Oligodendrocytes Remodel the Genomic Fabrics of Functional Pathways in Astrocytes
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Original Article Upregulation of HOXA13 As a Potential Tumorigenesis and Progression Promoter of LUSC Based on Qrt-PCR and Bioinformatics
Int J Clin Exp Pathol 2017;10(10):10650-10665 www.ijcep.com /ISSN:1936-2625/IJCEP0065149 Original Article Upregulation of HOXA13 as a potential tumorigenesis and progression promoter of LUSC based on qRT-PCR and bioinformatics Rui Zhang1*, Yun Deng1*, Yu Zhang1, Gao-Qiang Zhai1, Rong-Quan He2, Xiao-Hua Hu2, Dan-Ming Wei1, Zhen-Bo Feng1, Gang Chen1 Departments of 1Pathology, 2Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China. *Equal contributors. Received September 7, 2017; Accepted September 29, 2017; Epub October 1, 2017; Published October 15, 2017 Abstract: In this study, we investigated the levels of homeobox A13 (HOXA13) and the mechanisms underlying the co-expressed genes of HOXA13 in lung squamous cancer (LUSC), the signaling pathways in which the co-ex- pressed genes of HOXA13 are involved and their functional roles in LUSC. The clinical significance of 23 paired LUSC tissues and adjacent non-tumor tissues were gathered. HOXA13 levels in LUSC were detected by quantita- tive real-time polymerase chain reaction (qRT-PCR). HOXA13 levels in LUSC from The Cancer Genome Atlas (TCGA) and Oncomine were analyzed. We performed receiver operator characteristic (ROC) curves of various clinicopath- ological features of LUSC. Co-expressed of HOXA13 were collected from MEM, cBioPortal and GEPIA. The func- tions and pathways of the most reliable overlapped genes were achieved from the Gene Otology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively. The protein-protein interaction (PPI) net- works were mapped using STRING. HOXA13 in LUSC were markedly upregulated compared with those in the non- cancerous controls as demonstrated by qRT-PCR (LUSC: 0.330±0.360; CONTROLS: 0.155±0.142; P=0.021). -
Regulation of Dishevelled DEP Domain Swapping by Conserved Phosphorylation Sites
Regulation of Dishevelled DEP domain swapping by conserved phosphorylation sites Gonzalo J. Beitiaa,1, Trevor J. Rutherforda,1, Stefan M. V. Freunda, Hugh R. Pelhama, Mariann Bienza, and Melissa V. Gammonsa,2 aMedical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, United Kingdom Edited by Roeland Nusse, Stanford University School of Medicine, Stanford, CA, and approved May 13, 2021 (received for review February 20, 2021) Wnt signals bind to Frizzled receptors to trigger canonical and with these effectors even if present at a low cellular concentra- noncanonical signaling responses that control cell fates during tion (1, 3, 12). animal development and tissue homeostasis. All Wnt signals are The DEP domain is a small globular domain composed of three relayed by the hub protein Dishevelled. During canonical (β-catenin– α-helices and a flexible hinge loop between the first (H1) and sec- dependent) signaling, Dishevelled assembles signalosomes via dy- ond helix (H2), which, in the monomeric configuration, folds back namic head-to-tail polymerization of its Dishevelled and Axin (DIX) on itself to form a prominent “DEP finger” that is responsible domain, which are cross-linked by its Dishevelled, Egl-10, and Pleck- for binding to Frizzled (Fig. 1A) (13). DEP dimerization involves strin (DEP) domain through a conformational switch from monomer a highly unusual mechanism called “domain swapping” (14). During to domain-swapped dimer. The domain-swapped conformation of this process, H1 of one DEP monomer is exchanged with H1 from a DEP masks the site through which Dishevelled binds to Frizzled, im- reciprocal one through outward motions of the hinge loops, replacing plying that DEP domain swapping results in the detachment of Dish- intra- with intermolecular contacts. -
