DOCSLIB.ORG

Identification of Eight Genes Encoding Chemokine-Like

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Identification of Eight Genes Encoding Chemokine-Like 中国科技论文在线 http://www.paper.edu.cn Genomics 81 (2003) 609–617 Identification of eight genes encoding chemokine-like factor superfamily members 1–8 (CKLFSF1–8) by in silico cloning and experimental validation૾ Wenling Han,1 Peiguo Ding,1 Mingxu Xu, Lu Wang, Min Rui, Shuang Shi, Yanan Liu, Ying Zheng, Yingyu Chen, Tian Yang, and Dalong Ma* Center for Human Disease Genomics, Peking University, 38 Xueyuan Road, Beijing 100083, China Received 21 November 2002; accepted 14 March 2003 Abstract TM4SF11 is only 102 kb from the chemokine gene cluster composed of SCYA22, SCYD1, and SCYA17 on chromosome 16q13. CKLF maps on chromosome 16q22. CKLFs have some characteristics associated with the CCL22/MDC, CX3CL1/fractalkine, CCL17/TARC, and TM4SF proteins. Bioinformatics based on CKLF2 cDNA and protein sequences in combination with experimental validation identified eight novel genes designated chemokine-like factor superfamily members 1–8 (CKLFSF1–8). CKLFSF1–8 form gene clusters; the sequence identities between CKLF2 and CKLFSF1–8 are from 12.5 to 39.7%. Most of the CKLFSFs have alternative RNA splicing forms. CKLFSF1 has a CC motif and higher sequence similarity with chemokines than with any of the other CKLFSFs. CKLFSF8 shares 39.3% amino acid identity with TM4SF11. CKLFSF1 links the CKLFSF family with chemokines, and CKLFSF8 links it with TM4SF. The characteristics of CKLFSF2–7 are intermediate between CKLFSF1 and CKLFSF8. This indicates that CKLFSF represents a novel gene family between the SCY and the TM4SF gene families. © 2003 Elsevier Science (USA). All rights reserved. Keywords: CKLF; CKLFSF; Bioinformatics; Gene cluster; Chemokine; TM4SF11 Chemokines are small, secreted proteins that can be CXC chemokines (CXCL1–16), 2 C chemokines (XCL1– subdivided according to their NH2-terminal cysteine-motif 2), and one CX3C chemokine (CX3CL1/fractalkine) iden- into the CC, CXC, C, and CX3C classes. A systematic tified to date. Their corresponding genes have been named nomenclature for chemokines and their genes has gained SCYA1–28, SCYB1–16, SCYC1–2, and SCYD1, respectively wide acceptance, with 28 CC chemokines (CCL1–28),2 16 [1,2]. SCYA22 (CCL22/MDC), SCYD1 (CX3CL1/fracta- lkine), and SCYA17 (CCL17/TARC) are clustered on chro- mosome 16q13 [3]. TM4SF11, formerly named plasmo- ૾ Sequence data from this article have been deposited with the Gen- Bank Data Library under Accession Nos. AY174118 (CKLFSF1), lipin, is only 102 kb from SCYA22 [4]. Such a short distance AF479260 (CKLFSF2), AF479813 (CKLFSF3), AF479814 (CKLFSF4), suggests some relationship may exist between them. AF479262 (CKLFSF5), AF479261 (CKLFSF6), AF479263 (CKLFSF7), Chemokine-like factor was isolated from PHA-stimu- and AF474370 (CKLFSF8). lated U937 cells. It is composed of four exons and located * Corresponding author. Fax: ϩ1-8610-62091149. E-mail address: [email protected] (D. Ma). on chromosome 16q22. It maintains four alternative RNA 1 These authors contributed equally to this paper. splicing forms, which we designated CKLF1, 2, 3, and 4. 2 Abbreviations used: CKLF, chemokine-like factor; SCY, small se- CKLF1 has a CC motif and the key amino acids around the creted cytokine gene; CCL, CC chemokine ligand; TARC, thymus- and motif are identical with those of CCL22/MDC and CCL17/ activation-regulated chemokine; MDC, macrophage-derived chemokine; TARC, though lacking the additional two C-terminus cys- CX3CL, CX3C chemokine ligand; IL, interleukin; FXR, fragile-X-related protein; TM4SF, transmembrane 4 superfamily; HUGO, Human Genome teines. Mouse and rat CKLFs have some RNA splicing Organization; HGMP, Human Genome Mapping Project. forms similar to those of human CKLFs, but the key motif 0888-7543/03/$ – see front matter © 2003 Elsevier Science (USA). All rights reserved. doi:10.1016/S0888-7543(03)00095-8 转载 中国科技论文在线 http://www.paper.edu.cn 610 W. Han et al. / Genomics 81 (2003) 609–617 of their encoded proteins is not CC, but rather a CX3C motif (manuscript in preparation). Here, we report one of these similar to that of CX3CL1/fractalkine. Both human and rat splice variants, which encodes a protein of 169 amino acids CKLF1 have chemotactic activities on a wide spectrum of (AY174118). leukocytes. CKLF2 is the full-length cDNA product encod- When the cDNA sequence of mouse CKLF2 was used in ing 152 amino acids. It can stimulate the proliferation and a BLASTN search, several mouse EST fragments with high differentiation of C2C12 cells. In addition to possessing the sequence identity were identified. After EST assembly, a CC motif, it has four putative transmembrane regions and novel polypeptide with 169 amino acids was cloned the sequence identity between CKLF2 and TM4SF11 is (AY172740). After conducting a TBLASTN search against 15.4% [5,6]. It seems that CKLF may be an interim gene human EST databases with this protein sequence and EST between SCYA22, SCYD1, SCYA17, and TM4SF11. assembly, we obtained its human homologue and named it When CKLF was cloned in 1998, there was no human CKLFSF2. It is tightly linked with CKLFSF1 on chromo- gene product that had obvious sequence similarity with it. some 16q13, justifying the designation CKLFSF2. However, we suspected the existence of additional CKLF- When mouse CKLF2 was used for BLASTP searches, related genes because of the high frequency of gene dupli- four putative mouse proteins sharing obvious sequence sim- cation within chemokine clusters [7,8] and the rapidly ex- ilarity with it were found, but no human homologues of panded TM4SF proteins [9]. With the current availability of them existed in the public database at that time. TBLASTN large databases of expressed sequence tags (ESTs) and new searches against human EST databases with these sequences bioinformatics methods, we hypothesized that analysis of and the corresponding EST assemblies were performed. The the EST, nr, and HGP databases with multiple computa- accession numbers of the putative mouse genes used for tional tools would allow us to identify novel genes belong- TBLASTN analyses and the accession numbers for the ing to the CKLF family. In silico gene identification from corresponding EST assemblies may be found under Mate- human genome sequence and EST databases has become rials and methods. By using this approach, we successfully critically important in many projects seeking to discover obtained the human homologues of these four putative novel functional genes, especially structurally similar and mouse genes designated CKLFSF3, -5, -7, and -8. clustered genes. For example, some new members of the For CKLFSF4, we referred to a putative human gene FXR, IL-1, and ␤-defensin families have recently been encoding 133 amino acids (GenBank Accession No. cloned using a computational search strategy [10–12]. In XP_085368) that was identified by BLASTP searches with the current report, we describe the use of this strategy for the CKLFSF5 and CKLFSF7. Analyses revealed that this se- identification of eight novel genes designated chemokine- quence did not encode a complete gene product. By EST like factor superfamily members 1–8 (CKLFSF1–8), linking assembly, we obtained its full-length cDNA sequence en- SCYA22, SCYD1, SCYA17, and TM4SF11 further. coding 234 amino acids. For human CKLFSF6, we con- sulted the hypothetical National Center for Biotechnology Information (NCBI) protein FLJ20396 (GenBank Acces- Results sion Nos. BC002797, AK000403, and AAH02797), which has 31.1% sequence identity with CKLFSF4 on the overall Identification of the full-length cDNA sequences of amino acid sequence level. Using EST assembly based on CKLFSF1–8 the incomplete sequence information, we obtained the full- length cDNA sequence and named it CKLFSF6. We conducted bioinformatics analyses with the goal of After iterative BLAST searches and EST assemblies, we identifying novel CKLF-related genes. By searching the obtained the full-length cDNA sequences of human TBLASTN programs against human EST databases with CKLFSF1–8 with complete open reading frames. Most of human CKLF2, we found dozens of EST fragments whose them have a stop