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Reid XJ, Low JKK, Mackay JP. A NuRD for all seasons. Trends Biochem Sci 2023; 48:11-25. [PMID: 35798615 DOI: 10.1016/j.tibs.2022.06.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/02/2022] [Accepted: 06/08/2022] [Indexed: 12/27/2022]
Abstract
The nucleosome-remodeling and deacetylase (NuRD) complex is an essential transcriptional regulator in all complex animals. All seven core subunits of the complex exist as multiple paralogs, raising the question of whether the complex might utilize paralog switching to achieve cell type-specific functions. We examine the evidence for this idea, making use of published quantitative proteomic data to dissect NuRD composition in 20 different tissues, as well as a large-scale CRISPR knockout screen carried out in >1000 human cancer cell lines. These data, together with recent reports, provide strong support for the idea that distinct permutations of the NuRD complex with tailored functions might regulate tissue-specific gene expression programs.
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Affiliation(s)
- Xavier J Reid
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia.
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2
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Thamrongwaranggoon U, Detarya M, Seubwai W, Saengboonmee C, Hino S, Koga T, Nakao M, Wongkham S. Lactic acidosis promotes aggressive features of cholangiocarcinoma cells via upregulating ALDH1A3 expression through EGFR axis. Life Sci 2022; 302:120648. [PMID: 35598658 DOI: 10.1016/j.lfs.2022.120648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/14/2022] [Accepted: 05/14/2022] [Indexed: 02/06/2023]
Abstract
AIMS Lactic acidosis (LA) generated in tumor microenvironment promotes tumor metastasis and drug resistance. This study aimed to demonstrate the impacts and the mechanisms of LA on aldehyde dehydrogenase1A3 (ALDH1A3) in promoting aggressiveness and gemcitabine resistance in cholangiocarcinoma (CCA) cell lines. The clinical relevance and the molecular pathway related to the upregulation of ALDH1A3 in LA cells will be revealed. MAIN METHODS ALDH1A3 expression and its clinical significances in CCA tissues were analyzed using the GEO databases. Human CCA cell lines, KKU-213A-LA and KKU-213B-LA maintained in the LA medium were studied and compared with its parental cells cultured in normal medium. Aggressive features-proliferation, colony formation, migration, invasion, and gemcitabine response were determined. Expression of ALDH1A3, EGFR and the downstream effectors were analyzed using real-time PCR and Western blotting. KEY FINDINGS ALDH1A3 was upregulated in patient CCA tissues and correlated with LDHA and shorter survival of CCA patients. mRNA and protein of ALDH1A3 were increased in LA cells. Attenuation of ALDH1A3 expression by siRNA significantly reduced cell proliferation, colony formation, migration, invasion, and gemcitabine resistance of LA cells, and gemcitabine resistant cells. The EGF/EGFR signaling via Erk and STAT3 was pinned to be involved in the induction of ALDH1A3 expression in LA cells. The transcriptomic analysis from TCGA dataset supported the links between LDHA, EGFR and ALDH1A3 in several tumor tissues. SIGNIFICANCE Lactic acidosis upregulated EGFR and ALDH1A3 expression, leading to the aggressiveness of CCA cells. The EGFR/ALDH1A3 axis could be a novel therapeutic target to eradicate metastatic CCA.
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Affiliation(s)
- Ubonrat Thamrongwaranggoon
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand; Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand; Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 860-0811, Japan
| | - Marutpong Detarya
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand; Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Wunchana Seubwai
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand; Department of Forensic Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand; Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Charupong Saengboonmee
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand; Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Shinjiro Hino
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 860-0811, Japan
| | - Tomoaki Koga
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 860-0811, Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 860-0811, Japan.
| | - Sopit Wongkham
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand; Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand; Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand.
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3
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Garranzo-Asensio M, Rodríguez-Cobos J, Millán CS, Poves C, Fernández-Aceñero MJ, Pastor-Morate D, Viñal D, Montero-Calle A, Solís-Fernández G, Ceron MÁ, Gámez-Chiachio M, Rodríguez N, Guzmán-Aránguez A, Barderas R, Domínguez G. In-depth proteomics characterization of ∆Np73 effectors identifies key proteins with diagnostic potential implicated in lymphangiogenesis, vasculogenesis and metastasis in colorectal cancer. Mol Oncol 2022; 16:2672-2692. [PMID: 35586989 PMCID: PMC9298678 DOI: 10.1002/1878-0261.13228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 03/17/2022] [Accepted: 05/17/2022] [Indexed: 11/18/2022] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer and the second leading cause of cancer‐related death worldwide. Alterations in proteins of the p53‐family are a common event in CRC. ΔNp73, a p53‐family member, shows oncogenic properties and its effectors are largely unknown. We performed an in‐depth proteomics characterization of transcriptional control by ∆Np73 of the secretome of human colon cancer cells and validated its clinical potential. The secretome was analyzed using high‐density antibody microarrays and stable isotopic metabolic labeling. Validation was performed by semiquantitative PCR, ELISA, dot‐blot and western blot analysis. Evaluation of selected effectors was carried out using 60 plasma samples from CRC patients, individuals carrying premalignant colorectal lesions and colonoscopy‐negative controls. In total, 51 dysregulated proteins were observed showing at least 1.5‐foldchange in expression. We found an important association between the overexpression of ∆Np73 and effectors related to lymphangiogenesis, vasculogenesis and metastasis, such as brain‐derived neurotrophic factor (BDNF) and the putative aminoacyl tRNA synthase complex‐interacting multifunctional protein 1 (EMAP‐II)–vascular endothelial growth factor C–vascular endothelial growth factor receptor 3 axis. We further demonstrated the usefulness of BDNF as a potential CRC biomarker able to discriminate between CRC patients and premalignant individuals from controls with high sensitivity and specificity.
