University of Birmingham Novel Markers for Differentiation of Lobular
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Identification of SOX9 Interaction Sites in the Genome of Chondrocytes
Identification of SOX9 Interaction Sites in the Genome of Chondrocytes Chun-do Oh1, Sankar N. Maity1¤a, Jing-Fang Lu1¤a, Jiexin Zhang2, Shoudan Liang2, Francoise Coustry1¤b, Benoit de Crombrugghe1*, Hideyo Yasuda1* 1 Department of Genetics, M.D. Anderson Cancer Center, The University of Texas, Houston, Texas, United States of America, 2 Department of Bioinformatics and Computational Biology, M.D. Anderson Cancer Center, The University of Texas, Houston, Texas, United States of America Abstract Background: Our previous work has provided strong evidence that the transcription factor SOX9 is completely needed for chondrogenic differentiation and cartilage formation acting as a ‘‘master switch’’ in this differentiation. Heterozygous mutations in SOX9 cause campomelic dysplasia, a severe skeletal dysmorphology syndrome in humans characterized by a generalized hypoplasia of endochondral bones. To obtain insights into the logic used by SOX9 to control a network of target genes in chondrocytes, we performed a ChIP-on-chip experiment using SOX9 antibodies. Methodology/Principal Findings: The ChIP DNA was hybridized to a microarray, which covered 80 genes, many of which are involved in chondrocyte differentiation. Hybridization peaks were detected in a series of cartilage extracellular matrix (ECM) genes including Col2a1, Col11a2, Aggrecan and Cdrap as well as in genes for specific transcription factors and signaling molecules. Our results also showed SOX9 interaction sites in genes that code for proteins that enhance the transcriptional activity of SOX9. Interestingly, a strong SOX9 signal was also observed in genes such as Col1a1 and Osx, whose expression is strongly down regulated in chondrocytes but is high in osteoblasts. In the Col2a1 gene, in addition to an interaction site on a previously identified enhancer in intron 1, another strong interaction site was seen in intron 6. -
Genomic and Transcriptome Analysis Revealing an Oncogenic Functional Module in Meningiomas
Neurosurg Focus 35 (6):E3, 2013 ©AANS, 2013 Genomic and transcriptome analysis revealing an oncogenic functional module in meningiomas XIAO CHANG, PH.D.,1 LINGLING SHI, PH.D.,2 FAN GAO, PH.D.,1 JONATHAN RUssIN, M.D.,3 LIYUN ZENG, PH.D.,1 SHUHAN HE, B.S.,3 THOMAS C. CHEN, M.D.,3 STEVEN L. GIANNOTTA, M.D.,3 DANIEL J. WEISENBERGER, PH.D.,4 GAbrIEL ZADA, M.D.,3 KAI WANG, PH.D.,1,5,6 AND WIllIAM J. MAck, M.D.1,3 1Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California; 2GHM Institute of CNS Regeneration, Jinan University, Guangzhou, China; 3Department of Neurosurgery, Keck School of Medicine, University of Southern California, Los Angeles, California; 4USC Epigenome Center, Keck School of Medicine, University of Southern California, Los Angeles, California; 5Department of Psychiatry, Keck School of Medicine, University of Southern California, Los Angeles, California; and 6Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California Object. Meningiomas are among the most common primary adult brain tumors. Although typically benign, roughly 2%–5% display malignant pathological features. The key molecular pathways involved in malignant trans- formation remain to be determined. Methods. Illumina expression microarrays were used to assess gene expression levels, and Illumina single- nucleotide polymorphism arrays were used to identify copy number variants in benign, atypical, and malignant me- ningiomas (19 tumors, including 4 malignant ones). The authors also reanalyzed 2 expression data sets generated on Affymetrix microarrays (n = 68, including 6 malignant ones; n = 56, including 3 malignant ones). -
A Genome-Wide Study of Blood Pressure in African Americans Accounting for Gene-Smoking Interaction Jacquelyn Y