codon upstream of the translation initiation deduced amino acids have obvious sequence identity with site, a polyadenylation site, and a poly(A) tail at the 3Ј it. After EST assembly, we obtained a complete cDNA terminus. A promoter scan suggests there is a typical pro- sequence with a putative amino acid sequence that contains moter sequence in the upstream region of CKLFSF7. The a CC motif and has sequence similarity with CCL22/MDC, above results indicate we have obtained full cDNA se- CX3CL1/fractalkine, and CCL17/TARC. Therefore, we quences. propose that CKLF represents a novel gene family and that other related genes must exist. Under the approval of the Molecular cloning of cDNA sequences of CKLFSF1–8 HUGO Gene Nomenclature Committee, novel genes related to CKLF have been designated chemokine-like factor su- According to the predicted sequences, we designed spe- perfamily members (CKLFSFs) (previously called chemo- cific primers and amplified the complete open reading kine-like factor-related proteins). This first isolated gene frames of the putative genes from different cDNA libraries. was named CKLFSF1 and was confirmed by PCR amplifi- DNA sequencing verified our prediction. We deposited cation and DNA sequencing. CKLFSF1 is a complicated them with GenBank. In total, this iterative, computational gene having at least 23 alternative RNA splicing forms method has discovered eight novel human CKLFSF genes. 中国科技论文在线 http://www.paper.edu.cn W. Han et al. / Genomics 81 (2003) 609–617 611 Fig. 1. Northern blot analyses of CKLFSF1–8. CKLFSF1, -2, -3, -6, and -7 probes were hybridized with membranes prepared in our lab, and CKLFSF1, -5, and -8 were hybridized with membranes purchased from Clontech. The molecular weights of CKLFSF1–8 are in agreement with the predicted sizes. The expression of CKLFSF1, -2, -5, and -7 is restricted to some specific tissues, but CKLFSF3, -4, -6, and -8 are widely expressed. Northern blot analyses five gaps of ϳ117, 120, 192, 301, and 340 bp.
Load more

Recommended publications
  • SPATA33 Localizes Calcineurin to the Mitochondria and Regulates Sperm Motility in Mice
    SPATA33 localizes calcineurin to the mitochondria and regulates sperm motility in mice Haruhiko Miyataa, Seiya Ouraa,b, Akane Morohoshia,c, Keisuke Shimadaa, Daisuke Mashikoa,1, Yuki Oyamaa,b, Yuki Kanedaa,b, Takafumi Matsumuraa,2, Ferheen Abbasia,3, and Masahito Ikawaa,b,c,d,4 aResearch Institute for Microbial Diseases, Osaka University, Osaka 5650871, Japan; bGraduate School of Pharmaceutical Sciences, Osaka University, Osaka 5650871, Japan; cGraduate School of Medicine, Osaka University, Osaka 5650871, Japan; and dThe Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan Edited by Mariana F. Wolfner, Cornell University, Ithaca, NY, and approved July 27, 2021 (received for review April 8, 2021) Calcineurin is a calcium-dependent phosphatase that plays roles in calcineurin can be a target for reversible and rapidly acting male a variety of biological processes including immune responses. In sper- contraceptives (5). However, it is challenging to develop molecules matozoa, there is a testis-enriched calcineurin composed of PPP3CC and that specifically inhibit sperm calcineurin and not somatic calci- PPP3R2 (sperm calcineurin) that is essential for sperm motility and male neurin because of sequence similarities (82% amino acid identity fertility. Because sperm calcineurin has been proposed as a target for between human PPP3CA and PPP3CC and 85% amino acid reversible male contraceptives, identifying proteins that interact with identity between human PPP3R1 and PPP3R2). Therefore, identi- sperm calcineurin widens the choice for developing specific inhibitors. fying proteins that interact with sperm calcineurin widens the choice Here, by screening the calcineurin-interacting PxIxIT consensus motif of inhibitors that target the sperm calcineurin pathway. in silico and analyzing the function of candidate proteins through the The PxIxIT motif is a conserved sequence found in generation of gene-modified mice, we discovered that SPATA33 inter- calcineurin-binding proteins (8, 9).
