Smadinduced Alterations of Matrix Metabolism by a Myristoyl Tetra
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SUPPLEMENTAL DATA Supplemental Materials And
SUPPLEMENTAL DATA Supplemental Materials and Methods Cells and Cell Culture Human breast carcinoma cell lines, MDA-MB-231 and MCF7, were purchased from American Type Tissue Culture Collection (ATCC). 231BoM-1833, 231BrM-2a, CN34, CN34-BoM2d, CN34-BrM2c and MCF7- BoM2d cell lines were kindly provided by Dr. Joan Massagué (Memorial Sloan-Kettering Cancer Center) (1-3). Luciferase-labeled cells were generated by infecting the lentivirus carrying the firefly luciferase gene. The immortalized mouse bone microvascular endothelial cell (mBMEC) was a generous gift from Dr. Isaiah J. Fidler (M.D. Anderson Cancer Center) (4). MCF10A and MCF10DCIS.com cells were purchased from ATCC and Asterand, respectively. MDA-MB-231, its variant cells, MCF7 and MCF-BoM2d cells were cultured in DMEM medium supplemented with 10% FBS and antibiotics. CN34 and its variant cells were cultured in Medium199 supplemented with 2.5% FBS, 10 µg/ml insulin, 0.5 µg/ml hydrocortisone, 20 ng/ml EGF, 100 ng/ml cholera toxin and antibiotics. MCF10DCIS.com cells were cultured in RPMI-1640 medium supplemented with 10% FBS and antibiotics. MCF10A cells were cultured in MEGM mammary epithelial cell growth medium (Lonza). mBMEC was maintained at 8% CO2 at 33 °C in DMEM with 10% FBS, 2 mM L-glutamine, 1 mM sodium pyruvate, 1% non-essential amino acids and 1% vitamin mixture. Bone marrow stromal fibroblast cell lines HS5 and HS27A, and osteoblast cell line, hFOB1.19, were purchased from ATCC. Bone marrow derived human mesenchymal stem cells, BM-hMSC, were isolated for enrichment of plastic adherent cells from unprocessed bone marrow (Lonza) which was depleted of red blood cells. -
Alpha;-Actinin-4 Promotes Metastasis in Gastric Cancer
Laboratory Investigation (2017) 97, 1084–1094 © 2017 USCAP, Inc All rights reserved 0023-6837/17 α-Actinin-4 promotes metastasis in gastric cancer Xin Liu and Kent-Man Chu Metastasis increases the mortality rate of gastric cancer, which is the third leading cause of cancer-associated deaths worldwide. This study aims to identify the genes promoting metastasis of gastric cancer (GC). A human cell motility PCR array was used to analyze a pair of tumor and non-tumor tissue samples from a patient with stage IV GC (T3N3M1). Expression of the dysregulated genes was then evaluated in GC tissue samples (n = 10) and cell lines (n =6) via qPCR. Expression of α-actinin-4 (ACTN4) was validated in a larger sample size (n = 47) by qPCR, western blot and immunohistochemistry. Knockdown of ACTN4 with specific siRNAs was performed in GC cells, and adhesion assays, transwell invasion assays and migration assays were used to evaluate the function of these cells. Expression of potential targets of ACTN4 were then evaluated by qPCR. Thirty upregulated genes (greater than twofold) were revealed by the PCR array. We focused on ACTN4 because it was upregulated in 6 out of 10 pairs of tissue samples and 5 out of 6 GC cell lines. Further study indicated that ACTN4 was upregulated in 22/32 pairs of tissue samples at stage III & IV (P = 0.0069). Knockdown of ACTN4 in GC cells showed no significant effect on cell proliferation, but significantly increased cell-matrix adhesion, as well as reduced migration and invasion of AGS, MKN7 and NCI-N87 cells. -
Appendix 2. Significantly Differentially Regulated Genes in Term Compared with Second Trimester Amniotic Fluid Supernatant
