DOCSLIB.ORG

Towards the Mechanism of EGFR Inhibitor Resistance in Non-Small Lung Cancer Cells

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Towards the Mechanism of EGFR Inhibitor Resistance in Non-Small Lung Cancer Cells Towards the Mechanism of EGFR Inhibitor Resistance in Non-Small Lung Cancer Cells Michael Blank,1 Ryan Bomgarden, 2 John Rogers,2 Ryan Jacobs,3 Jason Fong,3 Neelu Puri,3 Vlad Zabrouskov,1 Rosa Viner1; 1ThermoFisher Scientific, San Jose, CA, USA; 2Thermo Fisher Scientific, Rockford, IL, USA; 3University of Illinois at Chicago, Rockford, IL, USA Towards the Mechanism of EGFR Inhibitor Resistance in Non-Small Lung Cancer Cells Michael Blank1; Ryan Bomgarden2; John Rogers2; Ryan Jacobs3; Jason Fong3; Neelu Puri3; Vlad Zabrouskov1; Rosa Viner1 1ThermoFisher Scientific, San Jose, CA; 2Thermo Fisher Scientific, Rockford, IL; 3University of Illinois at Chicago, Rockford, IL 3 FIGURE 3. Quantitative performance of the SPS MS3 fragmentation method on FIGURE 4. Elements of the Erb (A) and WnT (B) Signaling Pathways (KEGG). FIGURE 6. Clustering analysis based on SPS MS TMT quantitation highlighting Liquid Chromatography 2 2 Highlighted in blue are proteins identified and quantified proteins by either MS several patterns in the changes in protein expression between the two cell lines: Overview the Orbitrap Fusion compared to MS HCD fragmentation on the Orbitrap Elite. Samples were eluted by RP-HPLC using a Thermo Scientific™ EASY-nLC™ 1000 Results are the MUDPIT search of two replicate files or SPS methods. Pathway maps are generated by Protein Center 3.9 software H358 versus parental for the four treatment conditions. Purpose: To determine the mechanism of tyrosine kinase inhibitor (TKI) resistance nano-flow system connected to a Thermo Scientific™ EASY-Spray™ column, 25 cm × through analysis of differential changes in protein pathway expression levels by liquid 75 µm, Thermo Scientific™ Acclaim™ PepMap™ C18 Column and a 2 cm Acclaim 30000 chromatography-mass spectrometry (LC-MS). PepMap100 trap column. Mobile phase A consisted of 0.1% formic acid in water while 27005 A 3 RAB10 3 GFM1 mobile phase B was 0.1% formic acid in acetonitrile. A gradient beginning with 5% B EIF3K GSTM3 RAB11A HMGA1 Methods: Parental and tyrosine-kinase inhibitor (Erlotinib) resistant cell lines were 25000 2.5 2.5 EIF5A MCM5 increasing to 25% B over 180 minutes followed by 25% to 40% B over a further 30 APOA1BP treated with Epidermal Growth Factor (EGF), Erlotinib, Erlotinib and EGF, or left EIF1AX minutes was employed with a flow rate of 300 nL/min. 2 2 CMPK1 untreated. Samples from each condition were labeled with TMT8plex isobaric tags and 18487 DDB1 PGK2 20000 STRAP GSTO1 analyzed/quantified by LC-MS on two hybrid instruments based on the Thermo Mass Spectrometry 1.5 RAB14 1.5 EEF1B2 Scientific™ Orbitrap™ mass analyzer. RAB1B NME1-NME2 1 EIF3L 1 GALE Spectra were acquired on a an Thermo Scientific™ Orbitrap Elite™ hybrid mass 15000 12833 PDCD6IP EEF2 ® ® EIF4B The increased multiplexing capabilities of Tandem Mass Tag (TMT ) EIF3B Results: spectrometer using data-dependent MS/MS acquisition mode. The 15 most intense 0.5 0.5 HDGF labeling enables simultaneous comparison of 8 different treatment conditions. 