Relationship Between ETS Transcription Factor ETV1 and TGF
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Chromatin State Barriers Enforce an Irreversible Mammalian Cell Fate Decision
bioRxiv preprint doi: https://doi.org/10.1101/2021.05.12.443709; this version posted May 14, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Chromatin state barriers… Blanco et al. 2021 Chromatin state barriers enforce an irreversible mammalian cell fate decision M. Andrés Blanco1,19,*,†,, David B. Sykes6,8,19, Lei Gu2,15,17,18,19, Mengjun Wu2,4,15, Ricardo Petroni1, Rahul Karnik7,8,9, Mathias Wawer10, Joshua Rico1, Haitao Li1, William D. Jacobus2,12,15, Ashwini Jambhekar2,15,11, Sihem Cheloufi5, Alexander Meissner7,8,9,13, Konrad Hochedlinger6,7,8,14, David T. Scadden6,8,9,*, and Yang Shi2,3,* 1 Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA 2 Division of Newborn Medicine, Boston Children’s Hospital, Boston, MA 02115, USA 3 Ludwig Institute for Cancer Research, Oxford Branch, Oxford University, UK 4 Current address: The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark 5 Department of Biochemistry, Stem Cell Center, University of California, Riverside, Riverside, CA 92521, USA. 6 Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA. 7 Broad Institute of MIT and Harvard, Cambridge, MA, USA 8 Harvard Stem Cell Institute, Cambridge, Massachusetts, -
Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model
Downloaded from http://www.jimmunol.org/ by guest on September 25, 2021 T + is online at: average * The Journal of Immunology , 34 of which you can access for free at: 2016; 197:1477-1488; Prepublished online 1 July from submission to initial decision 4 weeks from acceptance to publication 2016; doi: 10.4049/jimmunol.1600589 http://www.jimmunol.org/content/197/4/1477 Molecular Profile of Tumor-Specific CD8 Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A. Waugh, Sonia M. Leach, Brandon L. Moore, Tullia C. Bruno, Jonathan D. Buhrman and Jill E. Slansky J Immunol cites 95 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html http://www.jimmunol.org/content/suppl/2016/07/01/jimmunol.160058 9.DCSupplemental This article http://www.jimmunol.org/content/197/4/1477.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2016 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 25, 2021. The Journal of Immunology Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A. -
Mediator of DNA Damage Checkpoint 1 (MDC1) Is a Novel Estrogen Receptor Co-Regulator in Invasive 6 Lobular Carcinoma of the Breast 7 8 Evelyn K
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.16.423142; this version posted December 16, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 1 Running Title: MDC1 co-regulates ER in ILC 2 3 Research article 4 5 Mediator of DNA damage checkpoint 1 (MDC1) is a novel estrogen receptor co-regulator in invasive 6 lobular carcinoma of the breast 7 8 Evelyn K. Bordeaux1+, Joseph L. Sottnik1+, Sanjana Mehrotra1, Sarah E. Ferrara2, Andrew E. Goodspeed2,3, James 9 C. Costello2,3, Matthew J. Sikora1 10 11 +EKB and JLS contributed equally to this project. 12 13 Affiliations 14 1Dept. of Pathology, University of Colorado Anschutz Medical Campus 15 2Biostatistics and Bioinformatics Shared Resource, University of Colorado Comprehensive Cancer Center 16 3Dept. of Pharmacology, University of Colorado Anschutz Medical Campus 17 18 Corresponding author 19 Matthew J. Sikora, PhD.; Mail Stop 8104, Research Complex 1 South, Room 5117, 12801 E. 17th Ave.; Aurora, 20 CO 80045. Tel: (303)724-4301; Fax: (303)724-3712; email: [email protected]. Twitter: 21 @mjsikora 22 23 Authors' contributions 24 MJS conceived of the project. MJS, EKB, and JLS designed and performed experiments. JLS developed models 25 for the project. EKB, JLS, SM, and AEG contributed to data analysis and interpretation. SEF, AEG, and JCC 26 developed and performed informatics analyses. MJS wrote the draft manuscript; all authors read and revised the 27 manuscript and have read and approved of this version of the manuscript. -
Proteasome System of Protein Degradation and Processing