Appendix 2. Significantly Differentially Regulated Genes in Term Compared With Second Trimester Amniotic Fluid Supernatant Fold Change in term vs second trimester Amniotic Affymetrix Duplicate Fluid Probe ID probes Symbol Entrez Gene Name 1019.9 217059_at D MUC7 mucin 7, secreted 424.5 211735_x_at D SFTPC surfactant protein C 416.2 206835_at STATH statherin 363.4 214387_x_at D SFTPC surfactant protein C 295.5 205982_x_at D SFTPC surfactant protein C 288.7 1553454_at RPTN repetin solute carrier family 34 (sodium 251.3 204124_at SLC34A2 phosphate), member 2 238.9 206786_at HTN3 histatin 3 161.5 220191_at GKN1 gastrokine 1 152.7 223678_s_at D SFTPA2 surfactant protein A2 130.9 207430_s_at D MSMB microseminoprotein, beta- 99.0 214199_at SFTPD surfactant protein D major histocompatibility complex, class II, 96.5 210982_s_at D HLA-DRA DR alpha 96.5 221133_s_at D CLDN18 claudin 18 94.4 238222_at GKN2 gastrokine 2 93.7 1557961_s_at D LOC100127983 uncharacterized LOC100127983 93.1 229584_at LRRK2 leucine-rich repeat kinase 2 HOXD cluster antisense RNA 1 (non- 88.6 242042_s_at D HOXD-AS1 protein coding) 86.0 205569_at LAMP3 lysosomal-associated membrane protein 3 85.4 232698_at BPIFB2 BPI fold containing family B, member 2 84.4 205979_at SCGB2A1 secretoglobin, family 2A, member 1 84.3 230469_at RTKN2 rhotekin 2 82.2 204130_at HSD11B2 hydroxysteroid (11-beta) dehydrogenase 2 81.9 222242_s_at KLK5 kallikrein-related peptidase 5 77.0 237281_at AKAP14 A kinase (PRKA) anchor protein 14 76.7 1553602_at MUCL1 mucin-like 1 76.3 216359_at D MUC7 mucin 7, -
Supplementary Methods
Supplementary methods Human lung tissues and tissue microarray (TMA) All human tissues were obtained from the Lung Cancer Specialized Program of Research Excellence (SPORE) Tissue Bank at the M.D. Anderson Cancer Center (Houston, TX). A collection of 26 lung adenocarcinomas and 24 non-tumoral paired tissues were snap-frozen and preserved in liquid nitrogen for total RNA extraction. For each tissue sample, the percentage of malignant tissue was calculated and the cellular composition of specimens was determined by histological examination (I.I.W.) following Hematoxylin-Eosin (H&E) staining. All malignant samples retained contained more than 50% tumor cells. Specimens resected from NSCLC stages I-IV patients who had no prior chemotherapy or radiotherapy were used for TMA analysis by immunohistochemistry. Patients who had smoked at least 100 cigarettes in their lifetime were defined as smokers. Samples were fixed in formalin, embedded in paraffin, stained with H&E, and reviewed by an experienced pathologist (I.I.W.). The 413 tissue specimens collected from 283 patients included 62 normal bronchial epithelia, 61 bronchial hyperplasias (Hyp), 15 squamous metaplasias (SqM), 9 squamous dysplasias (Dys), 26 carcinomas in situ (CIS), as well as 98 squamous cell carcinomas (SCC) and 141 adenocarcinomas. Normal bronchial epithelia, hyperplasia, squamous metaplasia, dysplasia, CIS, and SCC were considered to represent different steps in the development of SCCs. All tumors and lesions were classified according to the World Health Organization (WHO) 2004 criteria. The TMAs were prepared with a manual tissue arrayer (Advanced Tissue Arrayer ATA100, Chemicon International, Temecula, CA) using 1-mm-diameter cores in triplicate for tumors and 1.5 to 2-mm cores for normal epithelial and premalignant lesions. -
Proteomic Expression Profile in Human Temporomandibular Joint
diagnostics Article Proteomic Expression Profile in Human Temporomandibular Joint Dysfunction Andrea Duarte Doetzer 1,*, Roberto Hirochi Herai 1 , Marília Afonso Rabelo Buzalaf 2 and Paula Cristina Trevilatto 1 1 Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba 80215-901, Brazil; [email protected] (R.H.H.); [email protected] (P.C.T.) 2 Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru 17012-901, Brazil; [email protected] * Correspondence: [email protected]; Tel.: +55-41-991-864-747 Abstract: Temporomandibular joint dysfunction (TMD) is a multifactorial condition that impairs human’s health and quality of life. Its etiology is still a challenge due to its complex development and the great number of different conditions it comprises. One of the most common forms of TMD is anterior disc displacement without reduction (DDWoR) and other TMDs with distinct origins are condylar hyperplasia (CH) and mandibular dislocation (MD). Thus, the aim of this study is to identify the protein expression profile of synovial fluid and the temporomandibular joint disc of patients diagnosed with DDWoR, CH and MD. Synovial fluid and a fraction of the temporomandibular joint disc were collected from nine patients diagnosed with DDWoR (n = 3), CH (n = 4) and MD (n = 2). Samples were subjected to label-free nLC-MS/MS for proteomic data extraction, and then bioinformatics analysis were conducted for protein identification and functional annotation. The three Citation: Doetzer, A.D.; Herai, R.H.; TMD conditions showed different protein expression profiles, and novel proteins were identified Buzalaf, M.A.R.; Trevilatto, P.C. -
