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Paromov V, Uversky VN, Cooley A, Liburd LE, Mukherjee S, Na I, Dayhoff GW, Pratap S. The Proteomic Analysis of Cancer-Related Alterations in the Human Unfoldome. Int J Mol Sci 2024; 25:1552. [PMID: 38338831 PMCID: PMC10855131 DOI: 10.3390/ijms25031552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 02/12/2024] Open
Abstract
Many proteins lack stable 3D structures. These intrinsically disordered proteins (IDPs) or hybrid proteins containing ordered domains with intrinsically disordered protein regions (IDPRs) often carry out regulatory functions related to molecular recognition and signal transduction. IDPs/IDPRs constitute a substantial portion of the human proteome and are termed "the unfoldome". Herein, we probe the human breast cancer unfoldome and investigate relations between IDPs and key disease genes and pathways. We utilized bottom-up proteomics, MudPIT (Multidimensional Protein Identification Technology), to profile differentially expressed IDPs in human normal (MCF-10A) and breast cancer (BT-549) cell lines. Overall, we identified 2271 protein groups in the unfoldome of normal and cancer proteomes, with 148 IDPs found to be significantly differentially expressed in cancer cells. Further analysis produced annotations of 140 IDPs, which were then classified to GO (Gene Ontology) categories and pathways. In total, 65% (91 of 140) IDPs were related to various diseases, and 20% (28 of 140) mapped to cancer terms. A substantial portion of the differentially expressed IDPs contained disordered regions, confirmed by in silico characterization. Overall, our analyses suggest high levels of interactivity in the human cancer unfoldome and a prevalence of moderately and highly disordered proteins in the network.
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Affiliation(s)
- Victor Paromov
- Meharry Proteomics Core, RCMI Research Capacity Core, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA;
| | - Vladimir N. Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33613, USA; (V.N.U.); (I.N.)
| | - Ayorinde Cooley
- Meharry Bioinformatics Core, Department of Microbiology, Immunology and Physiology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA;
| | - Lincoln E. Liburd
- Department of Biochemistry, Cancer Biology, Neuroscience & Pharmacology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA (S.M.)
| | - Shyamali Mukherjee
- Department of Biochemistry, Cancer Biology, Neuroscience & Pharmacology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA (S.M.)
| | - Insung Na
- Department of Molecular Medicine, USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33613, USA; (V.N.U.); (I.N.)
| | - Guy W. Dayhoff
- Department of Chemistry, College of Art and Sciences, University of South Florida, Tampa, FL 33613, USA;
| | - Siddharth Pratap
- Meharry Proteomics Core, RCMI Research Capacity Core, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA;
- Meharry Bioinformatics Core, Department of Microbiology, Immunology and Physiology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA;
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Jayathirtha M, Jayaweera T, Whitham D, Petre BA, Neagu AN, Darie CC. Two-Dimensional Polyacrylamide Gel Electrophoresis Coupled with Nanoliquid Chromatography-Tandem Mass Spectrometry-Based Identification of Differentially Expressed Proteins and Tumorigenic Pathways in the MCF7 Breast Cancer Cell Line Transfected for Jumping Translocation Breakpoint Protein Overexpression. Int J Mol Sci 2023; 24:14714. [PMID: 37834160 PMCID: PMC10572688 DOI: 10.3390/ijms241914714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
The identification of new genes/proteins involved in breast cancer (BC) occurrence is widely used to discover novel biomarkers and understand the molecular mechanisms of BC initiation and progression. The jumping translocation breakpoint (JTB) gene may act both as a tumor suppressor or oncogene in various types of tumors, including BC. Thus, the JTB protein could have the potential to be used as a biomarker in BC, but its neoplastic mechanisms still remain unknown or controversial. We previously analyzed the interacting partners of JTBhigh protein extracted from transfected MCF7 BC cell line using SDS-PAGE complemented with in-solution digestion, respectively. The previous results suggested the JTB contributed to the development of a more aggressive phenotype and behavior for the MCF7 BC cell line through synergistic upregulation of epithelial-mesenchymal transition (EMT), mitotic spindle, and fatty acid metabolism-related pathways. In this work, we aim to complement the previously reported JTB proteomics-based experiments by investigating differentially expressed proteins (DEPs) and tumorigenic pathways associated with JTB overexpression using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). Statistically different gel spots were picked for protein digestion, followed by nanoliquid chromatography-tandem mass spectrometry (nLC-MS/MS) analysis. We identified six DEPs related to the JTBhigh condition vs. control that emphasize a pro-tumorigenic (PT) role. Twenty-one proteins, which are known to be usually overexpressed in cancer cells, emphasize an anti-tumorigenic (AT) role when low expression occurs. According to our previous results, proteins that have a PT role are mainly involved in the activation of the EMT process. Interestingly, JTB overexpression has been correlated here with a plethora of significant upregulated and downregulated proteins that sustain JTB tumor suppressive functions. Our present and previous results sustain the necessity of the complementary use of different proteomics-based methods (SDS-PAGE, 2D-PAGE, and in-solution digestion) followed by tandem mass spectrometry to avoid their limitations, with each method leading to the delineation of specific clusters of DEPs that may be merged for a better understanding of molecular pathways and neoplastic mechanisms related to the JTB's role in BC initiation and progression.