9953 GRB2 GSTP1 precursors selected from the FT MS1 full scan (resolution 120,000 FWHM) were 10000 EIF2S1 GSTM1 Changes in protein expression ratios between parent and TKI-resistant cell lines were isolated and fragmented by FT MS2 (HCD) at resolution of 30,000@m/z 400. SPS MS3 0 POLE3 0 SF3B3 Untreated EGF Erlotinib EGF + SF3B2 Untreated EGF Erlotinib EGF + TCEB2 observed in several important cell signaling pathways with improved quantitative quantification on the Thermo Scientific™ Orbitrap Fusion™ Tribrid™ mass Erlotinib G3BP1 Erlotinib RAB25 5000 2319 accuracy using synchronous precursor selection (SPS) acquisition methods compared spectrometer was performed using an FTMS full scan at 120,000 @ m/z 200 resolution 1507 1494 2112 to higher-energy collision dissociation (HCD) MS2 methods. 2 3 followed by IT MS CID and FT MS HCD (resolution 60000 @ m/z 200) on a total of 10 fragments from the MS2 spectra2. 0 Identified Quantified Identified Quantified 3 API5 3 RAN Introduction Data Analysis EIF3G GNB2L1 Protein Groups Unique Peptides PSMs CSDA PIN1 While tyrosine kinase inhibitors against Epidermal Growth Factor Receptor (EGFR) 2.5 GDI1 2.5 GNA13 Spectral data files were analyzed using Thermo Scientific™ Proteome Discoverer™ 1.4 © 2012 Kanehisa Laboratories MCM6 RAC1 have positive therapeutic effects in a subset of Non-Small Cell Lung Cancer (NSCLC) ® Orbitrap Elite HCD MS2 Orbitrap Fusion SPS MS3 RBBP4 ABCE1 software using the SEQUEST HT search engine, constrained with a precursor mass 2 MCM3 2 GDI2 patients, their clinical efficacies are limited due to the development of TKI resistance. EIF4A3 EIF3I tolerance of 10 ppm and fragment mass tolerance of 0.02 Da (0.8 Da for CID TAX1BP3 1.5 1.5 RPN1 To study the mechanism of TKI resistance, two NSCLC Erlotinib-resistant cell lines B SRSF7 GSTK1 identification using SPS). Carbamidomethylation (+57.021 Da) for cysteine and TMT Relative Quantitation Using TMT8plex Reagents PFKM GSTA1 NSFL1C were established. To identify differences in protein expression between parental and 1 1 BTF3 isobaric labeling (+229.162 Da) for lysine and N-terminus residues were treated as SH3BGRL drug-resistant cells after EGF and/or Erlotinib treatment, the high multiplexing The use of TMT6plex reagents with two additional isotope variants of the TMT6-127 KHSRP PRPS2 static modifications while methionine oxidation (+15.996 Da) and deamidation of EEF1A1 4,5 0.5 EIF6 0.5 capabilities of TMT reagents and MS analysis were utilized. Various pathways and TMT6-129 enabled the simultaneous comparison of relative protein abundances IQGAP1 CSNK2A1 asparagine and glutamine (+0.984 Da) were considered as variable peptide EIF1B EIF4H implicated in drug-resistance were examined in the context of expression differences ® in response to EGF stimulation, exposure to a tyrosine-kinase inhibitor, or both. Using 0 EIF3A 0 TSTD1 modifications. Data was searched against a Swiss-Prot complete human database EEF1A2 Untreated EGF Erlotinib EGF + FUBP1 Untreated EGF Erlotinib EGF + in key proteins using ion trap/Orbitrap mass spectrometer hybrids with a new 3 the Orbitrap Elite mass spectrometer, almost 1500 protein groups and 10,000 unique MCM2 NMT1 with a 1% FDR criteria using Percolator . Erlotinib PACSIN2 Erlotinib EIF2S2 synchronous precursor selection (SPS) MS3 fragmentation/quantitation method. peptides were able to be identified, with a quantitation rate exceeding 99% at the Pathway analysis/protein profiling was performed using Thermo Scientific™ peptide level employing HCD MS2 quantitation/fragmentation (Figure 3). This enabled ProteinCenter™ 3.9 software. The TMT8plex quantification method within Proteome the partial mapping of numerous important extra-cellular signaling pathways as well