Gene Expression Profiling Identifies STAT3 As a Novel Pathway for Immunomodulation by Cholera Toxin Adjuvant
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Mapping the Interface Between Calmodulin and MARCKS-Related Protein by Fluorescence Spectroscopy Andreas Ulrich*†‡, Arndt A
Mapping the interface between calmodulin and MARCKS-related protein by fluorescence spectroscopy Andreas Ulrich*†‡, Arndt A. P. Schmitz*‡§, Thomas Braun*‡¶, Tao Yuanʈ‡, Hans J. Vogelʈ, and Guy Verge` res*,** *Department of Biophysical Chemistry, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland; and ʈDepartment of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada Edited by H. Ronald Kaback, University of California, Los Angeles, CA, and approved March 3, 2000 (received for review November 16, 1999) MARCKS-related protein (MRP) is a myristoylated protein kinase C acid residues. The effector domain could be on the surface of substrate that binds calmodulin (CaM) with nanomolar affinity. To MARCKS proteins and partially exposed to water (model B). This obtain structural information on this protein, we have engineered model fits the proposed amphipathic structure of the effector 10 tryptophan residues between positions 89 and 104 in the domain (basic͞hydrophobic residues). Finally, the effector domain effector domain, a 24-residue-long amphipathic segment that could be completely exposed to water and either act as a hinge mediates binding of MRP to CaM. We show that the effector between the C- and N-terminal domains of MARCKS proteins domain is in a polar environment in free MRP, suggesting exposure (model C1) or form an exposed loop on the surface of the protein to water, in agreement with a rod-shaped structure of the protein. (model C2). The observation that MARCKS proteins are elon- The effector domain participates in the binding of MRP to CaM, as gated molecules (5, 10) supports model C1. -
BTG2: a Rising Star of Tumor Suppressors (Review)
INTERNATIONAL JOURNAL OF ONCOLOGY 46: 459-464, 2015 BTG2: A rising star of tumor suppressors (Review) BIjING MAO1, ZHIMIN ZHANG1,2 and GE WANG1 1Cancer Center, Institute of Surgical Research, Daping Hospital, Third Military Medical University, Chongqing 400042; 2Department of Oncology, Wuhan General Hospital of Guangzhou Command, People's Liberation Army, Wuhan, Hubei 430070, P.R. China Received September 22, 2014; Accepted November 3, 2014 DOI: 10.3892/ijo.2014.2765 Abstract. B-cell translocation gene 2 (BTG2), the first 1. Discovery of BTG2 in TOB/BTG gene family gene identified in the BTG/TOB gene family, is involved in many biological activities in cancer cells acting as a tumor The TOB/BTG genes belong to the anti-proliferative gene suppressor. The BTG2 expression is downregulated in many family that includes six different genes in vertebrates: TOB1, human cancers. It is an instantaneous early response gene and TOB2, BTG1 BTG2/TIS21/PC3, BTG3 and BTG4 (Fig. 1). plays important roles in cell differentiation, proliferation, DNA The conserved domain of BTG N-terminal contains two damage repair, and apoptosis in cancer cells. Moreover, BTG2 regions, named box A and box B, which show a high level of is regulated by many factors involving different signal path- homology to the other domains (1-5). Box A has a major effect ways. However, the regulatory mechanism of BTG2 is largely on cell proliferation, while box B plays a role in combination unknown. Recently, the relationship between microRNAs and with many target molecules. Compared with other family BTG2 has attracted much attention. MicroRNA-21 (miR-21) members, BTG1 and BTG2 have an additional region named has been found to regulate BTG2 gene during carcinogenesis. -
Original Article Long Noncoding RNA TOB1-AS1, an Epigenetically Silenced Gene, Functioned As a Novel Tumor Suppressor by Sponging Mir-27B in Cervical Cancer