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Affiliation(s)
- Madhuri Jayathirtha
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA; (M.J.); (T.J.); (D.W.); (B.A.P.)
| | - Taniya Jayaweera
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA; (M.J.); (T.J.); (D.W.); (B.A.P.)
| | - Danielle Whitham
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA; (M.J.); (T.J.); (D.W.); (B.A.P.)
| | - Brîndușa Alina Petre
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA; (M.J.); (T.J.); (D.W.); (B.A.P.)
- Laboratory of Biochemistry, Department of Chemistry, “Alexandru Ioan Cuza” University of Iasi, Carol I Bvd., No. 11, 700506 Iasi, Romania
- Center for Fundamental Research and Experimental Development in Translation Medicine—TRANSCEND, Regional Institute of Oncology, 700483 Iasi, Romania
| | - Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, “Alexandru Ioan Cuza” University of Iasi, Carol I Bvd., No. 20A, 700505 Iasi, Romania;
| | - Costel C. Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA; (M.J.); (T.J.); (D.W.); (B.A.P.)
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3
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Zhao N, Ruan M, Koestler DC, Lu J, Marsit CJ, Kelsey KT, Platz EA, Michaud DS. Epigenome-wide scan identifies differentially methylated regions for lung cancer using pre-diagnostic peripheral blood. Epigenetics 2021; 17:460-472. [PMID: 34008478 DOI: 10.1080/15592294.2021.1923615] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
BACKGROUND DNA methylation markers have been associated with lung cancer risk and may identify aetiologically relevant genomic regions, or alternatively, be markers of disease risk factors or biological processes associated with disease development. METHODS In a nested case-control study, we measured blood leukocyte DNA methylation levels in pre-diagnostic samples collected from 430 participants (208 cases; 222 controls) in the 1989 CLUE II cohort. We compared DNA methylation levels with case/control status to identify novel genomic regions, both single CpG sites and differentially methylated regions (DMRs), while controlling for known DNA methylation changes associated with smoking using a previously described pack-years-based smoking methylation score. Stratification analyses were conducted over time from blood draw to diagnosis, histology, and smoking status. RESULTS We identified 16 single CpG sites and 40 DMRs significantly associated with lung cancer risk (q < 0.05). The identified genomic regions were associated with genes including H19, HOXA3/HOXA4, RUNX3, BRICD5, PLXNB2, and RP13. For the single CpG sites, the strongest association was noted for cg09736286 in the DIABLO gene (OR [for 1 SD] = 2.99, 95% CI: 1.95-4.59, P-value = 4.81 × 10-7). We found that CpG sites in the HOXA3/HOXA4 region were hypermethylated in cases compared to controls. CONCLUSION The single CpG sites and DMRs that we identified represented significant measurable differences in lung cancer risk, providing potential biomarkers for lung cancer risk stratification. Future studies will need to examine whether these regions are causally related to lung cancer.
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Affiliation(s)
- Naisi Zhao
- Department of Public Health & Community Medicine, Tufts University School of Medicine, Tufts University, Boston, MA, USA
| | - Mengyuan Ruan
- Department of Public Health & Community Medicine, Tufts University School of Medicine, Tufts University, Boston, MA, USA
| | - Devin C Koestler
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, USA.,University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, USA
| | - Jiayun Lu
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Carmen J Marsit
- Department of Environmental Health and Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Karl T Kelsey
- Department of Epidemiology, Brown University, Providence, RI, USA.,Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.,The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - Dominique S Michaud
- Department of Public Health & Community Medicine, Tufts University School of Medicine, Tufts University, Boston, MA, USA.,Department of Epidemiology, Brown University, Providence, RI, USA
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Ling HZ, Xu SZ, Leng RX, Wu J, Pan HF, Fan YG, Wang B, Xia YR, Huang Q, Shuai ZW, Ye DQ. Discovery of new serum biomarker panels for systemic lupus erythematosus diagnosis. Rheumatology (Oxford) 2020; 59:1416-1425. [PMID: 31899518 DOI: 10.1093/rheumatology/kez634] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 11/26/2019] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE Clinical diagnosis of SLE is currently challenging due to its heterogeneity. Many autoantibodies are associated with SLE and are considered potential diagnostic markers, but systematic screening and validation of such autoantibodies is lacking. This study aimed to systematically discover new autoantibodies that may be good biomarkers for use in SLE diagnosis. METHODS Sera from 15 SLE patients and 5 healthy volunteers were analysed using human proteome microarrays to identify candidate SLE-related autoantibodies. The results were validated by screening of sera from 107 SLE patients, 94 healthy volunteers and 60 disease controls using focussed arrays comprised of autoantigens corresponding to the identified candidate antibodies. Logistic regression was used to derive and validate autoantibody panels that can discriminate SLE disease. Extensive ELISA screening of sera from 294 SLE patients and 461 controls was performed to validate one of the newly discovered autoantibodies. RESULTS A total of 31, 11 and 18 autoantibodies were identified to be expressed at significantly higher levels in the SLE group than in the healthy volunteers, disease controls and healthy volunteers plus disease control groups, respectively, with 25, 7 and 13 of these differentially expressed autoantibodies being previously unreported. Diagnostic panels comprising anti-RPLP2, anti-SNRPC and anti-PARP1, and anti-RPLP2, anti-PARP1, anti-MAK16 and anti- RPL7A were selected. Performance of the newly discovered anti-MAK16 autoantibody was confirmed by ELISA. Some associations were seen with clinical characteristics of SLE patients, such as disease activity with the level of anti-PARP1 and rash with the level of anti-RPLP2, anti-MAK16 and anti- RPL7A. CONCLUSION The combined autoantibody panels identified here show promise for the diagnosis of SLE and for differential diagnosis of other major rheumatic immune diseases.