Washington University School of Medicine Digital Commons@Becker Open Access Publications 2016 A genome-wide study of blood pressure in African Americans accounting for gene-smoking interaction Jacquelyn Y. Taylor Yale University Karen Schwander Washington University School of Medicine in St. Louis Sharon L. R. Kardia University of Michigan-Ann Arbor Donna Arnett University of Alabama, Birmingham Jingjing Liang Case Western Reserve University See next page for additional authors Follow this and additional works at: https://digitalcommons.wustl.edu/open_access_pubs Recommended Citation Taylor, Jacquelyn Y.; Schwander, Karen; Kardia, Sharon L. R.; Arnett, Donna; Liang, Jingjing; Hunt, Steven C.; Rao, D C.; and Sun, Yan V., ,"A genome-wide study of blood pressure in African Americans accounting for gene-smoking interaction." Scientific Reports.6,. 18812. (2016). https://digitalcommons.wustl.edu/open_access_pubs/4524 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 Jacquelyn Y. Taylor, Karen Schwander, Sharon L. R. Kardia, Donna Arnett, Jingjing Liang, Steven C. Hunt, D C. Rao, and Yan V. Sun This open access publication is available at Digital Commons@Becker: https://digitalcommons.wustl.edu/open_access_pubs/4524 www.nature.com/scientificreports OPEN A Genome-wide study of blood pressure in African Americans accounting for gene-smoking Received: 15 January 2015 Accepted: 09 November 2015 interaction Published: 11 January 2016 Jacquelyn Y. Taylor1, Karen Schwander2, Sharon L. R. Kardia3 & Donna Arnett4, Jingjing Liang5 Steven C. -
Glycoprotein Asporin As a Novel Player in Tumour Microenvironment and Cancer Progression Dana Simkovaa, Gvantsa Kharaishvilia, Eva Slabakovab, Paul G
Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub. 2016 Dec; 160(4):467-473. Glycoprotein asporin as a novel player in tumour microenvironment and cancer progression Dana Simkovaa, Gvantsa Kharaishvilia, Eva Slabakovab, Paul G. Murrayc, Jan Bouchala Background. Small leucine rich proteoglycans (SLRPs), major non-collagen components of the extracellular matrix (ECM), have multiple biological roles with diverse effects. Asporin, a member of the SLRPs class I, competes with other molecules in binding to collagen and affects its mineralization. Its role in cancer is only now being elucidated. Methods. The PubMed online database was used to search relevant reviews and original articles. Furthermore, altered asporin expression was analysed in publicly available genome-wide expression data at the Gene Expression Omnibus database. Results. Polymorphisms in the N-terminal polyaspartate domain, which binds calcium, are associated with osteoar- thritis and prostate cancer. Asporin also promotes the progression of scirrhous gastric cancer where it is required for coordinated invasion by cancer associated fibroblasts and cancer cells. Besides the enhanced expression of asporin observed in multiple cancer types, such as breast, prostate, gastric, pancreas and colon cancer, tumour suppressive effects of asporin were described in triple-negative breast cancer. We also discuss a number of factors modulating asporin expression in different cell types relevant for alterations toing the tumour microenvironment. Conclusion. The apparent contradicting tumour promoting and suppressive effects of asporin require further investiga- tion. Deciphering the role of asporin and other SLRPs in tumour-stroma interactions is needed for a better understand- ing of cancer progression and potentially also for novel tumour microenvironment based therapies. -
Mutation Analysis of Candidate Genes Within the 2Q33.3 Linkage Area for Familial Early-Onset Generalised Osteoarthritis
European Journal of Human Genetics (2007) 15, 791–799 & 2007 Nature Publishing Group All rights reserved 1018-4813/07 $30.00 www.nature.com/ejhg ARTICLE Mutation analysis of candidate genes within the 2q33.3 linkage area for familial early-onset generalised osteoarthritis Josine L Min1, Ingrid Meulenbelt*,1, Margreet Kloppenburg2, Cornelia M van Duijn3 and P Eline Slagboom1 1Molecular Epidemiology, Leiden University Medical Centre, Leiden, The Netherlands; 2Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands; 3Department of Epidemiology & Biostatistics, Erasmus Medical Centre, Rotterdam, The Netherlands In a genome-wide linkage scan of seven families with familial early-onset osteoarthritis (FOA), we mapped a FOA locus to a 5 cM region on chromosome 2q33.3–2q34 with a maximum LOD score of 6.05. To identify causal variants, 17 positional candidate genes and FRZB were sequenced for coding, splice sites, and 