Structure and Function of the Fgd Family of Divergent FYVE Domain Proteins
Biochemistry and Cell Biology Structure and Function of the Fgd Family of Divergent FYVE Domain Proteins Journal: Biochemistry and Cell Biology Manuscript ID bcb-2018-0185.R1 Manuscript Type: Mini Review Date Submitted by the 03-Aug-2018 Author: Complete List of Authors: Eitzen, Gary; University of Alberta Faculty of Medicine and Dentistry Smithers, Cameron C.; University of Alberta, Biochemistry Murray, Allan; University of Alberta Faculty of Medicine and Dentistry Overduin, Michael; University of Alberta Faculty of Medicine and Dentistry Draft Fgd, Pleckstrin Homology domain, FYVE domain, Dbl Homology Domain, Keyword: Rho GEF Is the invited manuscript for consideration in a Special CSMB Special Issue Issue? : https://mc06.manuscriptcentral.com/bcb-pubs Page 1 of 37 Biochemistry and Cell Biology Title: Structure and Function of the Fgd Family of Divergent FYVE Domain Proteins Authors: Gary Eitzen1, Cameron C. Smithers2, Allan G Murray3 and Michael Overduin2* Draft 1Department of Cell Biology, 2Department of Biochemistry, 3Department of Medicine, University of Alberta, Edmonton, Alberta, Canada *Corresponding author. Michael Overduin Telephone: +1 780 492 3518 Fax: +1 780 492-0886 E-mail: [email protected] https://mc06.manuscriptcentral.com/bcb-pubs Biochemistry and Cell Biology Page 2 of 37 Abstract FYVE domains are highly conserved protein modules that typically bind phosphatidylinositol 3-phosphate (PI3P) on the surface of early endosomes. Along with pleckstrin homology (PH) and phox homology (PX) domains, FYVE domains are the principal readers of the phosphoinositide (PI) code that mediate specific recognition of eukaryotic organelles. Of all the human FYVE domain-containing proteins, those within the Faciogenital dysplasia (Fgd) subfamily are particularly divergent, and couple with GTPases to exert unique cellular functions. -
Regulation of Cdc42 and Its Effectors in Epithelial Morphogenesis Franck Pichaud1,2,*, Rhian F
© 2019. Published by The Company of Biologists Ltd | Journal of Cell Science (2019) 132, jcs217869. doi:10.1242/jcs.217869 REVIEW SUBJECT COLLECTION: ADHESION Regulation of Cdc42 and its effectors in epithelial morphogenesis Franck Pichaud1,2,*, Rhian F. Walther1 and Francisca Nunes de Almeida1 ABSTRACT An overview of Cdc42 Cdc42 – a member of the small Rho GTPase family – regulates cell Cdc42 was discovered in yeast and belongs to a large family of small – polarity across organisms from yeast to humans. It is an essential (20 30 kDa) GTP-binding proteins (Adams et al., 1990; Johnson regulator of polarized morphogenesis in epithelial cells, through and Pringle, 1990). It is part of the Ras-homologous Rho subfamily coordination of apical membrane morphogenesis, lumen formation and of GTPases, of which there are 20 members in humans, including junction maturation. In parallel, work in yeast and Caenorhabditis elegans the RhoA and Rac GTPases, (Hall, 2012). Rho, Rac and Cdc42 has provided important clues as to how this molecular switch can homologues are found in all eukaryotes, except for plants, which do generate and regulate polarity through localized activation or inhibition, not have a clear homologue for Cdc42. Together, the function of and cytoskeleton regulation. Recent studies have revealed how Rho GTPases influences most, if not all, cellular processes. important and complex these regulations can be during epithelial In the early 1990s, seminal work from Alan Hall and his morphogenesis. This complexity is mirrored by the fact that Cdc42 can collaborators identified Rho, Rac and Cdc42 as main regulators of exert its function through many effector proteins. -
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. -
Table 2. Significant