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Affiliation(s)
- Hua-Zhi Ling
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical UniversityHefei, Anhui, China.,Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical UniversityHefei, Anhui, China.,Anhui Province Key Laboratory of Major Autoimmune Diseases, Hefei, Anhui, China
| | - Shu-Zhen Xu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical UniversityHefei, Anhui, China.,Anhui Province Key Laboratory of Major Autoimmune Diseases, Hefei, Anhui, China
| | - Rui-Xue Leng
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical UniversityHefei, Anhui, China.,Anhui Province Key Laboratory of Major Autoimmune Diseases, Hefei, Anhui, China
| | - Jun Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical UniversityHefei, Anhui, China
| | - Hai-Feng Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical UniversityHefei, Anhui, China.,Anhui Province Key Laboratory of Major Autoimmune Diseases, Hefei, Anhui, China
| | - Yin-Guang Fan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical UniversityHefei, Anhui, China
| | - Bin Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical UniversityHefei, Anhui, China
| | - Yuan-Rui Xia
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical UniversityHefei, Anhui, China
| | - Qian Huang
- Anhui Province Key Laboratory of Major Autoimmune Diseases, Hefei, Anhui, China
| | - Zong-Wen Shuai
- Department of Rheumatology and Immunology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Dong-Qing Ye
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical UniversityHefei, Anhui, China.,Anhui Province Key Laboratory of Major Autoimmune Diseases, Hefei, Anhui, China
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Schcolnik-Cabrera A, Chávez-Blanco A, Domínguez-Gómez G, Taja-Chayeb L, Morales-Barcenas R, Trejo-Becerril C, Perez-Cardenas E, Gonzalez-Fierro A, Dueñas-González A. Orlistat as a FASN inhibitor and multitargeted agent for cancer therapy. Expert Opin Investig Drugs 2018; 27:475-489. [PMID: 29723075 DOI: 10.1080/13543784.2018.1471132] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Cancer cells have increased glycolysis and glutaminolysis. Their third feature is increased de novo lipogenesis. As such, fatty acid (FA) synthesis enzymes are over-expressed in cancer and their depletion causes antitumor effects. As fatty acid synthase (FASN) plays a pivotal role in this process, it is an attractive target for cancer therapy. AREAS COVERED This is a review of the lipogenic phenotype of cancer and how this phenomenon can be exploited for cancer therapy using inhibitors of FASN, with particular emphasis on orlistat as a repurposing drug. EXPERT OPINION Disease stabilization only has been observed with a highly selective FASN inhibitor used as a single agent in clinical trials. It is too early to say whether the absence of tumor responses other than stabilization results because even full inhibition of FASN is not enough to elicit antitumor responses. The FASN inhibitor orlistat is a 'dirty' drug with target-off actions upon at least seven targets with a proven role in tumor biology. The development of orlistat formulations suited for its intravenous administration is a step ahead to shed light on the concept that drug promiscuity can or not be a virtue.