ISSN 0006-2979, Biochemistry (Moscow), 2009, Vol. 74, No. 13, pp. 1411-1442. © Pleiades Publishing, Ltd., 2009. Original Russian Text © A. V. Sorokin, E. R. Kim, L. P. Ovchinnikov, 2009, published in Uspekhi Biologicheskoi Khimii, 2009, Vol. 49, pp. 3-76. REVIEW Proteasome System of Protein Degradation and Processing A. V. Sorokin*, E. R. Kim, and L. P. Ovchinnikov Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia; E-mail: [email protected]; [email protected] Received February 5, 2009 Abstract—In eukaryotic cells, degradation of most intracellular proteins is realized by proteasomes. The substrates for pro- teolysis are selected by the fact that the gate to the proteolytic chamber of the proteasome is usually closed, and only pro- teins carrying a special “label” can get into it. A polyubiquitin chain plays the role of the “label”: degradation affects pro- teins conjugated with a ubiquitin (Ub) chain that consists at minimum of four molecules. Upon entering the proteasome channel, the polypeptide chain of the protein unfolds and stretches along it, being hydrolyzed to short peptides. Ubiquitin per se does not get into the proteasome, but, after destruction of the “labeled” molecule, it is released and labels another molecule. This process has been named “Ub-dependent protein degradation”. In this review we systematize current data on the Ub–proteasome system, describe in detail proteasome structure, the ubiquitination system, and the classical ATP/Ub- dependent mechanism of protein degradation, as well as try to focus readers’ attention on the existence of alternative mech- anisms of proteasomal degradation and processing of proteins. -
Figure S1. Representative Report Generated by the Ion Torrent System Server for Each of the KCC71 Panel Analysis and Pcafusion Analysis
Figure S1. Representative report generated by the Ion Torrent system server for each of the KCC71 panel analysis and PCaFusion analysis. (A) Details of the run summary report followed by the alignment summary report for the KCC71 panel analysis sequencing. (B) Details of the run summary report for the PCaFusion panel analysis. A Figure S1. Continued. Representative report generated by the Ion Torrent system server for each of the KCC71 panel analysis and PCaFusion analysis. (A) Details of the run summary report followed by the alignment summary report for the KCC71 panel analysis sequencing. (B) Details of the run summary report for the PCaFusion panel analysis. B Figure S2. Comparative analysis of the variant frequency found by the KCC71 panel and calculated from publicly available cBioPortal datasets. For each of the 71 genes in the KCC71 panel, the frequency of variants was calculated as the variant number found in the examined cases. Datasets marked with different colors and sample numbers of prostate cancer are presented in the upper right. *Significantly high in the present study. Figure S3. Seven subnetworks extracted from each of seven public prostate cancer gene networks in TCNG (Table SVI). Blue dots represent genes that include initial seed genes (parent nodes), and parent‑child and child‑grandchild genes in the network. Graphical representation of node‑to‑node associations and subnetwork structures that differed among and were unique to each of the seven subnetworks. TCNG, The Cancer Network Galaxy. Figure S4. REVIGO tree map showing the predicted biological processes of prostate cancer in the Japanese. Each rectangle represents a biological function in terms of a Gene Ontology (GO) term, with the size adjusted to represent the P‑value of the GO term in the underlying GO term database. -
PSMD10 Antibody Cat