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Affiliation(s)
- María Garranzo-Asensio
- Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Majadahonda, E-28222, Madrid, Spain
| | - Javier Rodríguez-Cobos
- Departamento de Bioquímica, Facultad de Medicina, Instituto de Investigaciones Biomédicas "Alberto Sols", CSIC-UAM, IdiPAZ, E-28029, Madrid, Spain
| | - Coral San Millán
- Departamento de Bioquímica, Facultad de Medicina, Instituto de Investigaciones Biomédicas "Alberto Sols", CSIC-UAM, IdiPAZ, E-28029, Madrid, Spain
| | - Carmen Poves
- Gastroenterology Unit, Hospital Universitario Clínico San Carlos, E-28040, Madrid, Spain
| | | | - Daniel Pastor-Morate
- Departamento de Bioquímica, Facultad de Medicina, Instituto de Investigaciones Biomédicas "Alberto Sols", CSIC-UAM, IdiPAZ, E-28029, Madrid, Spain
| | - David Viñal
- Medical Oncology Department, Hospital Universitario La Paz, E-28046, Madrid, Spain
| | - Ana Montero-Calle
- Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Majadahonda, E-28222, Madrid, Spain
| | - Guillermo Solís-Fernández
- Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Majadahonda, E-28222, Madrid, Spain
| | - María-Ángeles Ceron
- Surgical Pathology Department, Hospital Universitario Clínico San Carlos, E-28040, Madrid, Spain
| | - Manuel Gámez-Chiachio
- Departamento de Bioquímica, Facultad de Medicina, Instituto de Investigaciones Biomédicas "Alberto Sols", CSIC-UAM, IdiPAZ, E-28029, Madrid, Spain
| | - Nuria Rodríguez
- Medical Oncology Department, Hospital Universitario La Paz, E-28046, Madrid, Spain
| | - Ana Guzmán-Aránguez
- Departamento de Bioquímica y Biología Molecular, Facultad de Óptica y Optometría, Universidad Complutense de Madrid, E-28040, Madrid, Spain
| | - Rodrigo Barderas
- Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Majadahonda, E-28222, Madrid, Spain
| | - Gemma Domínguez
- Departamento de Bioquímica, Facultad de Medicina, Instituto de Investigaciones Biomédicas "Alberto Sols", CSIC-UAM, IdiPAZ, E-28029, Madrid, Spain
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Zhou M, Yuan M, Zhang M, Lei C, Aras O, Zhang X, An F. Combining histone deacetylase inhibitors (HDACis) with other therapies for cancer therapy. Eur J Med Chem 2021; 226:113825. [PMID: 34562854 DOI: 10.1016/j.ejmech.2021.113825] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 12/30/2022]
Abstract
Histone deacetylases (HDACs) play an important role in regulating the expression of genes involved in tumorigenesis and tumor maintenance, and hence they have been considered as key targets in cancer therapy. As a novel category of antitumor agents, histone deacetylase inhibitors (HDACis) can induce cell cycle arrest, apoptosis, and differentiation in cancer cells, ultimately combating cancer. Although in the United States, the use of HDACis for the treatment of certain cancers has been approved, the therapeutic efficacy of HDACis as a single therapeutic agent in solid tumorshas been unsatisfactory and drug resistance may yet occur. To enhance therapeutic efficacy and limit drug resistance, numerous combination therapies involving HDACis in synergy with other antitumor therapies have been studied. In this review, we describe the classification of HDACs. Moreover, we summarize the antitumor mechanism of the HDACis for targeting key cellular processes of cancers (cell cycle, apoptosis, angiogenesis, DNA repair, and immune response). In addition, we outline the major developments of other antitumor therapies in combination with HDACis, including chemotherapy, radiotherapy, phototherapy, targeted therapy, and immunotherapy. Finally, we discuss the current state and challenges of HDACis-drugs combinations in future clinical studies, with the aim of optimizing the antitumor effect of such combinations.