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Affiliation(s)
| | - Alma Chávez-Blanco
- a Division of Basic Research , Instituto Nacional de Cancerologia , Mexico City , Mexico
| | | | - Lucia Taja-Chayeb
- a Division of Basic Research , Instituto Nacional de Cancerologia , Mexico City , Mexico
| | - Rocio Morales-Barcenas
- a Division of Basic Research , Instituto Nacional de Cancerologia , Mexico City , Mexico
| | | | - Enrique Perez-Cardenas
- a Division of Basic Research , Instituto Nacional de Cancerologia , Mexico City , Mexico
| | - Aurora Gonzalez-Fierro
- a Division of Basic Research , Instituto Nacional de Cancerologia , Mexico City , Mexico
| | - Alfonso Dueñas-González
- b Unit of Biomedical Research in Cancer , Instituto de Investigaciones Biomedicas, UNAM/Instituto Nacional de Cancerologia , Mexico City , Mexico
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Marques SM, Chaves S, Gonçalves F, Pereira R. Differential gene expression in Iberian green frogs (Pelophylax perezi) inhabiting a deactivated uranium mine. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2013; 87:115-119. [PMID: 23146668 DOI: 10.1016/j.ecoenv.2012.10.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 10/02/2012] [Accepted: 10/12/2012] [Indexed: 06/01/2023]
Abstract
Iberian green frogs (Pelophylax perezi) were found inhabiting a deactivated uranium mine, especially an effluent pond, seriously contaminated with metals and radionuclides. These animals were previously assessed for oxidative stress parameters and did not revealed significant alterations. In order to better understand which mechanisms may be involved in the ability to withstand permanent contamination gene expression analysis was performed in the liver, through suppression subtractive hybridization (SSH). The SSH outcome in the liver revealed the up-regulation of genes coding for the ribosomal protein L7a and for several proteins typical from blood plasma: fibrinogen, hemoglobin and albumin. Besides their normal function, some of these proteins can play an important role as protective agents against oxidative stress. This work provides new insights on possible basal protection mechanisms that may act in organisms exposed chronically to contamination.
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Affiliation(s)
- Sérgio M Marques
- Departamento de Biologia da & CESAM-Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal.
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Wong AW, Paulson QX, Hong J, Stubbins RE, Poh K, Schrader E, Nunez NP. Alcohol promotes breast cancer cell invasion by regulating the Nm23-ITGA5 pathway. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2011; 30:75. [PMID: 21838876 PMCID: PMC3170226 DOI: 10.1186/1756-9966-30-75] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 08/12/2011] [Indexed: 01/03/2024]
Abstract
Background Alcohol consumption is an established risk factor for breast cancer metastasis. Yet, the mechanism by which alcohol promotes breast cancer metastases is unknown. The ability of cancer cells to invade through tissue barriers (such as basement membrane and interstitial stroma) is an essential step towards establishing cancer metastasis. In the present study, we identify and examine the roles of two genes, Nm23 and ITGA5, in alcohol-induced breast cancer cell invasion. Methods Human breast cancer T47D cells were treated with ethanol at various concentrations. Boyden chamber invasion assays were used to measure cellular invasive ability. The mRNA expression level of metastasis suppressor genes including Nm23 was determined by qRT-PCR. ITGA5 was identified using a qRT-PCR array of 84 genes important for cell-cell and cell-extracellular matrix interactions. Nm23 overexpression in addition to Nm23- and ITGA5 knock-down were used to determine the role of the Nm23-ITGA5 pathway on cellular invasive ability of T47D cells. Protein expression levels were verified by Western blot. Results Alcohol increased the invasive ability of human breast cancer T47D cells in a dose-dependent manner through the suppression of the Nm23 metastatic suppressor gene. In turn, Nm23 down-regulation increased expression of fibronectin receptor subunit ITGA5, which subsequently led to increased cellular invasion. Moreover, Nm23 overexpression was effective in suppressing the effects of alcohol on cell invasion. In addition, we show that the effects of alcohol on invasion were also inhibited by knock-down of ITGA5. Conclusions Our results suggest that the Nm23-ITGA5 pathway plays a critical role in alcohol-induced breast cancer cell invasion. Thus, regulation of this pathway may potentially be used to prevent the establishment of alcohol-promoted metastases in human breast cancers.
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Affiliation(s)
- Amy W Wong
- Institute for Cell and Molecular Biology, University of Texas, Austin, TX, USA
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Gao DM, Wang SP, He Z, Fung MC, Liu MS, Yu LX, Chen XC. Schistosoma japonicum: screening of cercariae cDNA library by specific single-chain antibody against SIEA26-28 ku and immunization experiment of the recombinant plasmids containing the selected genes. Parasitol Res 2010; 107:127-34. [DOI: 10.1007/s00436-010-1846-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2010] [Accepted: 03/11/2010] [Indexed: 10/19/2022]
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Menon R, Omenn GS. Proteomic characterization of novel alternative splice variant proteins in human epidermal growth factor receptor 2/neu-induced breast cancers. Cancer Res 2010; 70:3440-9. [PMID: 20388783 DOI: 10.1158/0008-5472.can-09-2631] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Multifaceted alternative splicing in cancer cells greatly diversifies protein structure independently of genome changes, but the characterization of cancer-associated splice variants is quite limited. In this study, we used mass spectrometric data to interrogate a custom-built database created with three-frame translations of mRNA sequences from Ensembl and ECgene to find alternative splice variant proteins. In mass spectrometric files from liquid chromatography tandem mass spectrometry (LC-MS/MS) analyses of normal mouse mammary glands or mammary tumors derived from conditional human epidermal growth factor receptor 2 (Her2)/neu transgenic mice, we identified a total of 608 alternative splice variants, of which peptides from 216 proteins were found only in the tumor sample. Among the 608 splice variants were 68 novel proteins that were not completely matched to any known protein sequence in mice, for which we found known functional motifs. Biological process enrichment analysis of the splice variants identified suggested the involvement of these proteins especially in cell motility and translation initiation. The cancer-associated differentially expressed splice variant proteins offer novel biomarker candidates that may function in breast cancer progression or metastasis.