    [Show full text]
  • Genetic and Genomic Analysis of Hyperlipidemia, Obesity and Diabetes Using (C57BL/6J × TALLYHO/Jngj) F2 Mice
    University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Nutrition Publications and Other Works Nutrition 12-19-2010 Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL/6J × TALLYHO/JngJ) F2 mice Taryn P. Stewart Marshall University Hyoung Y. Kim University of Tennessee - Knoxville, [email protected] Arnold M. Saxton University of Tennessee - Knoxville, [email protected] Jung H. Kim Marshall University Follow this and additional works at: https://trace.tennessee.edu/utk_nutrpubs Part of the Animal Sciences Commons, and the Nutrition Commons Recommended Citation BMC Genomics 2010, 11:713 doi:10.1186/1471-2164-11-713 This Article is brought to you for free and open access by the Nutrition at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Nutrition Publications and Other Works by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Stewart et al. BMC Genomics 2010, 11:713 http://www.biomedcentral.com/1471-2164/11/713 RESEARCH ARTICLE Open Access Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL/6J × TALLYHO/JngJ) F2 mice Taryn P Stewart1, Hyoung Yon Kim2, Arnold M Saxton3, Jung Han Kim1* Abstract Background: Type 2 diabetes (T2D) is the most common form of diabetes in humans and is closely associated with dyslipidemia and obesity that magnifies the mortality and morbidity related to T2D. The genetic contribution to human T2D and related metabolic disorders is evident, and mostly follows polygenic inheritance. The TALLYHO/ JngJ (TH) mice are a polygenic model for T2D characterized by obesity, hyperinsulinemia, impaired glucose uptake and tolerance, hyperlipidemia, and hyperglycemia.
    [Show full text]
  • Supplemental Information
    Supplemental information Dissection of the genomic structure of the miR-183/96/182 gene. Previously, we showed that the miR-183/96/182 cluster is an intergenic miRNA cluster, located in a ~60-kb interval between the genes encoding nuclear respiratory factor-1 (Nrf1) and ubiquitin-conjugating enzyme E2H (Ube2h) on mouse chr6qA3.3 (1). To start to uncover the genomic structure of the miR- 183/96/182 gene, we first studied genomic features around miR-183/96/182 in the UCSC genome browser (http://genome.UCSC.edu/), and identified two CpG islands 3.4-6.5 kb 5’ of pre-miR-183, the most 5’ miRNA of the cluster (Fig. 1A; Fig. S1 and Seq. S1). A cDNA clone, AK044220, located at 3.2-4.6 kb 5’ to pre-miR-183, encompasses the second CpG island (Fig. 1A; Fig. S1). We hypothesized that this cDNA clone was derived from 5’ exon(s) of the primary transcript of the miR-183/96/182 gene, as CpG islands are often associated with promoters (2). Supporting this hypothesis, multiple expressed sequences detected by gene-trap clones, including clone D016D06 (3, 4), were co-localized with the cDNA clone AK044220 (Fig. 1A; Fig. S1). Clone D016D06, deposited by the German GeneTrap Consortium (GGTC) (http://tikus.gsf.de) (3, 4), was derived from insertion of a retroviral construct, rFlpROSAβgeo in 129S2 ES cells (Fig. 1A and C). The rFlpROSAβgeo construct carries a promoterless reporter gene, the β−geo cassette - an in-frame fusion of the β-galactosidase and neomycin resistance (Neor) gene (5), with a splicing acceptor (SA) immediately upstream, and a polyA signal downstream of the β−geo cassette (Fig.