PSMD10 Antibody Cat. No.: 57-836 PSMD10 Antibody Western blot analysis of PSMD10 using rabbit polyclonal PSMD10 Antibody using 293 cell lysates (2 ug/lane) either nontransfected (Lane 1) or transiently transfected (Lane 2) with the PSMD10 gene. Specifications HOST SPECIES: Rabbit SPECIES REACTIVITY: Human HOMOLOGY: Predicted species reactivity based on immunogen sequence: Mouse, Rat This PSMD10 antibody is generated from rabbits immunized with a KLH conjugated IMMUNOGEN: synthetic peptide between 184-213 amino acids from the C-terminal region of human PSMD10. TESTED APPLICATIONS: WB APPLICATIONS: For WB starting dilution is: 1:1000 PREDICTED MOLECULAR 24 kDa WEIGHT: September 29, 2021 1 https://www.prosci-inc.com/psmd10-antibody-57-836.html Properties This antibody is purified through a protein A column, followed by peptide affinity PURIFICATION: purification. CLONALITY: Polyclonal ISOTYPE: Rabbit Ig CONJUGATE: Unconjugated PHYSICAL STATE: Liquid BUFFER: Supplied in PBS with 0.09% (W/V) sodium azide. CONCENTRATION: batch dependent Store at 4˚C for three months and -20˚C, stable for up to one year. As with all antibodies STORAGE CONDITIONS: care should be taken to avoid repeated freeze thaw cycles. Antibodies should not be exposed to prolonged high temperatures. Additional Info OFFICIAL SYMBOL: PSMD10 26S proteasome non-ATPase regulatory subunit 10, 26S proteasome regulatory subunit ALTERNATE NAMES: p28, Gankyrin, p28(GANK), PSMD10 ACCESSION NO.: O75832 GENE ID: 5716 USER NOTE: Optimal dilutions for each application to be determined by the researcher. Background and References The 26S proteasome is a multicatalytic proteinase complex with a highly ordered structure composed of 2 complexes, a 20S core and a 19S regulator. -
Anti-Inflammatory Role of Curcumin in LPS Treated A549 Cells at Global Proteome Level and on Mycobacterial Infection
Anti-inflammatory Role of Curcumin in LPS Treated A549 cells at Global Proteome level and on Mycobacterial infection. Suchita Singh1,+, Rakesh Arya2,3,+, Rhishikesh R Bargaje1, Mrinal Kumar Das2,4, Subia Akram2, Hossain Md. Faruquee2,5, Rajendra Kumar Behera3, Ranjan Kumar Nanda2,*, Anurag Agrawal1 1Center of Excellence for Translational Research in Asthma and Lung Disease, CSIR- Institute of Genomics and Integrative Biology, New Delhi, 110025, India. 2Translational Health Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India. 3School of Life Sciences, Sambalpur University, Jyoti Vihar, Sambalpur, Orissa, 768019, India. 4Department of Respiratory Sciences, #211, Maurice Shock Building, University of Leicester, LE1 9HN 5Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia- 7003, Bangladesh. +Contributed equally for this work. S-1 70 G1 S 60 G2/M 50 40 30 % of cells 20 10 0 CURI LPSI LPSCUR Figure S1: Effect of curcumin and/or LPS treatment on A549 cell viability A549 cells were treated with curcumin (10 µM) and/or LPS or 1 µg/ml for the indicated times and after fixation were stained with propidium iodide and Annexin V-FITC. The DNA contents were determined by flow cytometry to calculate percentage of cells present in each phase of the cell cycle (G1, S and G2/M) using Flowing analysis software. S-2 Figure S2: Total proteins identified in all the three experiments and their distribution betwee curcumin and/or LPS treated conditions. The proteins showing differential expressions (log2 fold change≥2) in these experiments were presented in the venn diagram and certain number of proteins are common in all three experiments. -
Produktinformation
Produktinformation Diagnostik & molekulare Diagnostik Laborgeräte & Service Zellkultur & Verbrauchsmaterial Forschungsprodukte & Biochemikalien Weitere Information auf den folgenden Seiten! See the following pages for more information! Lieferung & Zahlungsart Lieferung: frei Haus Bestellung auf Rechnung SZABO-SCANDIC Lieferung: € 10,- HandelsgmbH & Co KG Erstbestellung Vorauskassa Quellenstraße 110, A-1100 Wien T. +43(0)1 489 3961-0 Zuschläge F. +43(0)1 489 3961-7 [email protected] • Mindermengenzuschlag www.szabo-scandic.com • Trockeneiszuschlag • Gefahrgutzuschlag linkedin.com/company/szaboscandic • Expressversand facebook.com/szaboscandic PSMD10 Antibody, Biotin conjugated Product Code CSB-PA018899LD01HU Abbreviation 26S proteasome non-ATPase regulatory subunit 10 Storage Upon receipt, store at -20°C or -80°C. Avoid repeated freeze. Uniprot No. O75832 Immunogen Recombinant Human 26S proteasome non-ATPase regulatory subunit 10 protein (1-226AA) Raised In Rabbit Species Reactivity Human Tested Applications ELISA Relevance Acts as a chaperone