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Affiliation(s)
- Rajasree Menon
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109-2218, USA.
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Park S, Lee KM, Ju JH, Kim J, Noh DY, Lee T, Shin I. Protein expression profiling of primary mammary epithelial cells derived from MMTV-neu mice revealed that HER2/NEU-driven changes in protein expression are functionally clustered. IUBMB Life 2010; 62:41-50. [PMID: 19960538 DOI: 10.1002/iub.276] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
MMTV-neu transgenic mice overexpressing NEU in their mammary glands develop tumor after 6 months of age. To find a novel protein biomarker using this mouse model, we identified and characterized the proteins that were differently expressed between primary mammary epithelial cells from 2 months old MMTV-neu heterozygote mice and wild type (WT) littermates using two-dimensional digest (ChemDigest/Trypsin)-LC-MS/MS. The differentially expressed proteins were selected and analyzed using DAVID Bioinformatics resource. The proteins involved in anti-apoptosis, purine metabolism, ribosome and proteasome functions were upregulated, whereas cell adhesion-related proteins were downregulated in PMECs from MMTV-neu mice when compared with WT PMECs. The results indicate that several functional units are coregulated by HER2/NEU. We hypothesize that these changes in the cellular proteome may be responsible for early onset of HER2/NEU-driven tumorigenesis.
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Affiliation(s)
- Sungwoo Park
- Department of Life Science, Hanyang University, Seoul 133-791, Korea
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Yang PY, Liu K, Ngai MH, Lear MJ, Wenk MR, Yao SQ. Activity-based proteome profiling of potential cellular targets of Orlistat--an FDA-approved drug with anti-tumor activities. J Am Chem Soc 2010; 132:656-66. [PMID: 20028024 DOI: 10.1021/ja907716f] [Citation(s) in RCA: 186] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Orlistat, or tetrahydrolipstatin (THL), is an FDA-approved antiobesity drug with potential antitumor activities. Cellular off-targets and potential side effects of Orlistat in cancer therapies, however, have not been extensively explored thus far. In this study, we report the total of synthesis of THL-like protein-reactive probes, in which extremely conservative modifications (i.e., an alkyne handle) were introduced in the parental THL structure to maintain the native biological properties of Orlistat, while providing the necessary functionality for target identification via the bio-orthogonal click chemistry. With these natural productlike, cell-permeable probes, we were able to demonstrate, for the first time, this chemical proteomic approach is suitable for the identification of previously unknown cellular targets of Orlistat. In addition to the expected fatty acid synthase (FAS), we identified a total of eight new targets, some of which were further validated by experiments including Western blotting, recombinant protein expression, and site-directed mutagenesis. Our findings have important implications in the consideration of Orlistat as a potential anticancer drug at its early stages of development for cancer therapy. Our strategy should be broadly useful for off-target identification against quite a number of existing drugs and/or candidates, which are also covalent modifiers of their biological targets.
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Affiliation(s)
- Peng-Yu Yang
- Department of Chemistry, National University of Singapore, Singapore 117543
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12
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Lange A, Kistler C, Jutzi TB, Bazhin AV, Klemke CD, Schadendorf D, Eichmüller SB. Detergent fractionation with subsequent subtractive suppression hybridization as a tool for identifying genes coding for plasma membrane proteins. Exp Dermatol 2009; 18:527-35. [DOI: 10.1111/j.1600-0625.2008.00821.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Zhu Y, Wang Q, Xu W, Li S. The ethanol response gene Cab45 can modulate the impairment elicited by ethanol and ultraviolet in PC12 cells. J Genet Genomics 2009; 35:153-61. [PMID: 18355758 DOI: 10.1016/s1673-8527(08)60021-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Revised: 11/27/2007] [Accepted: 12/07/2007] [Indexed: 11/30/2022]
Abstract
High consumption of ethanolic beverages facilitates neurodegeneration, but the mechanism of this process still remained elusive. Suppression subtractive hybridization (SSH) is a technique for detection of rare transcripts. With SSH approach, we identified one ethanol response gene Cab45, which was down-regulated by ethanol with time-dependent manner in B104 cells. The full-length sequence of Cab45 gene was obtained by 5' -RACE (5' Rapid Amplification of cDNA Ends) for the first time in rat. Based on the sequence of deduced amino acid of rat Cab45, the alignment was conducted with its counterparts in different species and displayed a high conservation. Using different tissues in rat and cell lines, Cab45 was characterized by a ubiquitous expression and differentiation dependent down-regulation. Given that ethanol facilitates some cell differentiation, we hypothesize that Cab45 is involved in ethanol-mediated differentiation. With transient transfection, the function of Cab45 was investigated by up-regulation and down-regulation in PC12 cells. Ethanol treatment and UV exposure were conducted subsequently and cell proliferations were detected by MTT (Methyl Thiazolyl Tetrazolium) approach. It revealed that the up-regulation of Cab45 modulated the impairment elicited by ethanol and UV in transfected cells. As a member of new calcium binding protein family, the exact role of Cab45 still remains unclear.