    [Show full text]
  • MOCHI Enables Discovery of Heterogeneous Interactome Modules in 3D Nucleome
    Downloaded from genome.cshlp.org on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome Dechao Tian1,# , Ruochi Zhang1,# , Yang Zhang1, Xiaopeng Zhu1, and Jian Ma1,* 1Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA #These two authors contributed equally *Correspondence: [email protected] Contact To whom correspondence should be addressed: Jian Ma School of Computer Science Carnegie Mellon University 7705 Gates-Hillman Complex 5000 Forbes Avenue Pittsburgh, PA 15213 Phone: +1 (412) 268-2776 Email: [email protected] 1 Downloaded from genome.cshlp.org on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press Abstract The composition of the cell nucleus is highly heterogeneous, with different constituents forming complex interactomes. However, the global patterns of these interwoven heterogeneous interactomes remain poorly understood. Here we focus on two different interactomes, chromatin interaction network and gene regulatory network, as a proof-of-principle, to identify heterogeneous interactome modules (HIMs), each of which represents a cluster of gene loci that are in spatial contact more frequently than expected and that are regulated by the same group of transcription factors. HIM integrates transcription factor binding and 3D genome structure to reflect “transcriptional niche” in the nucleus. We develop a new algorithm MOCHI to facilitate the discovery of HIMs based on network motif clustering in heterogeneous interactomes. By applying MOCHI to five different cell types, we found that HIMs have strong spatial preference within the nucleus and exhibit distinct functional properties. Through integrative analysis, this work demonstrates the utility of MOCHI to identify HIMs, which may provide new perspectives on the interplay between transcriptional regulation and 3D genome organization.
    [Show full text]
  • A Tool to Identify Coordinately Expressed Genes
    The CO-Regulation Database (CORD): A Tool to Identify Coordinately Expressed Genes John P. Fahrenbach1*, Jorge Andrade2, Elizabeth M. McNally1,3 1 Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America, 2 Center for Research Informatics, The University of Chicago, Chicago, Illinois, United States of America, 3 Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America Abstract Background: Meta-analysis of gene expression array databases has the potential to reveal information about gene function. The identification of gene-gene interactions may be inferred from gene expression information but such meta-analysis is often limited to a single microarray platform. To address this limitation, we developed a gene-centered approach to analyze differential expression across thousands of gene expression experiments and created the CO-Regulation Database (CORD) to determine which genes are correlated with a queried gene. Results: Using the GEO and ArrayExpress database, we analyzed over 120,000 group by group experiments from gene microarrays to determine the correlating genes for over 30,000 different genes or hypothesized genes. CORD output data is presented for sample queries with focus on genes with well-known interaction networks including p16 (CDKN2A), vimentin (VIM), MyoD (MYOD1). CDKN2A, VIM, and MYOD1 all displayed gene correlations consistent with known interacting genes. Conclusions: We developed a facile, web-enabled program to determine gene-gene correlations across different gene expression microarray platforms. Using well-characterized genes, we illustrate how CORD’s identification of co-expressed genes contributes to a better understanding a gene’s potential function. The website is found at http://cord-db.org.