Am J Cancer Res 2018;8(8):1483-1498 www.ajcr.us /ISSN:2156-6976/ajcr0079106 Original Article Long noncoding RNA TOB1-AS1, an epigenetically silenced gene, functioned as a novel tumor suppressor by sponging miR-27b in cervical cancer Jihang Yao1, Zhenghong Li1, Ziwei Yang2, Hui Xue1, Hua Chang1, Xue Zhang1, Tianren Li1, Kejun Guo1 Departments of 1Gynecology, 2Clinical Laboratory, The First Hospital of China Medical University, Shenyang 110001, Liaoning, China Received April 21, 2018; Accepted July 9, 2018; Epub August 1, 2018; Published August 15, 2018 Abstract: Cervical cancer is one of the most common cancers in females, accounting for a majority of cancer- related deaths in worldwide. Long non-coding RNAs (lncRNAs) have been identified as critical regulators in many tumor-related biological processes. Thus, investigation into the function and mechanism of lncRNAs in the develop- ment of cervical cancer is very necessary. In this study, we found that the expression of TOB1-AS1 was significantly decreased in cervical cancer tissues compared with the adjacent normal tissues. The methylation status of TOB1- AS1-related CpG island was analyzed using methylation specific PCR and bisulfite sequencing analysis, revealing that the aberrant hypermethylation of TOB1-AS1-related CpG island was frequently observed in primary tumors and cervical cancer cells. The expression of TOB1-AS1 in cervical cancer cells could be reversed by demethylation agent treatment. Functionally, overexpression of TOB1-AS1 significantly inhibited cell proliferation, cell cycle progression, invasion and induced apoptosis, while knockdown of TOB1-AS1 exhibited the opposite effect. Furthermore, it was determined that TOB1-AS1 was able to bind and degrade the expression of miR-27b. -
A Deficiency in the Region Homologous to Human 17Q21.33
Copyright Ó 2006 by the Genetics Society of America DOI: 10.1534/genetics.105.054833 A Deficiency in the Region Homologous to Human 17q21.33–q23.2 Causes Heart Defects in Mice Y. Eugene Yu,*,†,1,2 Masae Morishima,‡ Annie Pao,* Ding-Yan Wang,§ Xiao-Yan Wen,§ Antonio Baldini*,‡,** and Allan Bradley††,1 *Department of Molecular and Human Genetics, ‡Department of Pediatrics (Cardiology), **Center for Cardiovascular Development, Baylor College of Medicine, Houston, Texas 77030, †Department of Cancer Genetics and Genetics Program, Roswell Park Cancer Institute, Buffalo, New York 14263, §Division of Cellular and Molecular Biology, Toronto General Research Institute, University of Toronto, Toronto, Ontario M5G 2C1, Canada and ††Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom Manuscript received December 17, 2005 Accepted for publication February 14, 2006 ABSTRACT Several constitutional chromosomal rearrangements occur on human chromosome 17. Patients who carry constitutional deletions of 17q21.3–q24 exhibit distinct phenotypic features. Within the deletion interval, there is a genomic segment that is bounded by the myeloperoxidase and homeobox B1 genes. This genomic segment is syntenically conserved on mouse chromosome 11 and is bounded by the mouse homologs of the same genes (Mpo and HoxB1). To attain functional information about this syntenic segment in mice, we have generated a 6.9-Mb deletion [Df(11)18], the reciprocal duplication [Dp(11)18] between Mpo and Chad (the chondroadherin gene), and a 1.8-Mb deletion between Chad and HoxB1. Phenotypic analyses of the mutant mouse lines showed that the Dp(11)18/Dp(11)18 genotype was responsible for embryonic or adolescent lethality, whereas the Df(11)18/1 genotype was responsible for heart defects. -
Novelty Indicator for Enhanced Prioritization of Predicted Gene Ontology Annotations
IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. X, NO. X, MONTHXXX 20XX 1 Novelty Indicator for Enhanced Prioritization of Predicted Gene Ontology Annotations Davide Chicco, Fernando Palluzzi, and Marco Masseroli Abstract—Biomolecular controlled annotations have become pivotal in computational biology, because they allow scientists to analyze large amounts of biological data to better understand their test results, and to infer new knowledge. Yet, biomolecular annotation databases are incomplete by definition, like our knowledge of biology, and may contain errors and inconsistent information. In this context, machine-learning algorithms able to predict and prioritize new biomolecular annotations are both effective and efficient, especially if compared with the time-consuming trials of biological validation. To limit the possibility that these techniques predict obvious and trivial high-level features, and to help prioritizing their results, we introduce here a new element that can improve the accuracy and relevance of the results of an annotation prediction and prioritization pipeline. We propose a novelty indicator able to state the level of ”newness” (or ”originality”) of the annotations predicted for a specific gene to Gene Ontology terms, and to help prioritizing the most novel and interesting annotations predicted. We performed a thorough biological functional analysis of the prioritized annotations predicted with high accuracy by using this indicator and our previously proposed prediction algorithms. The relevance -