during the assembly of the 26S proteasome, specifically of the PA700/19S regulatory complex (RC). In the initial step of the base subcomplex assembly is part of an intermediate PSMD10:PSMC4:PSMC5:PAAF1 module which probably assembles with a PSMD5:PSMC2:PSMC1:PSMD2 module. Independently of the proteasome, regulates EGF-induced AKT activation through inhibition of the RHOA/ROCK/PTEN pahway, leading to prolonged AKT activation. Plays an important role in RAS-induced tumorigenesis. Acts as an proto-oncoprotein by being involved in negative regulation of tumor suppressors RB1 and p53/TP53. Overexpression is leading to phosphorylation of RB1 and proteasomal degradation of RB1. Regulates CDK4-mediated phosphorylation of RB1 by competing with CDKN2A for binding with CDK4. Facilitates binding of MDM2 to p53/TP53 and the mono- and polyubiquitination of p53/TP53 by MDM2 suggesting a function in targeting the TP53:MDM2 complex to the 26S proteasome. -
PSMD10 Antibody (Center) Purified Rabbit Polyclonal Antibody (Pab) Catalog # AW5126
10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 PSMD10 Antibody (Center) Purified Rabbit Polyclonal Antibody (Pab) Catalog # AW5126 Specification PSMD10 Antibody (Center) - Product Information Application IF, WB, IHC-P,E Primary Accession O75832 Other Accession Q9Z2X2 Reactivity Human Predicted Mouse Host Rabbit Clonality Polyclonal Calculated MW H=24,16;M=25;Ra t=25 KDa Isotype Rabbit Ig Antigen Source HUMAN PSMD10 Antibody (Center) - Additional Information Gene ID 5716 Fluorescent image of Hela cells stained with PSMD10 Antibody (Center)(Cat#AW5126). Antigen Region AW5126 was diluted at 1:25 dilution. An 43-76 Alexa Fluor 488-conjugated goat anti-rabbit lgG at 1:400 dilution was used as the Other Names secondary antibody (green). Cytoplasmic 26S proteasome non-ATPase regulatory subunit 10, 26S proteasome regulatory actin was counterstained with Alexa Fluor® subunit p28, Gankyrin, p28(GANK), PSMD10 555 conjugated with Phalloidin (red). Dilution IF~~1:25 WB~~ 1:1000 IHC-P~~1:25 Target/Specificity This PSMD10 antibody is generated from a rabbit immunized with a KLH conjugated synthetic peptide between 43-76 amino acids from the Central region of human PSMD10. Format Purified polyclonal antibody supplied in PBS with 0.09% (W/V) sodium azide. This antibody is purified through a protein A column, followed by peptide affinity purification. Western blot analysis of lysates from MCF-7, PC-3, K562 cell line (from left to right), using Storage PSMD10 Antibody (Center)(Cat. #AW5126). Page 1/3 10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 Maintain refrigerated at 2-8°C for up to 2 AW5126 was diluted at 1:1000 at each lane. -
A Dissertation Entitled the Androgen Receptor
A Dissertation entitled The Androgen Receptor as a Transcriptional Co-activator: Implications in the Growth and Progression of Prostate Cancer By Mesfin Gonit Submitted to the Graduate Faculty as partial fulfillment of the requirements for the PhD Degree in Biomedical science Dr. Manohar Ratnam, Committee Chair Dr. Lirim Shemshedini, Committee Member Dr. Robert Trumbly, Committee Member Dr. Edwin Sanchez, Committee Member Dr. Beata Lecka -Czernik, Committee Member Dr. Patricia R. Komuniecki, Dean College of Graduate Studies The University of Toledo August 2011 Copyright 2011, Mesfin Gonit This document is copyrighted material. Under copyright law, no parts of this document may be reproduced without the expressed permission of the author. An Abstract of The Androgen Receptor as a Transcriptional Co-activator: Implications in the Growth and Progression of Prostate Cancer By Mesfin Gonit As partial fulfillment of the requirements for the PhD Degree in Biomedical science The University of Toledo August 2011 Prostate cancer depends on the androgen receptor (AR) for growth and survival even in the absence of androgen. In the classical models of gene activation by AR, ligand activated AR signals through binding to the androgen response elements (AREs) in the target gene promoter/enhancer. In the present study the role of AREs in the androgen- independent transcriptional signaling was investigated using LP50 cells, derived from parental LNCaP cells through extended passage in vitro. LP50 cells reflected the signature gene overexpression profile of advanced clinical prostate tumors. The growth of LP50 cells was profoundly dependent on nuclear localized AR but was independent of androgen. Nevertheless, in these cells AR was unable to bind to AREs in the absence of androgen. -