    [Show full text]
  • Characterization and Expression Profile of CMTM3/CKLFSF3
    Journal of Biochemistry and Molecular Biology, Vol. 39, No. 5, September 2006, pp. 537-545 Characterization and Expression Profile of CMTM3/CKLFSF3 Ji Zhong, Yu Wang, Xiaoyan Qiu, Xiaoning Mo, Yanan Liu, Ting Li, Quansheng Song, Dalong Ma and Wenling Han* Peking University Center for Human Disease Genomics, 38 Xueyuan Road, Beijing 100083, China Received 22 February 2006, Accepted 10 May 2006 CMTM/CKLFSF is a novel family of proteins linking Introduction chemokines and TM4SF. In humans, these proteins are encoded by nine genes, CKLF and CMTM1-8/CKLFSF1-8. CKLFSF is a novel family of proteins linking chemokines and Here we report the characteristics and expression profile Transmembrane 4 Super Family (TM4SF), which are encoded of CMTM3/CKLFSF3. Human CMTM3/CKLFSF3 has a by nine genes, CKLF and CKLFSF1-8, in humans. CKLF, high sequence identity among various species and similar CKLFSF1, and CKLFSF2 are active during evolution, and characteristics as its mouse and rat homologues. Established CKLFSF2 has two orthologues in rat and mouse designated by results both of RT-PCR and Quantitative Real-time Cklfsf2a and Cklfsf2b. CKLFSF3-8 are evolutionarily conserved. PCR, the gene is highly transcribed in testis, leukocytes CKLFSF members form two gene clusters: CKLF and and spleen. For further verification, we generated a CKLFSF1-4 at chromosome 16q22.1, and CKLFSF6-8 at polyclonal antibody against human CMTM3/CKLFSF3 chromosome 3p23. Most CKLFSFs have different spliced and found that the protein is highly expressed in the testis forms, and the protein product of at least one spliced form of and some cells of PBMCs.
    [Show full text]
  • SUPPLEMENTARY MATERIAL Supplementary Fig. S1. LD Mice Used in This Study Accumulate Polyglucosan Inclusions (Lafora Bodies) in the Brain
    1 SUPPLEMENTARY MATERIAL Supplementary Fig. S1. LD mice used in this study accumulate polyglucosan inclusions (Lafora bodies) in the brain. Samples from the hippocampus of five months old control, Epm2a-/- (lacking laforin) and Epm2b-/- mice (lacking malin) were stained with periodic acid Schiff reagent (PAS staining), which colors polysaccharide granules in red. Bar: 50 m. Supplementary Fig. S2. Principal component analysis (PCA) representing the first two components with the biggest level of phenotypic variability. Samples 1_S1 to 4_S4 corresponded to control, 5_S5, 6_S6 and 8_S8 to Epm2a-/- and 9_S9 to 12_S12 to Epm2b- /- samples, of animals of 16 months of age respectively. Supplementary Table S1. Primers used in this work to validate the expression of the corresponding genes by RT-qPCR. Supplementary Table S2: Genes downregulated more than 0.5 fold in Epm2a-/- and Epm2b-/- mice of 16 months of age. The gene name, false discovery rate (FDR), fold change (FC), description and MGI Id (mouse genome informatics) are indicated. Genes are arranged according to FC. Supplementary Table S3: Genes upregulated more than 1.5 fold in Epm2a-/- mice of 16 months of age. The gene name, false discovery rate (FDR), fold change (FC), description and MGI Id (mouse genome informatics) are indicated. Genes are arranged according to FC. Supplementary Table S4: Genes upregulated more than 1.5 fold in Epm2b-/- mice of 16 months of age. The gene name, false discovery rate (FDR), fold change (FC), description and MGI Id (mouse genome informatics) are indicated. Genes are arranged according to FC. 2 Supplementary Table S5: Genes upregulated in both Epm2a-/- and Epm2b-/- mice of 16 months of age.