50 and 30 untranslated regions. The pathogenicity of possible disease-causing variants was evaluated using predicted effects on protein structure and function, splicing enhancers, degree of conservation and frequency in 790 unrelated subjects from the population-based Rotterdam study scored for the presence of radiographic signs of OA (ROA). Nine novel variants, identified in NRP2, XM_371590, ADAM23, IDH1, PIP5K3 and PTHR2, cosegregated with FOA, of which two were promising. IDH1 Y183C cosegregated in one family, involved a conserved amino-acid change and showed a damaging effect predicted by PolyPhen and SIFT. In the Rotterdam sample, carriers of IDH1 Y183C (0.02) had an increased but insignificant risk for generalised ROA. The second variant, NRP2 c.1938-21T4C cosegregated in three families. -
Cytoplasmic Asporin Promotes Cell Migration by Regulating TGF-β
Li et al. Cell Death and Disease (2019) 10:109 https://doi.org/10.1038/s41419-019-1376-9 Cell Death & Disease ARTICLE Open Access Cytoplasmic Asporin promotes cell migration by regulating TGF-β/Smad2/3 pathway and indicates a poor prognosis in colorectal cancer Hengcun Li1, Zheng Zhang1, Lei Chen1, Xiujing Sun1, Yu Zhao1, Qingdong Guo1, Shengtao Zhu1,PengLi1,LiMin1 and Shutian Zhang 1 Abstract Previous studies revealed that Asporin (ASPN) is a potential mediator in the development of various types of cancer as a secreted stroma protein, but the function of ASPN inside the cancer cells remains largely unknown. Here, we demonstrated a higher expression level of ASPN in colorectal cancer (CRC) than matched normal tissues, and 25% (2/8) CRC showed copy number variation (CNV) gain/amplification in ASPN gene. Both higher ASPN expression levels and ASPN CNV gain/amplification indicated a worse prognosis in CRC patients. ASPN can promote proliferation, migration, and invasion of CRC cells, and inhibit apoptosis by activating Akt/Erk and TGF-β/Smad2/3 signalings. Further investigations revealed that ASPN interacts with Smad2/3, facilitates its translocation into nucleus, and up-regulates the expression of Epithelial-mesenchymal transition (EMT) related genes. Rescue assays confirmed that TGF-β signaling is essential for the effects of ASPN on promoting CRC cell migration and invasion. In conclusion, ASPN promotes the 1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; migration and invasion of CRC cells via TGF-β/Smad2/3 pathway and could serve as a potential prognostic biomarker in CRC patients. Introduction exhibited a very poor 5-year survival rate (11.7%)3. -
Identifying Loci Under Positive Selection in Complex Population Histories
bioRxiv preprint doi: https://doi.org/10.1101/453092; this version posted October 25, 2018. 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. Identifying loci under positive selection in complex population histories Alba Refoyo-Martínez1, Rute R. da Fonseca2, Katrín Halldórsdóttir3, Einar Árnason3;4, Thomas Mailund5, Fernando Racimo1;∗ 1 Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark. 2 Centre for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Denmark. 3 Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland. 4 Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, USA. 5 Bioinformatics Research Centre, Aarhus University, Denmark. * Corresponding author: [email protected] October 25, 2018 Abstract Detailed modeling of a species’ history is of prime importance for understanding how natural selection operates over time. Most methods designed to detect positive selection along sequenced genomes, however, use simplified representations of past histories as null models of genetic drift. Here, we present the first method that can detect signatures of strong local adaptation across the genome using arbitrarily complex admixture graphs, which are typically used to describe the history of past divergence and admixture events among any number of populations. The method—called Graph-aware Retrieval of Selective Sweeps (GRoSS)—has good power to detect loci in the genome with strong evidence for past selective sweeps and can also identify which branch of the graph was most affected by the sweep. -
Proteomic Analysis of Porcine-Derived Collagen Membrane and Matrix