Alpha Actinin (ACTN1) Mouse Monoclonal Antibody [Clone ID: OTI7A4] Product Data
OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for TA500072 alpha Actinin (ACTN1) Mouse Monoclonal Antibody [Clone ID: OTI7A4] Product data: Product Type: Primary Antibodies Clone Name: OTI7A4 Applications: IF, IHC, WB Recommend Dilution: WB 1:2000, IHC 1:50, IF 1:100 Reactivity: Human Host: Mouse Isotype: IgG2a Clonality: Monoclonal Immunogen: Human recombinant protein fragment corresponding to amino acids 650-893 of human alpha-actinin (NP_001093) produced in E.coli. Formulation: PBS (pH 7.3) containing 1% BSA, 50% glycerol and 0.02% sodium azide. Concentration: 1 mg/ml Purification: Purified from mouse ascites fluids or tissue culture supernatant by affinity chromatography (protein A/G) Predicted Protein Size: 102.9 kDa Gene Name: actinin alpha 1 Database Link: NP_001093 Entrez Gene 87 Human Background: Alpha actinins belong to the spectrin gene superfamily which represents a diverse group of cytoskeletal proteins, including the alpha and beta spectrins and dystrophins. Alpha actinin is an actin-binding protein with multiple roles in different cell types. In nonmuscle cells, the cytoskeletal isoform is found along microfilament bundles and adherens-type junctions, where it is involved in binding actin to the membrane. In contrast, skeletal, cardiac, and smooth muscle isoforms are localized to the Z-disc and analogous dense bodies, where they help anchor the myofibrillar actin filaments. Synonyms: BDPLT15 Protein Families: Druggable Genome, ES Cell Differentiation/IPS This product is to be used for laboratory only. Not for diagnostic or therapeutic use. -
Supplemental Figure Legends Figure S1. Expression of Mir-133A
Supplemental Figure legends Figure S1. Expression of miR-133a and miR-1 in adult mice. (A) Expression of miR-133a in heart samples of miR-133a-1-KO and miR-133a-2-KO adult mice as detected by real-time PCR. Expression level of miR-133a in mutant hearts were normalized to GAPDH and compared to WT hearts. N=3 for each genotype group. (B) Northern blot analysis of heart and skeletal muscle RNA from adult mice. Ten micrograms of RNA from skeletal muscle and heart tissues were used in the Northern blots. 32P-labeled Start-Fire probes for miR-133a and miR-1 were used. Genotypes of mice are labeled on top. U6 probe was used as a loading control. GP, gastrocnemius- plantaris. (C) Expression of Mib1 mRNA and protein in dKO mice at P1. mRNA level of Mib1 as detected by real-time PCR in dKO hearts were normalized to GAPDH and compared to WT hearts. Error bars indicate SEM. Western blot analysis was performed on hearts from P1 wild type and dKO mutant mice. α -tubulin was detected as a loading control. Figure S2. Abnormal cardiomyocyte proliferation in miR-133a dKO hearts. Representative images of proliferating cardiomyocytes in WT and dKO hearts at P1. High magnification of immunohistochemistry on heart sections at P1 using phospho- histone H3 (PH3, red) and -actinin (green) was shown. Bar = 20 m. Figure S3. Expression of miR-133a in wild-type and beta-MHC-miR-133a transgenic hearts at E13.5 as detected by real-time PCR. Figure S4. Expression of miR-133a target genes in hearts of WT and dKO mutant mice at P1. -
Chemical Agent and Antibodies B-Raf Inhibitor RAF265