A Master Autoantigen-Ome Links Alternative Splicing, Female Predilection, and COVID-19 to Autoimmune Diseases
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.30.454526; this version posted August 4, 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 4.0 International license. A Master Autoantigen-ome Links Alternative Splicing, Female Predilection, and COVID-19 to Autoimmune Diseases Julia Y. Wang1*, Michael W. Roehrl1, Victor B. Roehrl1, and Michael H. Roehrl2* 1 Curandis, New York, USA 2 Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA * Correspondence: [email protected] or [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.07.30.454526; this version posted August 4, 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 4.0 International license. Abstract Chronic and debilitating autoimmune sequelae pose a grave concern for the post-COVID-19 pandemic era. Based on our discovery that the glycosaminoglycan dermatan sulfate (DS) displays peculiar affinity to apoptotic cells and autoantigens (autoAgs) and that DS-autoAg complexes cooperatively stimulate autoreactive B1 cell responses, we compiled a database of 751 candidate autoAgs from six human cell types. At least 657 of these have been found to be affected by SARS-CoV-2 infection based on currently available multi-omic COVID data, and at least 400 are confirmed targets of autoantibodies in a wide array of autoimmune diseases and cancer. -
Transcriptome Analysis of Different Multidrug-Resistant Gastric Carcinoma Cells
in vivo 19: 583-590 (2005) Transcriptome Analysis of Different Multidrug-resistant Gastric Carcinoma Cells STEFFEN HEIM1 and HERMANN LAGE2 1Europroteome AG, Berlin-Hennigsdorf; 2Institute of Pathology, Charité Campus Mitte, Schumannstr. 20/21, D-10117 Berlin, Germany Abstract. Multidrug resistance (MDR) of human cancers is advanced cancer. These therapeutic protocols produce an the major cause of failure of chemotherapy. To better overall response rate of about 20% at best using a single- understand the molecular events associated with the agent, and up to 50% using combination chemotherapy. development of different types of MDR, two different multidrug- Thus, a large number of malignancies are incurable. resistant gastric carcinoma cell lines, the MDR1/P-glycoprotein- Generally, gastrointestinal cancers, including gastric expressing cell line EPG85-257RDB and the MDR1/P- carcinoma, are naturally resistant to many anticancer drugs. glycoprotein-negative cell variant EPG85-257RNOV, as well as Additionally, these tumors are able to develop acquired the corresponding drug-sensitive parental cell line EPG85-257P, drug resistance phenotypes, which include the multidrug were used for analyses of the mRNA expression profiles by resistance (MDR) phenomenon. cDNA array hybridization. Of more than 12,000 genes spotted The MDR phenotype is characterized by simultaneous on the arrays, 156 genes were detected as being significantly resistance of tumor cells to various antineoplastic agents regulated in the cell line EPG85-257RDB in comparison to the which are structurally and functionally unrelated. Besides non-resistant cell variant, and 61 genes were found to be the classical MDR phenotype, mediated by the enhanced differentially expressed in the cell line EPG85-257RNOV. -
Structural and Functional Studies of Mrna Stability Regulators