    [Show full text]
  • Diverse and Potent Chemokine Production by Lung Cd11bhigh Dendritic Cells in Homeostasis and in Allergic Lung Inflammation
    Diverse and Potent Chemokine Production by Lung CD11b high Dendritic Cells in Homeostasis and in Allergic Lung Inflammation This information is current as of September 29, 2021. Steven R. Beaty, C. Edward Rose, Jr. and Sun-sang J. Sung J Immunol 2007; 178:1882-1895; ; doi: 10.4049/jimmunol.178.3.1882 http://www.jimmunol.org/content/178/3/1882 Downloaded from References This article cites 69 articles, 42 of which you can access for free at: http://www.jimmunol.org/content/178/3/1882.full#ref-list-1 http://www.jimmunol.org/ Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication by guest on September 29, 2021 *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2007 by The American Association of Immunologists All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Diverse and Potent Chemokine Production by Lung CD11bhigh Dendritic Cells in Homeostasis and in Allergic Lung Inflammation1 Steven R. Beaty, C. Edward Rose, Jr., and Sun-Sang J. Sung2 Lung CD11chigh dendritic cells (DC) are comprised of two major phenotypically distinct populations, the CD11bhigh DC and the ؉ ؉ ␤ ␣ integrin E 7 DC (CD103 DC).
    [Show full text]
  • (CKLF) As a Potential Prognostic Marker in the MSI-Immune Consensus Molecular Subtype CMS1 of Colorectal Cancer Dunne, P
    Stratified analysis reveals chemokine-like factor (CKLF) as a potential prognostic marker in the MSI-immune consensus molecular subtype CMS1 of colorectal cancer Dunne, P. D., O'Reilly, P. G., Coleman, H. G., Gray, R. T., Longley, D. B., Johnston, P. G., Salto-Tellez, M., Lawler, M., & McArt, D. G. (2016). Stratified analysis reveals chemokine-like factor (CKLF) as a potential prognostic marker in the MSI-immune consensus molecular subtype CMS1 of colorectal cancer. Oncotarget, 36632-36644. https://doi.org/10.18632/oncotarget.9126 Published in: Oncotarget Document Version: Publisher's PDF, also known as Version of record Queen's University Belfast - Research Portal: Link to publication record in Queen's University Belfast Research Portal Publisher rights Copyright 2016 The Authors This is an open access article published under a Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited. General rights Copyright for the publications made accessible via the Queen's University Belfast Research Portal is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The Research Portal is Queen's institutional repository that provides access to Queen's research output. Every effort has been made to ensure that content in the Research Portal does not infringe any person's rights, or applicable UK laws. If you discover content in the Research Portal that you believe breaches copyright or violates any law, please contact [email protected].
    [Show full text]
  • Database Inteface—Entrez, Dbsnp, Hapmap, Perlegen
    SeattleSNPs Interactive Tutorial: Database Inteface—Entrez, dbSNP, HapMap, Perlegen The tutorial is designed to take you through the steps necessary to access SNP data from the primary database resources: 1. dbSNP/Entrez SNP 2. Perlegen Genotype Browser 3. HapMap Genome Browser 4. UCSC Genome Browser 5. SeattleSNPs Variation Discovery Resource As a launching point, we will begin our searching at the Entrez cross-database browser. This can be accessed on the NCBI home page (http://www.ncbi.nlm.nih.gov/). For these exercises we will be accessing data for the gene chemokine-like factor (HUGO name: CKLF). For a cross-database search: 1. Enter the gene symbol (CKLF) into the empty box next to the ‘Search All Databases’; type CKLF into the empty box and click on the GO button, or simply hit the return key on your keyboard. Why would our PGA sequence this gene? 2. Which NCBI database gives the most number of results? What is the database? (Hint: Mouse over the ‘?’ next to the icon and click for a popup explanation of this database.) 2. On the left column, note the results returned for the ‘SNP’ and ‘Gene’ database. 3. How many results were returned for the ‘SNP’ and ‘Gene’ database? 4. Why did the ‘Gene’ database return more than one result? Entrez Gene: 5. From the cross database search, click on the ‘Gene’ database icon. 6. Click on the result that corresponds to the ‘homo sapiens’ CKLF gene. 7. CKLF maps to which chromosome? 8. What are the genes 5’ and 3’ of CKLF? (Hint: look at the genomic context.) 9.