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Affiliation(s)
- Mengjiao Zhou
- Department of Pharmacology, School of Pharmacy, Nantong University, 226000, Nantong, Jiangsu, PR China
| | - Minjian Yuan
- Department of Pharmacology, School of Pharmacy, Nantong University, 226000, Nantong, Jiangsu, PR China
| | - Meng Zhang
- Institute of Medical Engineering, Department of Biophysics, School of Basic Medical Science, Health Science Center, Xi'an Jiaotong University, No.76 Yanta West Road, Xi'an, 710061, Shaanxi, People's Republic of China
| | - Chenyi Lei
- Institute of Medical Engineering, Department of Biophysics, School of Basic Medical Science, Health Science Center, Xi'an Jiaotong University, No.76 Yanta West Road, Xi'an, 710061, Shaanxi, People's Republic of China
| | - Omer Aras
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, United States
| | - Xiaohong Zhang
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Collaborative Innovation Center of Suzhou Nano Science & Technology, Soochow University, 199 Ren'ai Road, Suzhou, 215123, Jiangsu, PR China.
| | - Feifei An
- Institute of Medical Engineering, Department of Biophysics, School of Basic Medical Science, Health Science Center, Xi'an Jiaotong University, No.76 Yanta West Road, Xi'an, 710061, Shaanxi, People's Republic of China; Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Collaborative Innovation Center of Suzhou Nano Science & Technology, Soochow University, 199 Ren'ai Road, Suzhou, 215123, Jiangsu, PR China.
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Yu WW, Fu XL, Cai XW, Sun MH, Guo YM. Identification of differentially expressed proteins in the locoregional recurrent esophageal squamous cell carcinoma by quantitative proteomics. J Gastrointest Oncol 2021; 12:991-1006. [PMID: 34295551 DOI: 10.21037/jgo-21-278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/15/2021] [Indexed: 11/06/2022] Open
Abstract
Background This study aimed to identify potential biomarkers associated with locoregional recurrence in patients with esophageal squamous cell carcinoma (ESCC) after radical resection. Methods We performed a quantitative proteomics analysis using isobaric tags for relative and absolute quantification (iTRAQ) with reversed-phase liquid chromatography-mass spectrometry (RPLC-MS) to identify differential expression proteins (DEPs) between a locoregional recurrence group and good prognosis group of ESCC after radical esophagectomy. The bioinformatics analysis was performed with ingenuity pathway analysis software (IPA) and Gene Ontology (GO) database using the software of MAS 3.0. Kaplan-Meier (KM) Plotter Online Tool (http://www.kmplot.com) was used to evaluate the relationship between the differential expression of proteins and survival in patients with ESCC. Results More than 400 proteins were quantitated of which 27 proteins had upregulated expression and 55 proteins had downregulated expression in the locoregional recurrence group compared to the good prognosis group. These 82 DEPs were associated with biological procession of cancer development including cellular movement, cellular assembly and organization, cellular function and maintenance, cellular growth and proliferation, cell death and survival, DNA replication recombination and repair, and so on. Of these DEPs, SPTAN1 and AGT proteins were identified to be associated with RFS in ESCC. SPTAN1 was positively associated with RFS and AGT was negatively associated with RFS. Expression of SPTAN1 tended to have favorable OS while expression of AGT tended to have poor OS. Conclusions Our results demonstrated that quantitative proteomics is an effective discovery tool to identify biomarkers for prognosis prediction in ESCC. However, it needs more studies with large populations of ESCC to validate these potential biomarkers.
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Affiliation(s)
- Wei-Wei Yu
- Department of Radiation Oncology, Affiliated Hospital of Nantong University, Nantong, China
| | - Xiao-Long Fu
- Department of Radiation Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xu-Wei Cai
- Department of Radiation Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Meng-Hong Sun
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yan-Mei Guo
- Department of Gastroenterology, The Tenth People's Hospital of Tongji University, Shanghai, China
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Zhou B, Wang Y, Yan Y, Mariscal J, Di Vizio D, Freeman MR, Yang W. Low-Background Acyl-Biotinyl Exchange Largely Eliminates the Coisolation of Non- S-Acylated Proteins and Enables Deep S-Acylproteomic Analysis. Anal Chem 2019; 91:9858-9866. [PMID: 31251020 PMCID: PMC7451198 DOI: 10.1021/acs.analchem.9b01520] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein S-acylation (also called palmitoylation) is a common post-translational modification whose deregulation plays a key role in the pathogenesis of many diseases. Acyl-biotinyl exchange (ABE), a widely used method for the enrichment of S-acylated proteins, has the potential of capturing the entire S-acylproteome in any type of biological sample. Here, we showed that current ABE methods suffer from a high background arising from the coisolation of non-S-acylated proteins. The background can be substantially reduced by an additional blockage of residual free cysteine residues with 2,2'-dithiodipyridine prior to the biotin-HPDP reaction. Coupling the low-background ABE (LB-ABE) method with label-free proteomics, 2 895 high-confidence candidate S-acylated proteins (including 1 591 known S-acylated proteins) were identified from human prostate cancer LNCaP cells, representing so-far the largest S-acylproteome data set identified in a single study. Immunoblotting analysis confirmed the S-acylation of five known and five novel prostate cancer-related S-acylated proteins in LNCaP cells and suggested that their S-acylation levels were about 0.6-1.8%. In summary, the LB-ABE method largely eliminates the coisolation of non-S-acylated proteins and enables deep S-acylproteomic analysis. It is expected to facilitate a much more comprehensive and accurate quantification of S-acylproteomes than previous ABE methods.