Research Collection Doctoral Thesis Structural and Functional Studies of mRNA Stability Regulators Author(s): Ripin, Nina Publication Date: 2018-11 Permanent Link: https://doi.org/10.3929/ethz-b-000303696 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library DISS. ETH NO. 25327 Structural and functional studies of mRNA stability regulators A thesis submitted to attain the degree of DOCTOR OF SCIENCES of ETH ZÜRICH (Dr. sc. ETH Zürich) presented by NINA RIPIN Diplom-Biochemikerin, Goethe University, Frankfurt, Germany Born on 06.08.1986 citizen of Germany accepted on the recommendation of Prof. Dr. Frédéric Allain Prof. Dr. Stefanie Jonas Prof. Dr. Michael Sattler Prof. Dr. Witold Filipowicz 2018 “Success consists of going from failure to failure without loss of enthusiasm.” Winston Churchill Summary Posttranscriptional gene regulation (PTGR) is the process by which every step of the life cycle of an mRNA following transcription – maturation, transport, translation, subcellular localization and decay - is tightly regulated. This is accomplished by a complex network of multiple RNA binding proteins (RNPs) binding to several specific mRNA elements. Such cis-acting elements are or can be found within the 5’ cap, the 5’ untranslated region (UTR), the open reading frame (ORF), the 3’UTR and the poly(A) tail at the 3’ end of the mRNA. Adenylate-uridylate-rich elements (AU-rich elements; AREs) are heavily investigated regulatory cis- acting elements within 3’untranslated regions (3’UTRs). These are found in short-lived mRNAs and function as a signal for rapid degradation. -
Meta-Analysis of Genomewide Association Studies Reveals Genetic Variants for Hip Bone Geometry
HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author J Bone Miner Manuscript Author Res. Author Manuscript Author manuscript; available in PMC 2019 July 23. Published in final edited form as: J Bone Miner Res. 2019 July ; 34(7): 1284–1296. doi:10.1002/jbmr.3698. Meta-Analysis of Genomewide Association Studies Reveals Genetic Variants for Hip Bone Geometry A full list of authors and affiliations appears at the end of the article. Abstract Hip geometry is an important predictor of fracture. We performed a meta-analysis of GWAS studies in adults to identify genetic variants that are associated with proximal femur geometry phenotypes. We analyzed four phenotypes: (i) femoral neck length; (ii) neck-shaft angle; (iii) femoral neck width, and (iv) femoral neck section modulus, estimated from DXA scans using algorithms of hip structure analysis. In the Discovery stage, 10 cohort studies were included in the fixed-effect meta-analysis, with up to 18,719 men and women ages 16 to 93 years. Association analyses were performed with ~2.5 million polymorphisms under an additive model adjusted for age, body mass index, and height. Replication analyses of meta-GWAS significant loci (at adjusted genomewide significance [GWS], threshold p ≤ 2.6 × 10−8) were performed in seven additional cohorts in silico. We looked up SNPs associated in our analysis, for association with height, bone mineral density (BMD), and fracture. In meta-analysis (combined Discovery and Replication stages), GWS associations were found at 5p15 (IRX1 and ADAMTS16); 5q35 near FGFR4; at 12p11 (in CCDC91); 11q13 (near LRP5 and PPP6R3 (rs7102273)). Several hip geometry signals overlapped with BMD, including LRP5 (chr. -
MARCKS Regulates Membrane Targeting of Rab10 Vesicles to Promote Axon Development
npg MARCKS and axonal membrane addition Cell Research (2014) 24:576-594. 576 © 2014 IBCB, SIBS, CAS All rights reserved 1001-0602/14 $ 32.00 npg ORIGINAL ARTICLE www.nature.com/cr MARCKS regulates membrane targeting of Rab10 vesicles to promote axon development Xiao-Hui Xu1, 2, *, Cai-Yun Deng1, *, Yang Liu1, Miao He1, Jian Peng1, 3, Tong Wang1, Lei Yuan1, Zhi-Sheng Zheng1, Perry J Blackshear4, Zhen-Ge Luo1 1Institute of Neuroscience and State Key Laboratory of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Acad- emy of Sciences, Shanghai 200031, China; 2School of Life Sciences, Shanghai University, Shanghai 200444, China; 3School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China; 4Laboratory of Signal Transduction, National Insti- tute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA Axon development requires membrane addition from the intracellular supply, which has been shown to be medi- ated by Rab10-positive plasmalemmal precursor vesicles (PPVs). However, the molecular mechanisms underlying the membrane trafficking processes of PPVs remain unclear. Here, we show that myristoylated alanine-rich C-kinase substrate (MARCKS) mediates membrane targeting of Rab10-positive PPVs, and this regulation is critical for axon development. We found that the GTP-locked active form of Rab10 binds to membrane-associated MARCKS, whose affinity depends on the phosphorylation status of the MARCKS effector domain. Either genetic silencing of MARCKS or disruption of its interaction with Rab10 inhibited axon growth of cortical neurons, impaired docking and fusion of Rab10 vesicles with the plasma membrane, and consequently caused a loss of membrane insertion of axonal receptors responsive to extracellular axon growth factors. -