Integrative Epigenomic and Genomic Analysis of Malignant Pheochromocytoma
EXPERIMENTAL and MOLECULAR MEDICINE, Vol. 42, No. 7, 484-502, July 2010 Integrative epigenomic and genomic analysis of malignant pheochromocytoma Johanna Sandgren1,2* Robin Andersson3*, pression examination in a malignant pheochromocy- Alvaro Rada-Iglesias3, Stefan Enroth3, toma sample. The integrated analysis of the tumor ex- Goran̈ Akerstro̊ m̈ 1, Jan P. Dumanski2, pression levels, in relation to normal adrenal medulla, Jan Komorowski3,4, Gunnar Westin1 and indicated that either histone modifications or chromo- somal alterations, or both, have great impact on the ex- Claes Wadelius2,5 pression of a substantial fraction of the genes in the in- vestigated sample. Candidate tumor suppressor 1Department of Surgical Sciences genes identified with decreased expression, a Uppsala University, Uppsala University Hospital H3K27me3 mark and/or in regions of deletion were for SE-75185 Uppsala, Sweden 2 instance TGIF1, DSC3, TNFRSF10B, RASSF2, HOXA9, Department of Genetics and Pathology Rudbeck Laboratory, Uppsala University PTPRE and CDH11. More genes were found with in- SE-75185 Uppsala, Sweden creased expression, a H3K4me3 mark, and/or in re- 3The Linnaeus Centre for Bioinformatics gions of gain. Potential oncogenes detected among Uppsala University those were GNAS, INSM1, DOK5, ETV1, RET, NTRK1, SE-751 24 Uppsala, Sweden IGF2, and the H3K27 trimethylase gene EZH2. Our ap- 4Interdisciplinary Centre for Mathematical and proach to associate histone methylations and DNA Computational Modelling copy number changes to gene expression revealed ap- Warsaw University parent impact on global gene transcription, and en- PL-02-106 Warszawa, Poland abled the identification of candidate tumor genes for 5Corresponding author: Tel, 46-18-471-40-76; further exploration. -
Genetically Incorporated Crosslinkers Reveal Nlee Attenuates Host
RESEARCH ARTICLE Genetically incorporated crosslinkers reveal NleE attenuates host autophagy dependent on PSMD10 Jingxiang Li1, Shupan Guo1, Fangni Chai1, Qi Sun1, Pan Li1, Li Gao2, Lunzhi Dai2, Xiaoxiao Ouyang1, Zhihui Zhou1, Li Zhou1, Wei Cheng1, Shiqian Qi1, Kefeng Lu1, Haiyan Ren1* 1Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China; 2Department of General Practice and National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, and Sichuan University, Chengdu, China Abstract Autophagy acts as a pivotal innate immune response against infection. Some virulence effectors subvert the host autophagic machinery to escape the surveillance of autophagy. The mechanism by which pathogens interact with host autophagy remains mostly unclear. However, traditional strategies often have difficulty identifying host proteins that interact with effectors due to the weak, dynamic, and transient nature of these interactions. Here, we found that Enteropathogenic Escherichia coli (EPEC) regulates autophagosome formation in host cells dependent on effector NleE. The 26S Proteasome Regulatory Subunit 10 (PSMD10) was identified as a direct interaction partner of NleE in living cells by employing genetically incorporated crosslinkers. Pairwise chemical crosslinking revealed that NleE interacts with the N-terminus of PSMD10. We demonstrated that PSMD10 homodimerization is necessary for its interaction with ATG7 and promotion of autophagy, but not necessary for PSMD10 interaction with ATG12. Therefore, NleE-mediated PSMD10 in monomeric state attenuates host autophagosome formation. *For correspondence: Our study reveals the mechanism through which EPEC attenuates host autophagy activity. [email protected] Competing interests: The authors declare that no competing interests exist.