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Affiliation(s)
- Bo Zhou
- Division of Cancer Biology and Therapeutics, Departments of Surgery and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Yang Wang
- Division of Cancer Biology and Therapeutics, Departments of Surgery and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Yiwu Yan
- Division of Cancer Biology and Therapeutics, Departments of Surgery and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Javier Mariscal
- Division of Cancer Biology and Therapeutics, Departments of Surgery and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Dolores Di Vizio
- Division of Cancer Biology and Therapeutics, Departments of Surgery and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
- Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Michael R. Freeman
- Division of Cancer Biology and Therapeutics, Departments of Surgery and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
- Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Wei Yang
- Division of Cancer Biology and Therapeutics, Departments of Surgery and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
- Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, United States
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Miah S, Banks CAS, Adams MK, Florens L, Lukong KE, Washburn MP. Advancement of mass spectrometry-based proteomics technologies to explore triple negative breast cancer. MOLECULAR BIOSYSTEMS 2016; 13:42-55. [PMID: 27891540 PMCID: PMC5173390 DOI: 10.1039/c6mb00639f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Understanding the complexity of cancer biology requires extensive information about the cancer proteome over the course of the disease. The recent advances in mass spectrometry-based proteomics technologies have led to the accumulation of an incredible amount of such proteomic information. This information allows us to identify protein signatures or protein biomarkers, which can be used to improve cancer diagnosis, prognosis and treatment. For example, mass spectrometry-based proteomics has been used in breast cancer research for over two decades to elucidate protein function. Breast cancer is a heterogeneous group of diseases with distinct molecular features that are reflected in tumour characteristics and clinical outcomes. Compared with all other subtypes of breast cancer, triple-negative breast cancer is perhaps the most distinct in nature and heterogeneity. In this review, we provide an introductory overview of the application of advanced proteomic technologies to triple-negative breast cancer research.
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Affiliation(s)
- Sayem Miah
- Stowers Institute for Medical Research, 1000 E. 50th St, Kansas City, MO 64110, USA. and Department of Biochemistry, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Charles A S Banks
- Stowers Institute for Medical Research, 1000 E. 50th St, Kansas City, MO 64110, USA.
| | - Mark K Adams
- Stowers Institute for Medical Research, 1000 E. 50th St, Kansas City, MO 64110, USA.
| | - Laurence Florens
- Stowers Institute for Medical Research, 1000 E. 50th St, Kansas City, MO 64110, USA.
| | - Kiven E Lukong
- Department of Biochemistry, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Michael P Washburn
- Stowers Institute for Medical Research, 1000 E. 50th St, Kansas City, MO 64110, USA. and Departments of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
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Regulation of microtubule dynamics by DIAPH3 influences amoeboid tumor cell mechanics and sensitivity to taxanes. Sci Rep 2015; 5:12136. [PMID: 26179371 PMCID: PMC4503992 DOI: 10.1038/srep12136] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 05/05/2015] [Indexed: 12/20/2022] Open
Abstract
Taxanes are widely employed chemotherapies for patients with metastatic prostate and breast cancer. Here, we show that loss of Diaphanous-related formin-3 (DIAPH3), frequently associated with metastatic breast and prostate cancers, correlates with increased sensitivity to taxanes. DIAPH3 interacted with microtubules (MT), and its loss altered several parameters of MT dynamics as well as decreased polarized force generation, contractility, and response to substrate stiffness. Silencing of DIAPH3 increased the cytotoxic response to taxanes in prostate and breast cancer cell lines. Analysis of drug activity for tubulin-targeted agents in the NCI-60 cell line panel revealed a uniform positive correlation between reduced DIAPH3 expression and drug sensitivity. Low DIAPH3 expression correlated with improved relapse-free survival in breast cancer patients treated with chemotherapeutic regimens containing taxanes. Our results suggest that inhibition of MT stability arising from DIAPH3 downregulation enhances susceptibility to MT poisons, and that the DIAPH3 network potentially reports taxane sensitivity in human tumors.
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Chai YD, Zhang L, Yang Y, Su T, Charugundla P, Ai J, Messadi D, Wong DT, Hu S. Discovery of potential serum protein biomarkers for lymph node metastasis in oral cancer. Head Neck 2015; 38:118-25. [PMID: 25223295 DOI: 10.1002/hed.23870] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The purpose of our study was to identify serum protein biomarkers for node-positive oral squamous cell carcinoma (OSCC). Biomarkers indicating lymph node metastasis provides a valuable classification methodology to optimize treatment plans for patients with OSCC. METHODS Quantitative serum proteomic analysis of OSCCs with either node-positive or node-negative disease was performed with tandem mass spectrometry and isobaric tagging for relative and absolute quantitation (iTRAQ). Immunoassays were used to validate a panel of candidate protein biomarkers and receiver operating characteristic (ROC) analysis was used to evaluate the performance of the candidate biomarkers. RESULTS A total of 282 serum proteins were quantified between node-positive and node-negative OSCCs with the proteomic approach. Four candidate biomarkers, gelsolin, fibronectin, angiotensinogen, and haptoglobin, were validated in an independent group of patients with node-positive or node-negative OSCC. The best candidate biomarker, gelsolin, yielded a ROC value of 89% for node-positive OSCC, although the sample size for validation is relatively small. Fibronectin, gelsolin, and angiotensinogen were also found to be differentially expressed between cancer cell lines of node-positive and node-negative cancer origin. CONCLUSION Our studies suggest that testing of serum protein biomarkers might help detect lymph node metastasis of oral cancer. Because of limited sample size in our studies, long-term longitudinal studies with large populations of individuals with oral cancer are needed to validate these potential biomarkers.