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Affiliation(s)
- Yunfeng Zhu
- Department of Oncology in Beijing 307 Hospital, Fengtai District, Beijing 100071, China.
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Down-regulation of ribosomal protein L7A in human osteosarcoma. J Cancer Res Clin Oncol 2009; 135:1025-31. [DOI: 10.1007/s00432-008-0538-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2008] [Accepted: 12/15/2008] [Indexed: 10/21/2022]
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15
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Chattopadhyay I, Kapur S, Purkayastha J, Phukan R, Kataki A, Mahanta J, Saxena S. Gene expression profile of esophageal cancer in North East India by cDNA microarray analysis. World J Gastroenterol 2007; 13:1438-44. [PMID: 17457978 PMCID: PMC4146931 DOI: 10.3748/wjg.v13.i9.1438] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2006] [Revised: 12/29/2006] [Accepted: 01/26/2007] [Indexed: 02/07/2023] Open
Abstract
AIM To identify alterations in genes and molecular functional pathways in esophageal cancer in a high incidence region of India where there is a widespread use of tobacco and betel quid with fermented areca nuts. METHODS Total RNA was isolated from tumor and matched normal tissue of 16 patients with esophageal squamous cell carcinoma. Pooled tumor tissue RNA was labeled with Cy3-dUTP and pooled normal tissue RNA was labeled with Cy5-dUTP by direct labeling method. The labeled probes were hybridized with human 10K cDNA chip and expression profiles were analyzed by Genespring GX V 7.3 (Silicon Genetics). RESULTS Nine hundred twenty three genes were differentially expressed. Of these, 611 genes were upregulated and 312 genes were downregulated. Using stringent criteria (P < or = 0.05 and > or = 1.5 fold change), 127 differentially expressed genes (87 upregulated and 40 downregulated) were identified in tumor tissue. On the basis of Gene Ontology, four different molecular functional pathways (MAPK pathway, G-protein coupled receptor family, ion transport activity, and serine or threonine kinase activity) were most significantly upregulated and six different molecular functional pathways (structural constituent of ribosome, endopeptidase inhibitor activity, structural constituent of cytoskeleton, antioxidant activity, acyl group transferase activity, eukaryotic translation elongation factor activity) were most significantly downregulated. CONCLUSION Several genes that showed alterations in our study have also been reported from a high incidence area of esophageal cancer in China. This indicates that molecular profiles of esophageal cancer in these two different geographic locations are highly consistent.
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Affiliation(s)
- Indranil Chattopadhyay
- Institute of Pathology, Indian Council of Medical Research, Safdarjang Hospital Campus, Post Box No. 4909, New Delhi 110029, India
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Klener P, Szynal M, Cleuter Y, Merimi M, Duvillier H, Lallemand F, Bagnis C, Griebel P, Sotiriou C, Burny A, Martiat P, Van den Broeke A. Insights into gene expression changes impacting B-cell transformation: cross-species microarray analysis of bovine leukemia virus tax-responsive genes in ovine B cells. J Virol 2006; 80:1922-38. [PMID: 16439548 PMCID: PMC1367148 DOI: 10.1128/jvi.80.4.1922-1938.2006] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Large-animal models for leukemia have the potential to aid in the understanding of networks that contribute to oncogenesis. Infection of cattle and sheep with bovine leukemia virus (BLV), a complex retrovirus related to human T-cell leukemia virus type 1 (HTLV-1), is associated with the development of B-cell leukemia. Whereas the natural disease in cattle is characterized by a low tumor incidence, experimental infection of sheep leads to overt leukemia in the majority of infected animals, providing a model for studying the pathogenesis associated with BLV and HTLV-1. Tax(BLV), the major oncoprotein, initiates a cascade of events leading toward malignancy, although the basis of transformation is not fully understood. We have taken a cross-species ovine-to-human microarray approach to identify Tax(BLV)-responsive transcriptional changes in two sets of cultured ovine B cells following retroviral vector-mediated delivery of Tax(BLV). Using cDNA-spotted microarrays comprising 10,336 human genes/expressed sequence tags, we identified a cohort of differentially expressed genes, including genes related to apoptosis, DNA transcription, and repair; proto-oncogenes; cell cycle regulators; transcription factors; small Rho GTPases/GTPase-binding proteins; and previously reported Tax(HTLV-1)-responsive genes. Interestingly, genes known to be associated with human neoplasia, especially B-cell malignancies, were extensively represented. Others were novel or unexpected. The results suggest that Tax(BLV) deregulates a broad network of interrelated pathways rather than a single B-lineage-specific regulatory process. Although cross-species approaches do not permit a comprehensive analysis of gene expression patterns, they can provide initial clues for the functional roles of genes that participate in B-cell transformation and pinpoint molecular targets not identified using other methods in animal models.