Table 2. Significant (Q < 0.05 and |d | > 0.5) transcripts from the meta-analysis Gene Chr Mb Gene Name Affy ProbeSet cDNA_IDs d HAP/LAP d HAP/LAP d d IS Average d Ztest P values Q-value Symbol ID (study #5) 1 2 STS B2m 2 122 beta-2 microglobulin 1452428_a_at AI848245 1.75334941 4 3.2 4 3.2316485 1.07398E-09 5.69E-08 Man2b1 8 84.4 mannosidase 2, alpha B1 1416340_a_at H4049B01 3.75722111 3.87309653 2.1 1.6 2.84852656 5.32443E-07 1.58E-05 1110032A03Rik 9 50.9 RIKEN cDNA 1110032A03 gene 1417211_a_at H4035E05 4 1.66015788 4 1.7 2.82772795 2.94266E-05 0.000527 NA 9 48.5 --- 1456111_at 3.43701477 1.85785922 4 2 2.8237185 9.97969E-08 3.48E-06 Scn4b 9 45.3 Sodium channel, type IV, beta 1434008_at AI844796 3.79536664 1.63774235 3.3 2.3 2.75319499 1.48057E-08 6.21E-07 polypeptide Gadd45gip1 8 84.1 RIKEN cDNA 2310040G17 gene 1417619_at 4 3.38875643 1.4 2 2.69163229 8.84279E-06 0.0001904 BC056474 15 12.1 Mus musculus cDNA clone 1424117_at H3030A06 3.95752801 2.42838452 1.9 2.2 2.62132809 1.3344E-08 5.66E-07 MGC:67360 IMAGE:6823629, complete cds NA 4 153 guanine nucleotide binding protein, 1454696_at -3.46081884 -4 -1.3 -1.6 -2.6026947 8.58458E-05 0.0012617 beta 1 Gnb1 4 153 guanine nucleotide binding protein, 1417432_a_at H3094D02 -3.13334396 -4 -1.6 -1.7 -2.5946297 1.04542E-05 0.0002202 beta 1 Gadd45gip1 8 84.1 RAD23a homolog (S. -
Pancreatic Beta Cells Express a Diverse Set Ofhomeobox Genes
Proc. Nati. Acad. Sci. USA Vol. 91, pp. 12203-12207, December 1994 Biochemistry Pancreatic beta cells express a diverse set of homeobox genes (Lim motif/Lmx gene/Nkx gene/Alx gene/Vdx homeobox) ABRAHAM RUDNICK*t, THAI YEN LING*, HIROKI ODAGIRI*, WILLIAM J. RUTTER*t, AND MICHAEL S. GERMAN*t§ *Hormone Research Institute and Departments of tMedicine and tBiochemistry and Biophysics, University of California, San Francisco, CA 94143-0534 Contributed by William J. Rutter, August 22, 1994 ABSTRACT Homeobox genes, which are found in all RIPE3B element (16) and the P1 element (8) [also called CT1 eukaryotic organisms, encode transcriptional regulators in- (9)] lie on either side of the IEB1 element. The A/T elements volved in cell-type differentiation and development. Several and the E boxes function synergistically: none of the ele- homeobox genes encoding homeodomain proteins that bind and ments can function in isolation, but combination of an E box activate the insulin gene promoter have been described. In an and an A/T element results in dramatic activation of tran- attempt to identify additional beta-cell homeodomain proteins, scription (11, 16, 19). A number of complexes from beta-cell we designed primers based on the sequences of beta-cell nuclei bind to the A/T elements (6, 8-11, 16, 19). Some homeobox genes cdx3 and lmxl and the Drosophia homeodo- proteins in these complexes have been cloned, and they all main protein Antennapedia and used these primers to amplffy contain homeodomains. The A/T-binding proteins that have inserts by PCR from an insulinoma cDNA library. -
An Animal Model with a Cardiomyocyte-Specific Deletion of Estrogen Receptor Alpha: Functional, Metabolic, and Differential Netwo
Washington University School of Medicine Digital Commons@Becker Open Access Publications 2014 An animal model with a cardiomyocyte-specific deletion of estrogen receptor alpha: Functional, metabolic, and differential network analysis Sriram Devanathan Washington University School of Medicine in St. Louis Timothy Whitehead Washington University School of Medicine in St. Louis George G. Schweitzer Washington University School of Medicine in St. Louis Nicole Fettig Washington University School of Medicine in St. Louis Attila Kovacs Washington University School of Medicine in St. Louis See next page for additional authors Follow this and additional works at: https://digitalcommons.wustl.edu/open_access_pubs Recommended Citation Devanathan, Sriram; Whitehead, Timothy; Schweitzer, George G.; Fettig, Nicole; Kovacs, Attila; Korach, Kenneth