materials Article Proteomic Analysis of Porcine-Derived Collagen Membrane and Matrix Jung-Seok Lee 1,2 , Goran Mitulovi´c 3 , Layla Panahipour 1 and Reinhard Gruber 1,3,4,* 1 Department of Oral Biology, School of Dentistry, Medical University of Vienna, 1090 Vienna, Austria; [email protected] (J.-S.L.); [email protected] (L.P.) 2 Department of Periodontology, Research Institute for Periodontal Regeneration, College of Dentistry, Yonsei University, Seoul 03722, Korea 3 Proteomics Core Facility, Clinical Institute of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria; [email protected] 4 Department of Periodontology, School of Dental Medicine, University of Bern, 3010 Bern, Switzerland * Correspondence: [email protected] Received: 17 September 2020; Accepted: 11 November 2020; Published: 17 November 2020 Abstract: Collagen membranes and matrices being widely used in guided bone regeneration and soft tissue augmentation have characteristic properties based on their composition. The respective proteomic signatures have not been identified. Here, we performed a high-resolution shotgun proteomic analysis on two porcine collagen-based biomaterials designed for guided bone regeneration and soft tissue augmentation. Three lots each of a porcine-derived collagen membrane and a matrix derived from peritoneum and/or skin were digested and separated by nano-reverse-phase high-performance liquid chromatography. The peptides were subjected to mass spectrometric detection and analysis. A total of 37 proteins identified by two peptides were present in all collagen membranes and matrices, with 11 and 16 proteins being exclusively present in the membrane and matrix, respectively. The common extracellular matrix proteins include fibrillar collagens (COL1A1, COL1A2, COL2A1, COL3A1, COL5A1, COL5A2, COL5A3, COL11A2), non-fibrillar collagens (COL4A2, COL6A1, COL6A2, COL6A3, COL7A1, COL16A1, COL22A1), and leucine-rich repeat proteoglycans (DCN, LUM, BGN, PRELP, OGN). -
Asporin and Osteoarthritis
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Osteoarthritis and Cartilage 23 (2015) 933e939 Review Asporin and osteoarthritis * L. Xu, Z. Li, S.-Y. Liu, S.-Y. Xu, G.-X. Ni Department of Orthopeadics and Traumatology, Nanfang Hospital, Southern Medical University, China article info summary Article history: Objective: To provide an overview of the literature describing the role of asporin, a small leucine-rich Received 20 November 2014 proteoglycan (SLRP), in osteoarthritis (OA). Accepted 8 February 2015 Method: A literature search was performed and reviewed using the narrative approach. Results: As a class I SLRP member, asporin, is distinct from other SLRPs. Accumulating evidence dem- Keywords: onstrates the involvement of asporin in OA pathogenesis. Many human studies have been conducted to Asporin explore the association between the D-repeat polymorphisms and OA susceptibility, but these yield Small leucine-rich repeat proteoglycans inconsistent results. Possible mechanisms for the involvement of asporin in OA pathology include its Osteoarthritis influence on TGF-b (transforming growth factor-b) signaling pathways and collagen mineralization. To date, no studies were found to use an asporin-deficient animal model that would help to understand disease mechanisms. Many issues must be addressed to clarify the link between asporin and OA to provide a novel therapeutic strategy for OA, perhaps through controlling and modifying the TGF-b-ECM system. Conclusions: Studies examined demonstrate the involvement of asporin in OA pathogenesis, and possible mechanisms by which asporin may be involved in this process have been proposed. However, large-scale interracial studies should be conducted to investigate the association between asporin and OA, and further investigations are needed to obtain a better understanding of the disease mechanism, develop novel therapeutic strategies, and explore new approaches for diagnosis of OA. -
Autocrine IFN Signaling Inducing Profibrotic Fibroblast Responses By