Supplemental Materials and Methods: Chemical agent and antibodies B-Raf inhibitor RAF265 [5-(2-(5-(trifluromethyl)-1H-imidazol-2-yl)pyridin-4-yloxy)-N-(4-trifluoromethyl)phenyl-1-methyl-1H-benzp{D, }imidazol-2- amine] was kindly provided by Novartis Pharma AG and dissolved in solvent ethanol:propylene glycol:2.5% tween-80 (percentage 6:23:71) for oral delivery to mice by gavage. Antibodies to phospho-ERK1/2 Thr202/Tyr204(4370), phosphoMEK1/2(2338 and 9121)), phospho-cyclin D1(3300), cyclin D1 (2978), PLK1 (4513) BIM (2933), BAX (2772), BCL2 (2876) were from Cell Signaling Technology. Additional antibodies for phospho-ERK1,2 detection for western blot were from Promega (V803A), and Santa Cruz (E-Y, SC7383). Total ERK antibody for western blot analysis was K-23 from Santa Cruz (SC-94). Ki67 antibody (ab833) was from ABCAM, Mcl1 antibody (559027) was from BD Biosciences, Factor VIII antibody was from Dako (A082), CD31 antibody was from Dianova, (DIA310), and Cot antibody was from Santa Cruz Biotechnology (sc-373677). For the cyclin D1 second antibody staining was with an Alexa Fluor 568 donkey anti-rabbit IgG (Invitrogen, A10042) (1:200 dilution). The pMEK1 fluorescence was developed using the Alexa Fluor 488 chicken anti-rabbit IgG second antibody (1:200 dilution).TUNEL staining kits were from Promega (G2350). Mouse Implant Studies: Biopsy tissues were delivered to research laboratory in ice-cold Dulbecco's Modified Eagle Medium (DMEM) buffer solution. As the tissue mass available from each biopsy was limited, we first passaged the biopsy tissue in Balb/c nu/Foxn1 athymic nude mice (6-8 weeks of age and weighing 22-25g, purchased from Harlan Sprague Dawley, USA) to increase the volume of tumor for further implantation. -
Discovery of a Molecular Glue That Enhances Uprmt to Restore
bioRxiv preprint doi: https://doi.org/10.1101/2021.02.17.431525; this version posted February 17, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Title: Discovery of a molecular glue that enhances UPRmt to restore proteostasis via TRKA-GRB2-EVI1-CRLS1 axis Authors: Li-Feng-Rong Qi1, 2 †, Cheng Qian1, †, Shuai Liu1, 2†, Chao Peng3, 4, Mu Zhang1, Peng Yang1, Ping Wu3, 4, Ping Li1 and Xiaojun Xu1, 2 * † These authors share joint first authorship Running title: Ginsenoside Rg3 reverses Parkinson’s disease model by enhancing mitochondrial UPR Affiliations: 1 State Key Laboratory of Natural Medicines, China Pharmaceutical University, 210009, Nanjing, Jiangsu, China. 2 Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, China Pharmaceutical University, 210009, Nanjing, Jiangsu, China. 3. National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China 4. Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai, 201204, China. Corresponding author: Ping Li, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 210009, Nanjing, Jiangsu, China. Email: [email protected], Xiaojun Xu, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, China Pharmaceutical University, 210009, Nanjing, Jiangsu, China. Telephone number: +86-2583271203, E-mail: [email protected]. bioRxiv preprint doi: https://doi.org/10.1101/2021.02.17.431525; this version posted February 17, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. -
Electrophoresis
ELECTROPHORESIS Supporting Information for Electrophoresis DOI 10.1002/elps.200700936 Qiaozhen Lu, Nivetha Murugesan, Jennifer A. Macdonald, Shiaw-Lin Wu, Joel S. Pachter and William S. Hancock Analysis of mouse brain microvascular endothelium using immuno-laser capture microdissection coupled to a hybrid LTQ-FT-MS proteomics platform ª 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.electrophoresis-journal.com Table A. List of total proteins identified in CD31 immunostained LCM Sample Protein name Peptide (Hits) Coverag MW Accession (%) # keratin complex 1, acidic, gene 14 [Mus musculus] 15 (15 0 0 0 0) 2.56E+01 52866.70 21489935 neurofilament, light polypeptide [Mus musculus] 4 (4 0 0 0 0) 6.10E+00 61507.96 39204499 actin, beta, cytoplasmic [Mus musculus] 21 (21 0 0 0 0) 3.36E+01 41736.51 6671509 ATP synthase, H+ transporting, mitochondrial F1 complex, alpha 11 (11 0 0 0 0) 2.03E+01 59752.23 6680748 subunit, isoform 1 [Mus musculus] vesicle-associated membrane protein 2 [Mus musculus] 4 (4 0 0 0 0) 3.45E+01 12690.70 6678551 tubulin, beta 6 [Mus musculus] 1 (1 0 0 0 0) 4.00E+00 50090.05 27754056 actin-like [Mus musculus] 2 (2 0 0 0 0) 5.60E+00 43600.63 8850209 hemoglobin alpha 1 chain [Mus musculus] 3 (3 0 0 0 0) 2.39E+01 15085.06 6680175 keratinocyte associated protein 1 [Mus musculus] 23 (23 0 0 0 0) 1.22E+01 59740.13 29789317 ATP synthase, H+ transporting mitochondrial F1 complex, beta 18 (18 0 0 0 0) 4.03E+01 56300.11 31980648 subunit [Mus musculus] tyrosine 3-monooxygenase/tryptophan 5-monooxygenase 3 (3 0 0 0 0) 1.80E+01 27770.96 -