S.; Finck, Brian N.; and Shoghi, Kooresh I., ,"An animal model with a cardiomyocyte-specific deletion of estrogen receptor alpha: Functional, metabolic, and differential network analysis." PLoS One.9,7. e101900. (2014). https://digitalcommons.wustl.edu/open_access_pubs/3326 This Open Access Publication is brought to you for free and open access by Digital Commons@Becker. It has been accepted for inclusion in Open Access Publications by an authorized administrator of Digital Commons@Becker. For more information, please contact [email protected]. Authors Sriram Devanathan, Timothy Whitehead, George G. Schweitzer, Nicole Fettig, Attila Kovacs, Kenneth S. Korach, Brian N. Finck, and Kooresh I. Shoghi This open access publication is available at Digital Commons@Becker: https://digitalcommons.wustl.edu/open_access_pubs/3326 An Animal Model with a Cardiomyocyte-Specific Deletion of Estrogen Receptor Alpha: Functional, Metabolic, and Differential Network Analysis Sriram Devanathan1, Timothy Whitehead1, George G. Schweitzer2, Nicole Fettig1, Attila Kovacs3, Kenneth S. -
Molecular Dissection of G-Protein Coupled Receptor Signaling and Oligomerization
MOLECULAR DISSECTION OF G-PROTEIN COUPLED RECEPTOR SIGNALING AND OLIGOMERIZATION BY MICHAEL RIZZO A Dissertation Submitted to the Graduate Faculty of WAKE FOREST UNIVERSITY GRADUATE SCHOOL OF ARTS AND SCIENCES in Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY Biology December, 2019 Winston-Salem, North Carolina Approved By: Erik C. Johnson, Ph.D. Advisor Wayne E. Pratt, Ph.D. Chair Pat C. Lord, Ph.D. Gloria K. Muday, Ph.D. Ke Zhang, Ph.D. ACKNOWLEDGEMENTS I would first like to thank my advisor, Dr. Erik Johnson, for his support, expertise, and leadership during my time in his lab. Without him, the work herein would not be possible. I would also like to thank the members of my committee, Dr. Gloria Muday, Dr. Ke Zhang, Dr. Wayne Pratt, and Dr. Pat Lord, for their guidance and advice that helped improve the quality of the research presented here. I would also like to thank members of the Johnson lab, both past and present, for being valuable colleagues and friends. I would especially like to thank Dr. Jason Braco, Dr. Jon Fisher, Dr. Jake Saunders, and Becky Perry, all of whom spent a great deal of time offering me advice, proofreading grants and manuscripts, and overall supporting me through the ups and downs of the research process. Finally, I would like to thank my family, both for instilling in me a passion for knowledge and education, and for their continued support. In particular, I would like to thank my wife Emerald – I am forever indebted to you for your support throughout this process, and I will never forget the sacrifices you made to help me get to where I am today. -
Cyclin K Interacts with Β-Catenin to Induce Cyclin D1 Expression And
Theranostics 2020, Vol. 10, Issue 24 11144 Ivyspring International Publisher Theranostics 2020; 10(24): 11144-11158. doi: 10.7150/thno.42578 Research Paper Cyclin K interacts with β-catenin to induce Cyclin D1 expression and facilitates tumorigenesis and radioresistance in lung cancer Guojun Yao*, Jing Tang*, Xijie Yang, Ye Zhao, Rui Zhou, Rui Meng, Sheng Zhang, Xiaorong Dong, Tao Zhang, Kunyu Yang, Gang Wu and Shuangbing Xu Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China. *These authors contributed equally to this work. Corresponding author: Shuangbing Xu or Gang Wu, Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China. E-mail: [email protected] or [email protected]. © The author(s). This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/). See http://ivyspring.com/terms for full terms and conditions. Received: 2019.11.29; Accepted: 2020.08.24; Published: 2020.09.11 Abstract Rationale: Radioresistance remains the major cause of local relapse and distant metastasis in lung cancer. However, the underlying molecular mechanisms remain poorly defined. This study aimed to investigate the role and regulatory mechanism of Cyclin K in lung cancer radioresistance. Methods: Expression levels of Cyclin K were measured by immunohistochemistry in human lung cancer tissues and adjacent normal lung tissues. Cell growth and proliferation, neutral comet and foci formation assays, G2/M checkpoint and a xenograft mouse model were used for functional analyses. Gene expression was examined by RNA sequencing and quantitative real-time PCR. -
