad Feroze Fazaludeen, 7 Ahmed Elmouna, 6 Monica Ceccon, 2,8 Luca Mologni, 2,8 Carlo Gambacorti-Passerini, 2,8 Gerald Hoefler, 9 Cosimo Lobello, 2,10 Sarka Pospisilova, 2,10,11 Andrea Janikova, 2,11 Wilhelm Woessmann, 2,12 Christine Damm-Welk, 2,12 Martin Zimmermann, 13 Alina Fedorova, 14 Andrea Malone, 15 Owen Smith, 15 Mariusz Wasik, 2,16 Giorgio Inghirami, 17 Laurence Lamant, 18 Tom L. Blundell, 5 Wolfram Klapper, 19 Olaf Merkel, 2,3 G. A. Amos Burke, 20 Shahid Mian, 6 Ibraheem Ashankyty, 21 Lukas Kenner 2,3,22 and Suzanne D. Turner 1,2,10 1Department of Pathology, University of Cambridge, Cambridge, UK; 2European Research Initiative for ALK Related Malignancies (ERIA; www.ERIALCL.net ); 3Department of Pathology, Medical University of Vienna, Vienna, Austria; 4Unit of Laboratory Animal Pathology, Uni - versity of Veterinary Medicine Vienna, Vienna, Austria; 5Department of Biochemistry, University of Cambridge, Tennis Court Road, Cam - bridge, UK; 6Molecular Diagnostics and Personalised Therapeutics Unit, Colleges of Medicine and Applied Medical Sciences, University of Ha’il, Ha’il, Saudi Arabia; 7Neuroinflammation Research Group, Department of Neurobiology, A.I Virtanen Institute -
Molecular Genetics of Schizophrenia and Related Intermediate
Juho Wedenoja c R Molecular Genetics of e S Schizophrenia and Related Rea h Intermediate Phenotypes in a Founder Population Phenotypes in a Founder Population Founder a in Phenotypes Intermediate Related and Schizophrenia of Genetics Molecular 28 2010 28 Juho Wedenoja Molecular Genetics of Schizophrenia and Related Intermediate Phenotypes in a Founder Population ACADEMIC DISSERTATION To be presented, with the permission of the Faculty of Medicine, University of Helsinki, for public examination in the Small Hall, University of Helsinki Main Building, on 5 February 2010, at 12 noon. National Institute for Health and Welfare, Helsinki, Finland and Institute for Molecular Medicine Finland FIMM, Helsinki, Finland and Department of Medical Genetics, University of Helsinki, Helsinki, Finland RESEARCH 28 Helsinki 2010 Helsinki University Biomedical Dissertations No 131 ISSN 1457-8433 Publications of the National Institute for Health and Welfare Research 28 © Juho Wedenoja & National Institute for Health and Welfare 2010 ISBN 978-952-245-219-1 (print) ISSN 1798-0054 (print) ISBN 978-952-245-220-7 (pdf) ISSN 1798-0062 (pdf) Cover picture: Satu Wedenoja (Monterey, CA, USA on 7 November 2007) http://www.thl.fi/julkaisut http://ethesis.helsinki.fi/ Helsinki University Print Helsinki, Finland 2010 Supervisors Academician Leena Peltonen-Palotie, MD, PhD Professor, Research Director Institute for Molecular Medicine Finland FIMM Nordic EMBL Partnership for Molecular Medicine National Institute for Health and Welfare and University of Helsinki and Department -
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.