as Methods Discoverer 1.4 software was used to calculate the reporter ratios with mass tolerance those associated with cancer from the KEGG™ reference set with corresponding Conclusion TABLE 1: Response of the H358 and Parental cells to treatment versus the Sample Preparation ±10 ppm without applying the isotopic correction factors. A protein ratio was expressed relative abundance information (Figure 4A). untreated controls using quantitative information from the SPS MS3 method on . TMT labeling with additional isobaric tags allows for the simultaneous as a median value of the ratios for all quantifiable spectra of the peptides pertaining to Two NSCLC cell lines (H2170 and H358) were established with resistance to the Repeating the MS analysis with the enhanced capabilities of the Orbitrap Fusion mass the Orbitrap Fusion mass spectrometer. A 1.5-fold change up or down was used quantification of protein expression ratios under numerous experimental that protein5. EGFR-tyrosine kinase inhibitor, Erlotinib, exhibiting a 4-5 fold higher IC50 than the spectrometer resulted in a substantial increase in identified protein groups using the as the threshold for differences in regulation. conditions when coupled with the high resolution/accurate mass of the Orbitrap parent cell line1. Parental and drug-resistant NSCLC cell lines were left untreated or new SPS functionality (Figure 3). We identified nearly13,000 unique peptides instrument. treated with EGF or 10µM Erlotinib alone, or treated with both EGF and Erlotinib, for Results corresponding to over 2300 protein groups (a 40% increase over previous Quantifiable Proteins . The enhanced identification rate of the Orbitrap Fusion instrument coupled with 2.5 minutes. After reduction and alkylation, proteins from the eight conditions were Immunoblot Analysis performance) with a quantitation rate above 90%. This resulted in increased coverage the improved accuracy of quantitation using the SPS MS3 method enables digested with trypsin and then labeled with Thermo Scientific TMT6plex reagents plus of the pathways of interest to better understand of the impact of EGF stimulation and Parental H358 markedly improved pathway profiling. two 13C/15N isotope variants of the TMT6-127 and TMT6-129 reagents according to Targeted antibodies revealed little change in the degree of mTOR, EGFR, S6 kinase, Erlotinib treatment upon the H358 NSCLC cell line. Down No Up Down No Up 2 3 the manufacture’s protocol. The peptides were then combined and analyzed by LC/MS ERK, and β-actin expression between the parental and drug-resistant cell lines under EGF Erlotinib . MS and SPS MS methods resulted in similar protein expression trends, but the Even without treatment, we found evidence of marked upregulation of HER2/erbB26 in Regulated Change Regulated Regulated Change Regulated (Figure 1). Immunoblotting using antibodies against phospho-EGFR, EGFR, mTOR, all treatment conditions (Figure 2A). Autophosphorylation of EGFR was noticeably SPS method yields a larger dynamic range of protein expression ratios resulting the H358 erlotinib-resistant cell line. HER2/erbB2 is a closely related receptor tyrosine phospho-mTOR, S6 kinase, phospho-S6 kinase, phospho-ERK and ERK was also suppressed in the H358 cell line, while p-mTOR (S2448) and its downstream signaling + - 102 1804 126 62 1801 248 in significantly more identified up or down regulated proteins. kinase to EGFR/erbB1 which can activate the classical MAPK pathway or other performed.