4-6 Weeks Old Female C57BL/6 Mice Obtained from Jackson Labs Were Used for Cell Isolation
Methods Mice: 4-6 weeks old female C57BL/6 mice obtained from Jackson labs were used for cell isolation. Female Foxp3-IRES-GFP reporter mice (1), backcrossed to B6/C57 background for 10 generations, were used for the isolation of naïve CD4 and naïve CD8 cells for the RNAseq experiments. The mice were housed in pathogen-free animal facility in the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee. Preparation of cells: Subsets of thymocytes were isolated by cell sorting as previously described (2), after cell surface staining using CD4 (GK1.5), CD8 (53-6.7), CD3ε (145- 2C11), CD24 (M1/69) (all from Biolegend). DP cells: CD4+CD8 int/hi; CD4 SP cells: CD4CD3 hi, CD24 int/lo; CD8 SP cells: CD8 int/hi CD4 CD3 hi, CD24 int/lo (Fig S2). Peripheral subsets were isolated after pooling spleen and lymph nodes. T cells were enriched by negative isolation using Dynabeads (Dynabeads untouched mouse T cells, 11413D, Invitrogen). After surface staining for CD4 (GK1.5), CD8 (53-6.7), CD62L (MEL-14), CD25 (PC61) and CD44 (IM7), naïve CD4+CD62L hiCD25-CD44lo and naïve CD8+CD62L hiCD25-CD44lo were obtained by sorting (BD FACS Aria). Additionally, for the RNAseq experiments, CD4 and CD8 naïve cells were isolated by sorting T cells from the Foxp3- IRES-GFP mice: CD4+CD62LhiCD25–CD44lo GFP(FOXP3)– and CD8+CD62LhiCD25– CD44lo GFP(FOXP3)– (antibodies were from Biolegend). In some cases, naïve CD4 cells were cultured in vitro under Th1 or Th2 polarizing conditions (3, 4). -
The Uvomorulin-Anchorage Protein a Catenin Is a Vinculin
Proc. Nail. Acad. Sci. USA Vol. 88, pp. 9156-9160, October 1991 Cell Biology The uvomorulin-anchorage protein a catenin is a vinculin homologue KURT HERRENKNECHT*, MASAYUKI OZAWA*t, CHRISTOPH ECKERSKORN*, FRIEDRICH LOTTSPEICHt, MARTIN LENTER*, AND ROLF KEMLER*§ *Max-Planck-Institut ffir Immunbiologie, FG Molekulare Embryologie, D-7800 Freiburg, Federal Republic of Germany; and tMax-Planck-Institut ffr Biochemie, D-8033 Martinsried, Federal Republic of Germany Communicated by Franqois Jacob, July 18, 1991 (receivedfor review June 25, 1991) ABSTRACT The cytoplasmic region of the Ca2+- domain is well conserved in other cadherins, it is possible that dependent cell-adhesion molecule (CAM) uvomorulin associ- catenins may also complex with other members of this gene ates with distinct cytoplasmic proteins with molecular masses family (13, 14). Here we have produced antibodies against a of 102, 88, and 80 kDa termed a, (3, and ycatenin, respectively. catenin and show that a catenin is indeed associated with This complex formation links uvomorulin to the actin filament cadherins from human, mouse, and Xenopus. We have network, which seems to be of primary importance for its cloned and sequenced¶ the cDNA coding for a catenin and cell-adhesion properties. We show here that antibodies against have established the primary protein structure. Sequence a catenin also immunoprecipitate complexes that contain hu- comparison reveals homology to vinculin, a well-known man N-cadherin, mouse P-cadherin, chicken A-CAM (adhe- adherens-type and focal contact protein. rens junction-specific CAM; also called N-cadherin) or Xeno- pus U-cadherin, demonstrating that a catenin is complexed with other cadherins.