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Affiliation(s)
- Yang D Chai
- School of Dentistry, University of California-Los Angeles, Los Angeles, California
| | - Lifeng Zhang
- School of Dentistry, University of California-Los Angeles, Los Angeles, California
| | - Yan Yang
- School of Dentistry, University of California-Los Angeles, Los Angeles, California
| | - Trent Su
- School of Dentistry, University of California-Los Angeles, Los Angeles, California
| | - Prashant Charugundla
- School of Dentistry, University of California-Los Angeles, Los Angeles, California
| | - Jiye Ai
- School of Dentistry, University of California-Los Angeles, Los Angeles, California
| | - Diana Messadi
- School of Dentistry, University of California-Los Angeles, Los Angeles, California.,Jonsson Comprehensive Cancer Center, School of Dentistry, University of California-Los Angeles, Los Angeles, California
| | - David T Wong
- School of Dentistry, University of California-Los Angeles, Los Angeles, California.,Jonsson Comprehensive Cancer Center, School of Dentistry, University of California-Los Angeles, Los Angeles, California
| | - Shen Hu
- School of Dentistry, University of California-Los Angeles, Los Angeles, California.,Jonsson Comprehensive Cancer Center, School of Dentistry, University of California-Los Angeles, Los Angeles, California
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Yeh CC, Hsu CH, Shao YY, Ho WC, Tsai MH, Feng WC, Chow LP. Integrated Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) Quantitative Proteomic Analysis Identifies Galectin-1 as a Potential Biomarker for Predicting Sorafenib Resistance in Liver Cancer. Mol Cell Proteomics 2015; 14:1527-45. [PMID: 25850433 DOI: 10.1074/mcp.m114.046417] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Indexed: 01/06/2023] Open
Abstract
Sorafenib has become the standard therapy for patients with advanced hepatocellular carcinoma (HCC). Unfortunately, most patients eventually develop acquired resistance. Therefore, it is important to identify potential biomarkers that could predict the efficacy of sorafenib. To identify target proteins associated with the development of sorafenib resistance, we applied stable isotope labelling with amino acids in cell culture (SILAC)-based quantitative proteomic approach to analyze differences in protein expression levels between parental HuH-7 and sorafenib-acquired resistance HuH-7 (HuH-7(R)) cells in vitro, combined with an isobaric tags for relative and absolute quantitation (iTRAQ) quantitative analysis of HuH-7 and HuH-7(R) tumors in vivo. In total, 2,450 quantified proteins were identified in common in SILAC and iTRAQ experiments, with 81 showing increased expression (>2.0-fold) with sorafenib resistance and 75 showing decreased expression (<0.5-fold). In silico analyses of these differentially expressed proteins predicted that 10 proteins were related to cancer with involvements in cell adhesion, migration, and invasion. Knockdown of one of these candidate proteins, galectin-1, decreased cell proliferation and metastasis in HuH-7(R) cells and restored sensitivity to sorafenib. We verified galectin-1 as a predictive marker of sorafenib resistance and a downstream target of the AKT/mTOR/HIF-1α signaling pathway. In addition, increased galectin-1 expression in HCC patients' serum was associated with poor tumor control and low response rate. We also found that a high serum galectin-1 level was an independent factor associated with poor progression-free survival and overall survival. In conclusion, these results suggest that galectin-1 is a possible biomarker for predicting the response of HCC patients to treatment with sorafenib. As such, it may assist in the stratification of HCC and help direct personalized therapy.
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Affiliation(s)
- Chao-Chi Yeh
- From the ‡Graduate Institute of Biochemistry and Molecular Biology
| | - Chih-Hung Hsu
- §Graduate Institute of Oncology, College of Medicine, ‖Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
| | - Yu-Yun Shao
- §Graduate Institute of Oncology, College of Medicine, ‖Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
| | - Wen-Ching Ho
- From the ‡Graduate Institute of Biochemistry and Molecular Biology
| | - Mong-Hsun Tsai
- ¶Institute of Biotechnology, National Taiwan University and
| | - Wen-Chi Feng
- From the ‡Graduate Institute of Biochemistry and Molecular Biology
| | - Lu-Ping Chow
- From the ‡Graduate Institute of Biochemistry and Molecular Biology,
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Beck KL, Weber D, Phinney BS, Smilowitz JT, Hinde K, Lönnerdal B, Korf I, Lemay DG. Comparative Proteomics of Human and Macaque Milk Reveals Species-Specific Nutrition during Postnatal Development. J Proteome Res 2015; 14:2143-57. [PMID: 25757574 DOI: 10.1021/pr501243m] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Milk has been well established as the optimal nutrition source for infants, yet there is still much to be understood about its molecular composition. Therefore, our objective was to develop and compare comprehensive milk proteomes for human and rhesus macaques to highlight differences in neonatal nutrition. We developed a milk proteomics technique that overcomes previous technical barriers including pervasive post-translational modifications and limited sample volume. We identified 1606 and 518 proteins in human and macaque milk, respectively. During analysis of detected protein orthologs, we identified 88 differentially abundant proteins. Of these, 93% exhibited increased abundance in human milk relative to macaque and include lactoferrin, polymeric immunoglobulin receptor, alpha-1 antichymotrypsin, vitamin D-binding protein, and haptocorrin. Furthermore, proteins more abundant in human milk compared with macaque are associated with development of the gastrointestinal tract, the immune system, and the brain. Overall, our novel proteomics method reveals the first comprehensive macaque milk proteome and 524 newly identified human milk proteins. The differentially abundant proteins observed are consistent with the perspective that human infants, compared with nonhuman primates, are born at a slightly earlier stage of somatic development and require additional support through higher quantities of specific proteins to nurture human infant maturation.