Load more

Recommended publications
  • New Approaches to Functional Process Discovery in HPV 16-Associated Cervical Cancer Cells by Gene Ontology
    Cancer Research and Treatment 2003;35(4):304-313 New Approaches to Functional Process Discovery in HPV 16-Associated Cervical Cancer Cells by Gene Ontology Yong-Wan Kim, Ph.D.1, Min-Je Suh, M.S.1, Jin-Sik Bae, M.S.1, Su Mi Bae, M.S.1, Joo Hee Yoon, M.D.2, Soo Young Hur, M.D.2, Jae Hoon Kim, M.D.2, Duck Young Ro, M.D.2, Joon Mo Lee, M.D.2, Sung Eun Namkoong, M.D.2, Chong Kook Kim, Ph.D.3 and Woong Shick Ahn, M.D.2 1Catholic Research Institutes of Medical Science, 2Department of Obstetrics and Gynecology, College of Medicine, The Catholic University of Korea, Seoul; 3College of Pharmacy, Seoul National University, Seoul, Korea Purpose: This study utilized both mRNA differential significant genes of unknown function affected by the display and the Gene Ontology (GO) analysis to char- HPV-16-derived pathway. The GO analysis suggested that acterize the multiple interactions of a number of genes the cervical cancer cells underwent repression of the with gene expression profiles involved in the HPV-16- cancer-specific cell adhesive properties. Also, genes induced cervical carcinogenesis. belonging to DNA metabolism, such as DNA repair and Materials and Methods: mRNA differential displays, replication, were strongly down-regulated, whereas sig- with HPV-16 positive cervical cancer cell line (SiHa), and nificant increases were shown in the protein degradation normal human keratinocyte cell line (HaCaT) as a con- and synthesis. trol, were used. Each human gene has several biological Conclusion: The GO analysis can overcome the com- functions in the Gene Ontology; therefore, several func- plexity of the gene expression profile of the HPV-16- tions of each gene were chosen to establish a powerful associated pathway, identify several cancer-specific cel- cervical carcinogenesis pathway.
    [Show full text]
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
    [Show full text]
  • Proteomics Provides Insights Into the Inhibition of Chinese Hamster V79
    www.nature.com/scientificreports OPEN Proteomics provides insights into the inhibition of Chinese hamster V79 cell proliferation in the deep underground environment Jifeng Liu1,2, Tengfei Ma1,2, Mingzhong Gao3, Yilin Liu4, Jun Liu1, Shichao Wang2, Yike Xie2, Ling Wang2, Juan Cheng2, Shixi Liu1*, Jian Zou1,2*, Jiang Wu2, Weimin Li2 & Heping Xie2,3,5 As resources in the shallow depths of the earth exhausted, people will spend extended periods of time in the deep underground space. However, little is known about the deep underground environment afecting the health of organisms. Hence, we established both deep underground laboratory (DUGL) and above ground laboratory (AGL) to investigate the efect of environmental factors on organisms. Six environmental parameters were monitored in the DUGL and AGL. Growth curves were recorded and tandem mass tag (TMT) proteomics analysis were performed to explore the proliferative ability and diferentially abundant proteins (DAPs) in V79 cells (a cell line widely used in biological study in DUGLs) cultured in the DUGL and AGL. Parallel Reaction Monitoring was conducted to verify the TMT results. γ ray dose rate showed the most detectable diference between the two laboratories, whereby γ ray dose rate was signifcantly lower in the DUGL compared to the AGL. V79 cell proliferation was slower in the DUGL. Quantitative proteomics detected 980 DAPs (absolute fold change ≥ 1.2, p < 0.05) between V79 cells cultured in the DUGL and AGL. Of these, 576 proteins were up-regulated and 404 proteins were down-regulated in V79 cells cultured in the DUGL. KEGG pathway analysis revealed that seven pathways (e.g.
    [Show full text]
  • Quantitative Analysis of the Human Ovarian Carcinoma Mitochondrial Phosphoproteome
    www.aging-us.com AGING 2019, Vol. 11, No. 16 Research Paper Quantitative analysis of the human ovarian carcinoma mitochondrial phosphoproteome Na Li1,2,3, Shehua Qian1,2,3, Biao Li1,2,3, Xianquan Zhan1,2,3,4 1Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China 2Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China 3State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China 4National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan P. R. China Correspondence to: Xianquan Zhan; email: [email protected] Keywords: ovarian cancer, mitochondria, TiO2 enrichment, iTRAQ quantitative proteomics, mitochondrial phosphoprotein (mtPP) Received: June 15, 2019 Accepted: August 10, 2019 Published: August 22, 2019 Copyright: Li et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT To investigate the existence and their potential biological roles of mitochondrial phosphoproteins (mtPPs) in human ovarian carcinoma (OC), mitochondria purified from OC and control tissues were analyzed with TiO2 enrichment-based iTRAQ quantitative proteomics. Totally 67 mtPPs with 124 phosphorylation sites were identified, which of them included 48 differential mtPPs (mtDPPs). Eighteen mtPPs were reported previously in OCs, and they were consistent in this study compared to previous literature.