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Affiliation(s)
- Pavel Klener
- Laboratory of Experimental Hematology, Bordet Institute, 121 Blvd. de Waterloo, 1000 Brussels, Belgium
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Liu J, Li JP, Chen DL, Zhang HW, Wang WZ. Expression and functional study of ribosomal protein L5 in gastric cancer. Shijie Huaren Xiaohua Zazhi 2005; 13:2731-2735. [DOI: 10.11569/wcjd.v13.i23.2731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the expression of ribosomal protein L15 (RPL5) in gastric cancer as well as its effect on the proliferation of gastric cancer cells.
METHODS: The expression of RPL5 was detected in gastric cancer cell lines AGS, MKN45, SGC7901 and MGC803 by Western blot. The specific siRNA vector of RPL5 was constructed and then transfected into AGS cells. The expression of RPL5 in the transfectants was examined by Western blot. The growth of transfected cells was evaluated by MTT assay and flow cytometry.
RESULTS: The expression of RPL5 in gastric cancer cell lines AGS, MKN45, SGC7901 and MGC803 were all significantly higher than that in GES-1 and normal epithelial cells of gastric mucosa. The specific siRNA vectors of RPL5, named U6-RPL5A and U6-RPL5B, were successfully constructed and transfected into AGS cells. U6-RPL5A could inhibit the expression of RPL5 significantly. The growth rate of U6-RPL5A transfected cells, named AGS-U6-RPL5A, was lower than the control cells, and the percentage of the cells that was in proliferation phase was decreased by about 5%.
CONCLUSION: RPL5 can inhibit the proliferation of gastric cancer cells, and further investigation of RPL5 function will be helpful in the diagnosis and treatment of gastric cancer.
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Eichbaum MHR, Schneeweiss A, Bastert G. Long-term remission of excessive liver metastases in a breast cancer patient with chronic alcohol abuse using a monotherapy with trastuzumab. Anticancer Drugs 2005; 16:199-200. [PMID: 15655418 DOI: 10.1097/00001813-200502000-00012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We report on the successful treatment of a 43-year-old breast cancer patient with excessive liver metastases and chronic alcohol abuse. After first occurrence of hepatic metastases, systemic and interventional therapies were performed, and resulted in short-term partial remission. Finally, an excessive progression of the hepatic metastases was diagnosed. A systemic therapy with weekly trastuzumab (Herceptin) infusions was induced and a complete remission was achieved that is ongoing now for over 45 months.
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Affiliation(s)
- Michael H R Eichbaum
- Department of Gynecology and Obstetrics, University of Heidelberg Medical School, Heidelberg, Germany.
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Ma C, Lin H, Leonard SS, Shi X, Ye J, Luo J. Overexpression of ErbB2 enhances ethanol-stimulated intracellular signaling and invasion of human mammary epithelial and breast cancer cells in vitro. Oncogene 2003; 22:5281-90. [PMID: 12917629 DOI: 10.1038/sj.onc.1206675] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Both epidemiological and experimental studies indicate that ethanol is a tumor promoter and may promote metastasis of breast cancer. However, the molecular mechanisms underlying ethanol-mediated tumor promotion remain unknown. Overexpression of ErbB proteins in breast cancer patients is generally associated with poor prognosis. The ErbB proteins are a family of receptor kinases that include four closely related members: epidermal growth factor receptor (EGFR/ErbB1), ErbB2/neu, ErbB3, and ErbB4. Particularly, ErbB2 plays a pivotal role in ErbB-mediated activities. Here we demonstrated that amplification of ErbB2 expression sensitized a specific cellular response to ethanol. Human breast cancer cells or mammary epithelial cells with a high expression of ErbB2 exhibited an enhanced response to ethanol-stimulated cell invasion in vitro. Ethanol also stimulated cell proliferation; however, this stimulation was independent of ErbB2 levels. Ethanol triggered divergent intracellular signaling among cells expressing different ErbB2 levels. In the cells overexpressing ErbB2, ethanol was more effective in the activation of c-Jun NH2 terminal protein kinases (JNKs) and p38 mitogen-activated protein kinase (p38 MAPK) as well as the induction of reactive oxygen species (ROS) than the cells with normal ErbB2 expression. Blockage of either JNKs or p38 MAPK activation eliminated ethanol-mediated cell invasion. In contrast, the reduction of hydrogen peroxide concentration by catalase exposure had little effect on ethanol-induced cell invasion. These results indicated that ethanol-induced cell invasion was primarily mediated by JNKs and p38 MAPK, whereas the involvement of ROS formation might be minimal. Our study suggests that overexpression of ErbB2 may augment ethanol-elicited signaling and promote ethanol-stimulated tumor metastasis.