Mechanisms of Membrane Remodeling by Peripheral Proteins and Divalent Cations
University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2015 Mechanisms of Membrane Remodeling by Peripheral Proteins and Divalent Cations Zheng Shi University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Biophysics Commons, and the Physical Chemistry Commons Recommended Citation Shi, Zheng, "Mechanisms of Membrane Remodeling by Peripheral Proteins and Divalent Cations" (2015). Publicly Accessible Penn Dissertations. 2011. https://repository.upenn.edu/edissertations/2011 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/2011 For more information, please contact [email protected]. Mechanisms of Membrane Remodeling by Peripheral Proteins and Divalent Cations Abstract Biological membranes undergo constant shape remodeling involving the formation of highly curved structures. As one of the most extensively studied membrane remodeling events, endocytosis is a ubiquitous eukaryotic membrane budding, vesiculation, and internalization process fulfilling numerous roles including compensation of membrane area increase after bursts of exocytosis. There are multiple independent endocytic pathways which differ by their speed as well as the proteins that are involved in. Bin/Amphiphysin/Rvs (BAR) domain proteins, such as endophilin, are responsible for sensing or generating membrane curvature in multiple endocytic pathways. In this dissertation, I elucidate the mechanisms of membrane remodeling through in vitro experimental studies with synthetic lipid bilayers. Firstly, I investigated the binding and assembly of endophilin on planar membranes. Endophilin was found to be attracted to the membrane through electrostatic forces and to subsequently oligomerize on the membrane with the help of the protein’s N-terminal helices. Next, I studied the mechanisms that govern membrane shape transitions induced by BAR domain proteins. -
MARCKS Deficiency in Mice Leads to Abnormal Brain
Proc. Natl. Acad. Sci. USA Vol. 92, pp. 944-948, February 1995 Developmental Biology MARCKS deficiency in mice leads to abnormal brain development and perinatal death (myristoylated, alanine-rich C kinase substrate/protein kinase C/Macs gene) DEBORAH J. STUMPO*t, CHERYL B. BOCKt, JANE S. TUTTLE*t, AND PERRY J. BLACKSHEAR*t#§ tHoward Hughes Medical Institute Laboratories, Durham, NC; *Division of Endocrinology, Metabolism and Nutrition, Departments of Medicine and Biochemistry; and tComprehensive Cancer Center, Duke University Medical Center, Durham, NC 27710 Communicated by Robert L. Hill, Duke University Medical Center, Durham, NC, October 14, 1994 ABSTRACT The MARCKS protein is a widely distributed To elucidate possible roles of MARCKS in both develop- cellular substrate for protein kinase C. It is a myristoylprotein ment and normal cellular function, we disrupted its gene in that binds calmodulin and actin in a manner reversible by mice by using the techniques of homologous recombination in protein kinase C-dependent phosphorylation. It is also highly embryonic stem (ES) cells. This gene, Macs, has been localized expressed in nervous tissue, particularly during development. to mouse chromosome 10 in a region of synteny with human To evaluate a possible developmental role for MARCKS, we chromosome 6q21, where the human gene (MACS) has been disrupted its gene in mice by using the techniques of homol- mapped (10, 11). Our results indicate that expression of ogous recombination. Pups homozygous for the disrupted MARCKS during embryonic and fetal life in the mouse is allele lacked detectable MARCKS mRNA and protein. All necessary for normal development of the central nervous MARCKS-deficient pups died before or within a few hours of system as well as for extrauterine survival.