    [Show full text]
  • EIF2S1 Antibody Cat
    EIF2S1 Antibody Cat. No.: 57-063 EIF2S1 Antibody Confocal immunofluorescent analysis of EIF2S1 Antibody EIF2S1 Antibody immunohistochemistry analysis in with Hela cell followed by Alexa Fluor 488-conjugated goat formalin fixed and paraffin embedded human stomach anti-rabbit lgG (green). DAPI was used to stain the cell tissue followed by peroxidase conjugation of the nuclear (blue). secondary antibody and DAB staining. Specifications HOST SPECIES: Rabbit SPECIES REACTIVITY: Mouse Predicted species reactivity based on immunogen sequence: Rat, Chicken, Yeast, Bovine, HOMOLOGY: Drosophila This EIF2S1 antibody is generated from rabbits immunized with a KLH conjugated IMMUNOGEN: synthetic peptide between 60-89 amino acids from the N-terminal region of human EIF2S1. TESTED APPLICATIONS: IF, IHC-P, WB September 30, 2021 1 https://www.prosci-inc.com/eif2s1-antibody-57-063.html For WB starting dilution is: 1:1000 APPLICATIONS: For IF starting dilution is: 1:10~50 For IHC-P starting dilution is: 1:10~50 PREDICTED MOLECULAR 36 kDa WEIGHT: Properties This antibody is purified through a protein A column, followed by peptide affinity PURIFICATION: purification. CLONALITY: Polyclonal ISOTYPE: Rabbit Ig CONJUGATE: Unconjugated PHYSICAL STATE: Liquid BUFFER: Supplied in PBS with 0.09% (W/V) sodium azide. CONCENTRATION: batch dependent Store at 4˚C for three months and -20˚C, stable for up to one year. As with all antibodies STORAGE CONDITIONS: care should be taken to avoid repeated freeze thaw cycles. Antibodies should not be exposed to prolonged high temperatures. Additional Info OFFICIAL SYMBOL: EIF2S1 Eukaryotic translation initiation factor 2 subunit 1, Eukaryotic translation initiation factor 2 ALTERNATE NAMES: subunit alpha, eIF-2-alpha, eIF-2A, eIF-2alpha, EIF2S1, EIF2A ACCESSION NO.: P05198 PROTEIN GI NO.: 124200 GENE ID: 1965 USER NOTE: Optimal dilutions for each application to be determined by the researcher.
    [Show full text]
  • Identification of Molecular Targets in Head and Neck Squamous Cell Carcinomas Based on Genome-Wide Gene Expression Profiling
    1489-1497 7/11/07 18:41 Page 1489 ONCOLOGY REPORTS 18: 1489-1497, 2007 Identification of molecular targets in head and neck squamous cell carcinomas based on genome-wide gene expression profiling SATOYA SHIMIZU1,2, NAOHIKO SEKI2, TAKASHI SUGIMOTO2, SHIGETOSHI HORIGUCHI1, HIDEKI TANZAWA3, TOYOYUKI HANAZAWA1 and YOSHITAKA OKAMOTO1 Departments of 1Otorhinolaryngology, 2Functional Genomics and 3Clinical Molecular Biology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan Received May 21, 2007; Accepted June 28, 2007 Abstract. DNA amplifications activate oncogenes and are patients and metastases develop in 15-25% of patients (1). hallmarks of nearly all advanced cancers including head and Many factors, such as TNM stage, pathological grade and neck squamous cell carcinoma (HNSCC). Some oncogenes tumor site, influence the prognosis of HNSCC but are not show both DNA copy number gain and mRNA overexpression. sufficient to predict outcome. In addition, treatment often Chromosomal comparative genomic hybridization and oligo- results in impairment of functions such as speech and nucleotide microarrays were used to examine 8 HNSCC cell swallowing, cosmetic disfiguration and mental pain. These lines and a plot of gene expression levels relative to their inflictions significantly erode quality of life. To overcome this position on the chromosome was produced. Three highly situation, there is a need to find novel biomarkers that classify up-regulated genes, NT5C3, ANLN and INHBA, were patients into prognostic groups, to aid identification of high- identified on chromosome 7p14. These genes were subjected risk patients who may benefit from different treatments. to quantitative real-time RT-PCR on cDNA and genomic Comparative genomic hybridization (CGH) has facilitated DNA derived from 8 HNSCC cell lines.