    [Show full text]
  • KLF5 Rabbit Pab
    Leader in Biomolecular Solutions for Life Science KLF5 Rabbit pAb Catalog No.: A2989 Basic Information Background Catalog No. This gene encodes a member of the Kruppel-like factor subfamily of zinc finger proteins. A2989 The encoded protein is a transcriptional activator that binds directly to a specific recognition motif in the promoters of target genes. This protein acts downstream of Observed MW multiple different signaling pathways and is regulated by post-translational 55kDa modification. It may participate in both promoting and suppressing cell proliferation. Expression of this gene may be changed in a variety of different cancers and in Calculated MW cardiovascular disease. Alternative splicing results in multiple transcript variants. 18kDa/33kDa/41kDa/50kDa Category Primary antibody Applications WB, IHC, IF Cross-Reactivity Human, Mouse Recommended Dilutions Immunogen Information WB 1:200 - 1:1000 Gene ID Swiss Prot 688 Q13887 IHC 1:50 - 1:200 Immunogen 1:50 - 1:200 IF Recombinant fusion protein containing a sequence corresponding to amino acids 1-250 of human KLF5 (NP_001721.2). Synonyms KLF5;BTEB2;CKLF;IKLF Contact Product Information www.abclonal.com Source Isotype Purification Rabbit IgG Affinity purification Storage Store at -20℃. Avoid freeze / thaw cycles. Buffer: PBS with 0.02% sodium azide,50% glycerol,pH7.3. Validation Data Western blot analysis of extracts of various cell lines, using KLF5 antibody (A2989) at 1:1000 dilution. Secondary antibody: HRP Goat Anti-Rabbit IgG (H+L) (AS014) at 1:10000 dilution. Lysates/proteins: 25ug per lane. Blocking buffer: 3% nonfat dry milk in TBST. Detection: ECL Basic Kit (RM00020). Exposure time: 15s. Immunohistochemistry of paraffin- Immunofluorescence analysis of A375 cells embedded human placenta using KLF5 using KLF5 antibody (A2989) at dilution of antibody (A2989) at dilution of 1:100 (40x 1:100.
    [Show full text]
  • Medicine® OBSERVATIONAL STUDY
    Medicine® OBSERVATIONAL STUDY Chemokine-Like Factor 1 (CKLF-1) is Overexpressed in Keloid Patients A Potential Indicating Factor for Keloid-Predisposed Individuals Mingzi Zhang, MB, Ying Xu, MB, Yifang Liu, MS, Yingying Cheng, PhD, Pengxiang Zhao, PhD, Hao Liu, MB, Youbin Wang, MD, and Xuemei Ma, PhD Abstract: Chemokine-like factor 1 (CKLF-1) is a novel cytokine Abbreviations: CKLF-1 = chemokine-like factor 1, IL = which have a crucial role in immune and inflammatory responses. interleukin, RT-qPCR = real-time quantitative polymerase chain In this study, the expression level of CKLF-1 was measured to reaction, TGF-b = transforming growth factor-b. assess the difference between keloid patients and people without keloid. Fifty samples were taken from 30 patients: 10 keloid patients; 10 INTRODUCTION scar patients; and 10 patients without obvious scarring. Patients were eloid, considered to be a result of abnormal wound healing, randomly selected from the hospitalized patients of Peking Union K is defined as excessive scar tissue formation extending Medical College Hospital from September 2013 to July 2015. Five beyond the area of the original skin injury and occurring in 1 groups of samples were established: keloid samples from keloid predisposed individuals. The main symptoms of keloid patients patients (K); normal skin samples from keloid patients (KS); scar are pain, itching, functional limitation, and disfigurement, samples from scar patients (C); normal skin samples from scar patients which may cause psychological distress and seriously affect 2 (CS); and normal skin samples from patients without obvious scarring patients’ quality of life. The mechanism of keloid formation is (S).
    [Show full text]