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Affiliation(s)
| | | | | | | | - Katie Hinde
- ⊥Department of Human Evolutionary Biology, Harvard University, 11 Divinity Avenue, Cambridge, Massachusetts 02138, United States
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Wu Q, Cheng Z, Zhu J, Xu W, Peng X, Chen C, Li W, Wang F, Cao L, Yi X, Wu Z, Li J, Fan P. Suberoylanilide hydroxamic acid treatment reveals crosstalks among proteome, ubiquitylome and acetylome in non-small cell lung cancer A549 cell line. Sci Rep 2015; 5:9520. [PMID: 25825284 PMCID: PMC4379480 DOI: 10.1038/srep09520] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 03/03/2015] [Indexed: 12/31/2022] Open
Abstract
Suberoylanilide hydroxamic acid (SAHA) is a well-known histone deacetylase (HDAC) inhibitor and has been used as practical therapy for breast cancer and non-small cell lung cancer (NSCLC). It is previously demonstrated that SAHA treatment could extensively change the profile of acetylome and proteome in cancer cells. However, little is known about the impact of SAHA on other protein modifications and the crosstalks among different modifications and proteome, hindering the deep understanding of SAHA-mediated cancer therapy. In this work, by using SILAC technique, antibody-based affinity enrichment and high-resolution LC-MS/MS analysis, we investigated quantitative proteome, acetylome and ubiquitylome as well as crosstalks among the three datasets in A549 cells toward SAHA treatment. In total, 2968 proteins, 1099 acetylation sites and 1012 ubiquitination sites were quantified in response to SAHA treatment, respectively. With the aid of intensive bioinformatics, we revealed that the proteome and ubiquitylome were negatively related upon SAHA treatment. Moreover, the impact of SAHA on acetylome resulted in 258 up-regulated and 99 down-regulated acetylation sites at the threshold of 1.5 folds. Finally, we identified 55 common sites with both acetylation and ubiquitination, among which ubiquitination level in 43 sites (78.2%) was positive related to acetylation level.
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Affiliation(s)
- Quan Wu
- Central Laboratory of Medical Research Centre, Affiliated Provincial Hospital, Anhui Medical University, Hefei, 230001, China
| | - Zhongyi Cheng
- Institute for Advanced Study of Translational Medicine, Tongji University, Shanghai, 200092, China
| | - Jun Zhu
- Jingjie PTM Biolab (Hangzhou) Co. Ltd, Hangzhou 310018, China
| | - Weiqing Xu
- Central Laboratory of Medical Research Centre, Affiliated Provincial Hospital, Anhui Medical University, Hefei, 230001, China
| | - Xiaojun Peng
- Jingjie PTM Biolab (Hangzhou) Co. Ltd, Hangzhou 310018, China
| | - Chuangbin Chen
- Jingjie PTM Biolab (Hangzhou) Co. Ltd, Hangzhou 310018, China
| | - Wenting Li
- Central Laboratory of Medical Research Centre, Affiliated Provincial Hospital, Anhui Medical University, Hefei, 230001, China
| | - Fengsong Wang
- School of Life science, Anhui Medical University, Hefei, 230032, China
| | - Lejie Cao
- Department of Respiration, Affiliated Provincial Hospital, Anhui Medical University, Hefei, 230001, China
| | - Xingling Yi
- Jingjie PTM Biolab (Hangzhou) Co. Ltd, Hangzhou 310018, China
| | - Zhiwei Wu
- Central Laboratory of Medical Research Centre, Affiliated Provincial Hospital, Anhui Medical University, Hefei, 230001, China
| | - Jing Li
- Central Laboratory of Medical Research Centre, Affiliated Provincial Hospital, Anhui Medical University, Hefei, 230001, China
| | - Pingsheng Fan
- Department of Oncology, Affiliated Provincial Hospital, Anhui Medical University, Hefei, 230001, China
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Li LY, Zhang K, Jiang H, Xie YM, Liao LD, Chen B, Du ZP, Zhang PX, Chen H, Huang W, Jia W, Cao HH, Zheng W, Li EM, Xu LY. Quantitative proteomics reveals the downregulation of GRB2 as a prominent node of F806-targeted cell proliferation network. J Proteomics 2015; 117:145-55. [PMID: 25659534 DOI: 10.1016/j.jprot.2015.01.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Revised: 12/15/2014] [Accepted: 01/18/2015] [Indexed: 02/05/2023]
Abstract
UNLABELLED High-throughput proteomics has successfully identified thousands of proteins as potential therapeutic targets during investigations into mechanisms of drug action. A novel macrolide analog, denoted F806, is a potential antitumor drug. Here, using the quantitative proteomic approach of stable isotope labeling with amino acids in cell culture (SILAC) coupled to high-resolution mass spectrometry (MS), we characterize the F806-regulating protein profiles and identify the potential target molecules or pathways of F806 in esophageal squamous cell carcinoma (ESCC) cells. From a total of 1931 quantified proteins, 181 proteins were found to be down-regulated (FDR p-value<0.1, H/L ratio<0.738), and 119 proteins were up-regulated (FDR p-value<0.1, H/L ratio>1.156). Among