    [Show full text]
  • Relevance of Translation Initiation in Diffuse Glioma Biology and Its
    cells Review Relevance of Translation Initiation in Diffuse Glioma Biology and its Therapeutic Potential Digregorio Marina 1, Lombard Arnaud 1,2, Lumapat Paul Noel 1, Scholtes Felix 1,2, Rogister Bernard 1,3 and Coppieters Natacha 1,* 1 Laboratory of Nervous System Disorders and Therapy, GIGA-Neurosciences Research Centre, University of Liège, 4000 Liège, Belgium; [email protected] (D.M.); [email protected] (L.A.); [email protected] (L.P.N.); [email protected] (S.F.); [email protected] (R.B.) 2 Department of Neurosurgery, CHU of Liège, 4000 Liège, Belgium 3 Department of Neurology, CHU of Liège, 4000 Liège, Belgium * Correspondence: [email protected] Received: 18 October 2019; Accepted: 26 November 2019; Published: 29 November 2019 Abstract: Cancer cells are continually exposed to environmental stressors forcing them to adapt their protein production to survive. The translational machinery can be recruited by malignant cells to synthesize proteins required to promote their survival, even in times of high physiological and pathological stress. This phenomenon has been described in several cancers including in gliomas. Abnormal regulation of translation has encouraged the development of new therapeutics targeting the protein synthesis pathway. This approach could be meaningful for glioma given the fact that the median survival following diagnosis of the highest grade of glioma remains short despite current therapy. The identification of new targets for the development of novel therapeutics is therefore needed in order to improve this devastating overall survival rate. This review discusses current literature on translation in gliomas with a focus on the initiation step covering both the cap-dependent and cap-independent modes of initiation.
    [Show full text]
  • The DNA Sequence and Comparative Analysis of Human Chromosome 20
    articles The DNA sequence and comparative analysis of human chromosome 20 P. Deloukas, L. H. Matthews, J. Ashurst, J. Burton, J. G. R. Gilbert, M. Jones, G. Stavrides, J. P. Almeida, A. K. Babbage, C. L. Bagguley, J. Bailey, K. F. Barlow, K. N. Bates, L. M. Beard, D. M. Beare, O. P. Beasley, C. P. Bird, S. E. Blakey, A. M. Bridgeman, A. J. Brown, D. Buck, W. Burrill, A. P. Butler, C. Carder, N. P. Carter, J. C. Chapman, M. Clamp, G. Clark, L. N. Clark, S. Y. Clark, C. M. Clee, S. Clegg, V. E. Cobley, R. E. Collier, R. Connor, N. R. Corby, A. Coulson, G. J. Coville, R. Deadman, P. Dhami, M. Dunn, A. G. Ellington, J. A. Frankland, A. Fraser, L. French, P. Garner, D. V. Grafham, C. Grif®ths, M. N. D. Grif®ths, R. Gwilliam, R. E. Hall, S. Hammond, J. L. Harley, P. D. Heath, S. Ho, J. L. Holden, P. J. Howden, E. Huckle, A. R. Hunt, S. E. Hunt, K. Jekosch, C. M. Johnson, D. Johnson, M. P. Kay, A. M. Kimberley, A. King, A. Knights, G. K. Laird, S. Lawlor, M. H. Lehvaslaiho, M. Leversha, C. Lloyd, D. M. Lloyd, J. D. Lovell, V. L. Marsh, S. L. Martin, L. J. McConnachie, K. McLay, A. A. McMurray, S. Milne, D. Mistry, M. J. F. Moore, J. C. Mullikin, T. Nickerson, K. Oliver, A. Parker, R. Patel, T. A. V. Pearce, A. I. Peck, B. J. C. T. Phillimore, S. R. Prathalingam, R. W. Plumb, H. Ramsay, C. M.