Sox2 Promotes Malignancy in Glioblastoma by Regulating
Volume 16 Number 3 March 2014 pp. 193–206.e25 193 www.neoplasia.com Artem D. Berezovsky*, Laila M. Poisson†, Sox2 Promotes Malignancy in ‡ ‡ David Cherba , Craig P. Webb , Glioblastoma by Regulating Andrea D. Transou*, Nancy W. Lemke*, Xin Hong*, Laura A. Hasselbach*, Susan M. Irtenkauf*, Plasticity and Astrocytic Tom Mikkelsen*,§ and Ana C. deCarvalho* Differentiation1,2 *Department of Neurosurgery, Henry Ford Hospital, Detroit, MI; †Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI; ‡Program of Translational Medicine, Van Andel Research Institute, Grand Rapids, MI; §Department of Neurology, Henry Ford Hospital, Detroit, MI Abstract The high-mobility group–box transcription factor sex-determining region Y–box 2 (Sox2) is essential for the maintenance of stem cells from early development to adult tissues. Sox2 can reprogram differentiated cells into pluripotent cells in concert with other factors and is overexpressed in various cancers. In glioblastoma (GBM), Sox2 is a marker of cancer stemlike cells (CSCs) in neurosphere cultures and is associated with the proneural molecular subtype. Here, we report that Sox2 expression pattern in GBM tumors and patient-derived mouse xenografts is not restricted to a small percentage of cells and is coexpressed with various lineage markers, suggesting that its expression extends beyond CSCs to encompass more differentiated neoplastic cells across molecular subtypes. Employing a CSC derived from a patient with GBM and isogenic differentiated cell model, we show that Sox2 knockdown in the differentiated state abolished dedifferentiation and acquisition of CSC phenotype. Furthermore, Sox2 deficiency specifically impaired the astrocytic component of a biphasic gliosarcoma xenograft model while allowing the formation of tumors with sarcomatous phenotype. -
Immune-Mediated Inflammation May Contribute to the Pathogenesis of Cardiovascular Disease in Mucopolysaccharidosis Type I
UC San Diego UC San Diego Previously Published Works Title Immune-Mediated Inflammation May Contribute to the Pathogenesis of Cardiovascular Disease in Mucopolysaccharidosis Type I. Permalink https://escholarship.org/uc/item/5r90p78m Journal PloS one, 11(3) ISSN 1932-6203 Authors Khalid, Omar Vera, Moin U Gordts, Philip L et al. Publication Date 2016 DOI 10.1371/journal.pone.0150850 Peer reviewed eScholarship.org Powered by the California Digital Library University of California RESEARCH ARTICLE Immune-Mediated Inflammation May Contribute to the Pathogenesis of Cardiovascular Disease in Mucopolysaccharidosis Type I Omar Khalid1☯, Moin U. Vera2☯, Philip L. Gordts3, N. Matthew Ellinwood4, Philip H. Schwartz1,5, Patricia I. Dickson2, Jeffrey D. Esko3, Raymond Y. Wang3,6* 1 National Human Neural Stem Cell Resource, CHOC Research Institute, Orange, California, United States of America, 2 Division of Medical Genetics, Los Angeles Biomedical Research Institute at Harbor-UCLA, Torrance, California, United States of America, 3 University of California-San Diego, La Jolla, California, United States of America, 4 Iowa State University College of Agriculture and Life Sciences, Ames, Iowa, United States of America, 5 Sue and Bill Gross Stem Cell Research Center, University of California-Irvine, Irvine, California, United States of America, 6 Division of Metabolic Disorders, CHOC Children’s Hospital, Orange, California, United States of America ☯ These authors contributed equally to this work. OPEN ACCESS * [email protected] Citation: Khalid O, Vera MU, Gordts PL, Ellinwood NM, Schwartz PH, Dickson PI, et al. (2016) Immune- Mediated Inflammation May Contribute to the Pathogenesis of Cardiovascular Disease in Abstract Mucopolysaccharidosis Type I. PLoS ONE 11(3): e0150850.