the down-regulated proteins, we uncovered the over- and under-represented protein clusters in biological process and molecular function respectively by Gene Ontology analysis. Furthermore, down-regulated and up-regulated proteins were significantly enriched in 37 pathways and 60 sub-pathways by bioinformatic analysis (FDR p-value<0.1), while a down-regulated molecule growth factor receptor-bound protein 2 (GRB2) was a prominent node in fourteen cell proliferation-related sub-pathways. We concluded that GRB2 downregulation would be a potential target of F806 in ESCC cells. BIOLOGICAL SIGNIFICANCE This study used SILAC-based quantitative proteomics screen to systematically characterize molecular changes induced by a novel macrolide analog F806 in esophageal squamous cell carcinoma (ESCC) cells. Followed by bioinformatic analyses, signal pathway networks generated from the quantified proteins, would facilitate future investigation into the further mechanisms of F806 in ESCC cells. Notably, it provided information that growth factor receptor-bound protein 2 (GRB2) would be a prominent node in the F806-targeted cell proliferation network.
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Affiliation(s)
- Li-Yan Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, Guangdong, PR China; Institute of Oncologic Pathology, Shantou University Medical College, Shantou, Guangdong, PR China
| | - Kai Zhang
- Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, PR China
| | - Hong Jiang
- Fujian Provincial Key Laboratory of Screening for Novel Microbial Products, Fujian Institute of Microbiology, Fuzhou, Fujian, PR China
| | - Yang-Min Xie
- Experimental Animal Center, Shantou University Medical College, Shantou, Guangdong, PR China
| | - Lian-Di Liao
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, Guangdong, PR China; Institute of Oncologic Pathology, Shantou University Medical College, Shantou, Guangdong, PR China
| | - Bo Chen
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, Guangdong, PR China; Institute of Oncologic Pathology, Shantou University Medical College, Shantou, Guangdong, PR China
| | - Ze-Peng Du
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, Guangdong, PR China; Institute of Oncologic Pathology, Shantou University Medical College, Shantou, Guangdong, PR China
| | - Pi-Xian Zhang
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, Guangdong, PR China; Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong, PR China
| | - Hong Chen
- Fujian Provincial Key Laboratory of Screening for Novel Microbial Products, Fujian Institute of Microbiology, Fuzhou, Fujian, PR China
| | - Wei Huang
- Fujian Provincial Key Laboratory of Screening for Novel Microbial Products, Fujian Institute of Microbiology, Fuzhou, Fujian, PR China
| | - Wei Jia
- Fujian Provincial Key Laboratory of Screening for Novel Microbial Products, Fujian Institute of Microbiology, Fuzhou, Fujian, PR China
| | - Hui-Hui Cao
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, Guangdong, PR China; Institute of Oncologic Pathology, Shantou University Medical College, Shantou, Guangdong, PR China
| | - Wei Zheng
- Fujian Provincial Key Laboratory of Screening for Novel Microbial Products, Fujian Institute of Microbiology, Fuzhou, Fujian, PR China.
| | - En-Min Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, Guangdong, PR China; Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong, PR China.
| | - Li-Yan Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, Guangdong, PR China; Institute of Oncologic Pathology, Shantou University Medical College, Shantou, Guangdong, PR China.
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Abstract
Head and neck cancers usually originate in the squamous cells that line the inner mucosal surfaces of the oral and the neck region. These cancers follow multifocal steps for progression that include risk of developing metastasis. Although therapeutics has advanced in the past decades, head and neck cancers continue to cause much morbidity and mortality. Even with the promising effect of targeted therapies, there is a need for a better evaluation of patients with head and neck cancers. Metastasis-associated tumour antigen 1 (MTA1), a chromatin modifier, is found as an integral part of nucleosome remodelling and histone deacetylation (NuRD) complex. MTA1 is a biomarker for several solid tumours, and the overexpression of which have been documented in various cancers such as breast, ovarian, colon, prostrate etc. Interestingly also, a set of head and neck cancers shows MTA1 overexpression. However, recent evidences from clinical data raise a critical question on the role of MTA1 in head and neck cancers. This calls for a detailed review to the role of MTA1 in oral cancer. This review gives a brief account on the existing biological and molecular data in the context of head and neck cancer invasion and metastasis in relation to MTA1.