    [Show full text]
  • Global Analysis of Trna and Translation Factor Expression Reveals a Dynamic Landscape of Translational Regulation in Human Cancers
    ARTICLE https://doi.org/10.1038/s42003-018-0239-8 OPEN Global analysis of tRNA and translation factor expression reveals a dynamic landscape of translational regulation in human cancers Zhao Zhang1, Youqiong Ye1, Jing Gong1, Hang Ruan1, Chun-Jie Liu2, Yu Xiang1, Chunyan Cai3, An-Yuan Guo2, 1234567890():,; Jiqiang Ling4, Lixia Diao5, John N. Weinstein5 & Leng Han 1,6 The protein translational system, including transfer RNAs (tRNAs) and several categories of enzymes, plays a key role in regulating cell proliferation. Translation dysregulation also contributes to cancer development, though relatively little is known about the changes that occur to the translational system in cancer. Here, we present global analyses of tRNAs and three categories of enzymes involved in translational regulation in ~10,000 cancer patients across 31 cancer types from The Cancer Genome Atlas. By analyzing the expression levels of tRNAs at the gene, codon, and amino acid levels, we identified unequal alterations in tRNA expression, likely due to the uneven distribution of tRNAs decoding different codons. We find that overexpression of tRNAs recognizing codons with a low observed-over-expected ratio may overcome the translational bottleneck in tumorigenesis. We further observed overall overexpression and amplification of tRNA modification enzymes, aminoacyl-tRNA synthe- tases, and translation factors, which may play synergistic roles with overexpression of tRNAs to activate the translational systems across multiple cancer types. 1 Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA. 2 Department of Bioinformatics and Systems Biology, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology Wuhan, 430074 Hubei, People’s Republic of China.
    [Show full text]
  • Supplementary Table 1
    Up-regulated accession # Development M93275 ADFP, adipose differentiation related protein D43694 MATH-1, homolog of atonal 1 M64068 Bmi-1, zinc finger protein AW124785 Midnolin, midbrain nucleolar protein AI843178 Cla3, Cerebellar ataxia 3 D10712 Nedd1, Neural precursor cell expressed, developmentally down-regulated gene 1 AB011678 Doublecortin, for neurogenesis M57683 mPDGF-alpha-R, PDGF alpha receptor U41626 DSS1, deleted in split hand/split foot 1 homolog (Dss1), for limb development AB010833 PTCH2, patched 2, Mouse homolog of yeast CDC46 NP_034226 Ebf3, early B-cell factor 3 AI846695 Qk, Quaking U63386 Edr1 Early development regulator 1 (homolog of polyhomeotic 1), Mph1 AI043016 Rnf2, Ring finger protein 2 X69942 Enhancer-trap-locus 1, for transcription regulation AF100694 Ruvbl1, Ruv-B like protein 1, DNA helicase AW123618 Fzd2, Frizzled homolog 2 U88566 Sfrp1, secreted frizzled related protein 1 AA681520 Geminin-pending, for embryogenesis and morphogenesis U88567 Sfrp2, secreted frizzled related protein 2 AB025922 Gli1, GLI-Kruppel family member 1 AF089721 Smo, Smoothened X99104 Gli2, GLI-Kruppel family member 2 AF009414 SOX11, SRY-box containing gene 11 U61362 Grg1, groucho-related gene 1, Tle1, transducin-like enhancer of split 1 U85614 SRG3, Smarcc1, SWI/SNF related, matrix associated, action dependent regulator of chromatin, subfamily, member 1 M97506 Hen1, helix-loop-helix protein AI837838 Tmeff1, Transmembrane protein with EGF-like and two follistatin-like domains 1 U79748 Madh4, MAD homolog 4, for transcription regulation