Downloaded from http://www.jimmunol.org/ by guest on September 23, 2021 Inducing is online at: average * The Journal of Immunology , 11 of which you can access for free at: 2013; 191:2956-2966; Prepublished online 16 from submission to initial decision 4 weeks from acceptance to publication August 2013; doi: 10.4049/jimmunol.1300376 http://www.jimmunol.org/content/191/6/2956 A Synthetic TLR3 Ligand Mitigates Profibrotic Fibroblast Responses by Autocrine IFN Signaling Feng Fang, Kohtaro Ooka, Xiaoyong Sun, Ruchi Shah, Swati Bhattacharyya, Jun Wei and John Varga J Immunol cites 49 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/2013/08/20/jimmunol.130037 6.DC1 This article http://www.jimmunol.org/content/191/6/2956.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 © 2013 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 23, 2021. The Journal of Immunology A Synthetic TLR3 Ligand Mitigates Profibrotic Fibroblast Responses by Inducing Autocrine IFN Signaling Feng Fang,* Kohtaro Ooka,* Xiaoyong Sun,† Ruchi Shah,* Swati Bhattacharyya,* Jun Wei,* and John Varga* Activation of TLR3 by exogenous microbial ligands or endogenous injury-associated ligands leads to production of type I IFN. -
CYB5R2 (Y-12): Sc-161510
SAN TA C RUZ BI OTEC HNOL OG Y, INC . CYB5R2 (Y-12): sc-161510 BACKGROUND SOURCE NADH-cytochrome b5 reductases participate in a variety of physiological pro - CYB5R2 (Y-12) is an affinity purified goat polyclonal antibody raised against cesses including biosynthesis of cholesterol, methemoglobin reduction of a peptide mapping within an internal region of CYB5R2 of human origin. erythrocytes, elongation of fatty acids and metabolism of drugs. CYB5R2 (cytochrome b5 reductase 2), also known as B5R.2, is a 276 amino acid pro - PRODUCT tein that contains one FAD-binding FR-type domain and belongs to the flavo - Each vial contains 200 µg IgG in 1.0 ml of PBS with < 0.1% sodium azide protein pyridine nucleotide cytochrome reductase family. Existing as two and 0.1% gelatin. alternatively spliced isoforms, CYB5R2 reduces 2-[4-iodophenyl]-3-[4-nitro - phenyl]-5-[2,4-disulfophenyl]-2H tetrazolium monosodium salt and lucigenin Blocking peptide available for competition studies, sc-161510 P, (100 µg in spermatozoa, which results in NADH-dependent lucigenin chemilumines - peptide in 0.5 ml PBS containing < 0.1% sodium azide and 0.2% BSA). cence. CYB5R2 binds FAD as a cofactor and is encoded by a gene located on human chromosome 11, which houses over 1,400 genes and comprises nearly APPLICATIONS 4% of the human genome. Jervell and Lange-Nielsen syndrome, Jacobsen CYB5R2 (Y-12) is recommended for detection of CYB5R2 of mouse, rat and syndrome and Smith-Lemli-Opitz syndrome are associated with defects in human origin by Western Blotting (starting dilution 1:200, dilution range genes that maps to chromosome 11. -
Analysis of Transcriptome and Mirnaome in the Muscle of Bamei Pigs at Different Developmental Stages
animals Communication Analysis of Transcriptome and miRNAome in the Muscle of Bamei Pigs at Different Developmental Stages Guofang Wu y, Lin Ma y, Lei Wang *, Jiping Zhou, Yuhong Ma and Chen Yang Stake Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining 810016, China; [email protected] (G.W.); [email protected] (L.M.); [email protected] (J.Z.); [email protected] (Y.M.); [email protected] (C.Y.) * Correspondence: [email protected]; Tel.: +86-097-1625-4161 These authors contributed equally to this study. y Received: 28 November 2019; Accepted: 11 July 2020; Published: 15 July 2020 Simple Summary: The pigs is the most popular agricultural animal in the world. Muscle growth—which has the highest economic value in pigs—can be regulated by multiple genes and involves complex regulatory mechanisms. It is necessary to understand the dynamics of muscle transcriptome during development to understand the muscle development mechanism. However, the genes and miRNAs that play regulatory roles underlying differences in the meat quality of pigs remain unclear. In the current study, qRT-PCR, miRNA-Seq, and RNA-Seq were applied to analyze and verify muscle tissues of pigs from three different developmental stages and screened genes, miRNAs and pathways related to pig muscle development. This study focused on analyzing the mechanisms of muscle development and uncover the development differences in muscle from embryo to adult. Abstract: The growth of skeletal muscle involves complex developmental processes that play an important part in the determinization of pork quality.