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Affiliation(s)
- Cuiling Ma
- Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, Morgantown, WV 26506, USA
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Qian Y, Luo J, Leonard SS, Harris GK, Millecchia L, Flynn DC, Shi X. Hydrogen peroxide formation and actin filament reorganization by Cdc42 are essential for ethanol-induced in vitro angiogenesis. J Biol Chem 2003; 278:16189-97. [PMID: 12598535 DOI: 10.1074/jbc.m207517200] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
This report focuses on the identification of the molecular mechanisms of ethanol-induced in vitro angiogenesis. The manipulation of angiogenesis is an important therapeutic approach for the treatment of cancer, cardiovascular diseases, and chronic inflammation. Our results showed that ethanol stimulation altered the integrity of actin filaments and increased the formation of lamellipodia and filopodia in SVEC4-10 cells. Further experiments demonstrated that ethanol stimulation increased cell migration and invasion and induced in vitro angiogenesis in SVEC4-10 cells. Mechanistically, ethanol stimulation activated Cdc42 and produced H(2)O(2) a reactive oxygen species intermediate in SVEC4-10 cells. Measuring the time course of Cdc42 activation and H(2)O(2) production upon ethanol stimulation revealed that the Cdc42 activation and the increase of H(2)O(2) lasted more than 3 h, which indicates the mechanisms of the long duration effects of ethanol on the cells. Furthermore, either overexpression of a constitutive dominant negative Cdc42 or inhibition of H(2)O(2) production abrogated the effects of ethanol on SVEC4-10 cells, indicating that both the activation of Cdc42 and the production of H(2)O(2) are essential for the actions of ethanol. Interestingly, we also found that overexpression of a constitutive dominant positive Cdc42 itself was sufficient to produce H(2)O(2) and to induce in vitro angiogenesis. Taken together, our results suggest that ethanol stimulation can induce H(2)O(2) production through the activation of Cdc42, which results in reorganizing actin filaments and increasing cell motility and in vitro angiogenesis.
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Affiliation(s)
- Yong Qian
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA.
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Sun Y, Lin H, Zhu Y, Ma C, Ye J, Luo J. Induction or suppression of expression of cytochrome C oxidase subunit II by heregulin beta 1 in human mammary epithelial cells is dependent on the levels of ErbB2 expression. J Cell Physiol 2002; 192:225-33. [PMID: 12115729 DOI: 10.1002/jcp.10132] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The ErbB family of receptor kinases is composed of four members: epidermal growth factor receptor (EGFR/ErbB1), ErbB2/neu, ErbB3, and ErbB4. Amplification of the ErbB2/neu is found in about 30% of breast cancer patients and is associated with a poor prognosis. Heregulin (HRG) activates the ErbB2 via induction of heterodimerization with ErbB3 and ErbB4 receptors. With suppression subtractive hybridization, we demonstrated that the expression of cytochrome c oxidase subunit II (COXII) is HRG-responsive. Two nontransformed human mammary epithelial cell lines, the HB2 and the HB2(ErbB2) (the HB2 engineered to overexpress ErbB2), displayed an opposite response to HRG-mediated regulation. HRG upregulated mRNA expression of COXII in the HB2 cells, but suppressed COXII expression in the HB2(ErbB2) cells. A human breast cancer cell line (T47D), which expresses ErbB2 at a level similar to that of the HB2 cells, also responded to HRG by increasing COXII mRNA levels. Therefore, HRG regulation of COXII expression depends on the levels of ErbB2 expression. Furthermore, the expression of COXII was inversely correlated to the levels of ErbB2, i.e., the cells overexpressing ErbB2 exhibited lower COXII levels. HRG-evoked signal transduction differed between the cells with normal ErbB expression and the cells overexpressing ErbB2. The activation of both ERK and PI3-K was essential for HRG regulation of COXII, i.e., blockage of either pathway eliminated HRG-mediated alteration. This is the first report demonstrating that the expression of mitochondria-encoded COXII is HRG-responsive. The levels of ErbB2 expression are decisive for the diverse biological activities of HRG.
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Affiliation(s)
- Yanbo Sun
- Department of Microbiology, Immunology & Cell Biology, West Virginia University School of Medicine, Morgantown, West Virginia 26506-9177, USA.
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