    [Show full text]
  • Divergent Selection for Residual Feed Intake Affects the Transcriptomic And
    Divergent selection for residual feed intake affects the transcriptomic and proteomic profiles of pig skeletal muscle Annie Vincent, Isabelle Louveau, Florence Gondret, Christine Trefeu, Hélène Gilbert, Louis Lefaucheur To cite this version: Annie Vincent, Isabelle Louveau, Florence Gondret, Christine Trefeu, Hélène Gilbert, et al.. Diver- gent selection for residual feed intake affects the transcriptomic and proteomic profiles of pig skeletal muscle. Journal of Animal Science, American Society of Animal Science, 2015, 93 (6), pp.2745-2758. 10.2527/jas2015-8928. hal-01211015 HAL Id: hal-01211015 https://hal.archives-ouvertes.fr/hal-01211015 Submitted on 28 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Published June 25, 2015 Divergent selection for residual feed intake affects the transcriptomic and proteomic profiles of pig skeletal muscle1,2 A. Vincent,*† I. Louveau,*† F. Gondret,*† C. Tréfeu,*† H. Gilbert,‡§# and L. Lefaucheur*†3 *INRA, UMR1348 Pegase, F-35590 Saint-Gilles, France; †Agrocampus Ouest, UMR1348 Pegase, F-35000 Rennes, France; ‡INRA, UMR1388 GenPhySE, F-31326 Castanet-Tolosan, France; §Université de Toulouse, INP, ENSAT, UMR1388 GenPhySE, F-31326 Castanet-Tolosan, France; #Université de Toulouse, INP, ENVT, UMR1388 GenPhySE, F-31076 Toulouse, France ABSTRACT: Improving feed efficiency is a rel- involved in protein synthesis and a lower expres- evant strategy to reduce feed cost and environmental sion of genes associated with mitochondrial energy waste in livestock production.
    [Show full text]
  • Expression of EIF2 Family Genes Under Newcastle Disease Virus Infection in Two Chicken Lines
    Iowa State University Animal Industry Report 2019 Expression of EIF2 Family Genes under Newcastle Disease Virus Infection in Two Chicken Lines A.S. Leaflet R3323 controlling immune response to NDV. We hypothesize that the lines differentially regulate the expression of genes Ana Paula Del Vesco, Visiting Scholar1,2; related to host protein synthesis as a defense mechanism in Melissa S. Monson, Postdoc Research Associate1; response to NDV infection, and that this genetic control Michael G. Kaiser, Research Associate1; may contribute to the level of host resistance to NDV. Huaijun Zhou, Professor3; Jack C. M. Dekkers, Distinguished Professor1; Materials and Methods Susan J. Lamont, Distinguished Professor1 The effect of NDV challenge on gene expression in the 1Iowa State University, USA; 2Universidade Federal de spleen of the Fayoumis and the Leghorns at two- and six- Sergipe, Brazil; 3University of California, Davis, USA. days post infection (dpi) was evaluated. Chickens from both lines were either challenged with a concentrated NDV Summary and Implications vaccine strain via the eyes and nostrils or non-challenged Newcastle Disease Virus (NDV) causes large economic (control). The chickens from both lines and challenge losses around the world and recent outbreaks have occurred statuses (NDV challenged or control) were euthanized at 2- in the US. We assessed the expression of eukaryotic or 6-dpi for spleen harvest. The RNA was isolated from translation initiation factor 2 (eIF2)-related genes in the spleen samples and used to assess the expression of seven spleens of two genetically different, inbred chicken lines genes related to the eIF2 family using quantitative PCR. The from the Iowa State University Poultry Genetics program.
    [Show full text]