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Affiliation(s)
- Hezlin Marzook
- Cancer Research Program 9, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
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15
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Zhang H, Xu Y, Papanastasopoulos P, Stebbing J, Giamas G. Broader implications of SILAC-based proteomics for dissecting signaling dynamics in cancer. Expert Rev Proteomics 2014; 11:713-31. [PMID: 25345469 DOI: 10.1586/14789450.2014.971115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Large-scale transcriptome and epigenome analyses have been widely utilized to discover gene alterations implicated in cancer development at the genetic level. However, mapping of signaling dynamics at the protein level is likely to be more insightful and needed to complement massive genomic data. Stable isotope labeling with amino acids in cell culture (SILAC)-based proteomic analysis represents one of the most promising comparative quantitative methods that has been extensively employed in proteomic research. This technology allows for global, robust and confident identification and quantification of signal perturbations important for the progress of human diseases, particularly malignancies. The present review summarizes the latest applications of in vitro and in vivo SILAC-based proteomics in identifying global proteome/phosphoproteome and genome-wide protein-protein interactions that contribute to oncogenesis, highlighting the recent advances in dissecting signaling dynamics in cancer.
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Affiliation(s)
- Hua Zhang
- Department of Surgery and Cancer, Division of Cancer, Imperial College London, Hammersmith Hospital Campus, ICTEM Building, Du Cane Road, London, W12 ONN, UK
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Integration of proteomic and transcriptomic profiles identifies a novel PDGF-MYC network in human smooth muscle cells. Cell Commun Signal 2014; 12:44. [PMID: 25080971 PMCID: PMC4422302 DOI: 10.1186/s12964-014-0044-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 06/23/2014] [Indexed: 12/12/2022] Open
Abstract
Background Platelet-derived growth factor-BB (PDGF-BB) has been implicated in the proliferation, migration and synthetic activities of smooth muscle cells that characterize physiologic and pathologic tissue remodeling in hollow organs. However, neither the molecular basis of PDGFR-regulated signaling webs, nor the extent to which specific components within these networks could be exploited for therapeutic benefit has been fully elucidated. Results Expression profiling and quantitative proteomics analysis of PDGF-treated primary human bladder smooth muscle cells identified 1,695 genes and 241 proteins as differentially expressed versus non-treated cells. Analysis of gene expression data revealed MYC, JUN, EGR1, MYB, RUNX1, as the transcription factors most significantly networked with up-regulated genes. Forty targets were significantly altered at both the mRNA and protein levels. Proliferation, migration and angiogenesis were the biological processes most significantly associated with this signature, and MYC was the most highly networked master regulator. Alterations in master regulators and gene targets were validated in PDGF-stimulated smooth muscle cells in vitro and in a model of bladder injury in vivo. Pharmacologic inhibition of MYC and JUN confirmed their role in SMC proliferation and migration. Network analysis identified the diaphanous-related formin 3 as a novel PDGF target regulated by MYC and JUN, which was necessary for PDGF-stimulated lamellipodium formation. Conclusions These findings provide the first systems-level analysis of the PDGF-regulated transcriptome and proteome in normal smooth muscle cells. The analyses revealed an extensive cohort of PDGF-dependent biological processes and connected key transcriptional effectors to their regulation, significantly expanding current knowledge of PDGF-stimulated signaling cascades. These observations also implicate MYC as a novel target for pharmacological intervention in fibroproliferative expansion of smooth muscle, and potentially in cancers in which PDGFR-dependent signaling or MYC activation promote tumor progression.
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Barderas R, Mendes M, Torres S, Bartolomé RA, López-Lucendo M, Villar-Vázquez R, Peláez-García A, Fuente E, Bonilla F, Casal JI. In-depth characterization of the secretome of colorectal cancer metastatic cells identifies key proteins in cell adhesion, migration, and invasion. Mol Cell Proteomics 2013; 12:1602-20. [PMID: 23443137 DOI: 10.1074/mcp.m112.022848] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Liver metastasis in colorectal cancer is the major cause of cancer-related deaths. To identify and characterize proteins associated with colon cancer metastasis, we have compared the conditioned serum-free medium of highly metastatic KM12SM colorectal cancer cells with the parental, poorly metastatic KM12C cells using quantitative stable isotope labeling by amino acids in cell culture (SILAC) analyses on a linear ion trap-Orbitrap Velos mass spectrometer. In total, 1337 proteins were simultaneously identified in SILAC forward and reverse experiments. For quantification, 1098 proteins were selected in both experiments, with 155 proteins showing >1.5-fold change. About 52% of these proteins were secreted directly or using alternative secretion pathways. GDF15, S100A8/A9, and SERPINI1 showed capacity to discriminate cancer serum samples from healthy controls using ELISAs. In silico analyses of deregulated proteins in the secretome of metastatic cells showed a major abundance of proteins involved in cell adhesion, migration, and invasion. To characterize the tumorigenic and metastatic properties of some top up- and down-regulated proteins, we used siRNA silencing and antibody blocking. Knockdown expression of NEO1, SERPINI1, and PODXL showed a significant effect on cellular adhesion. Silencing or blocking experiments with SOSTDC1, CTSS, EFNA3, CD137L/TNFSF9, ZG16B, and Midkine caused a significant decrease in migration and invasion of highly metastatic cells. In addition, silencing of SOSTDC1, EFNA3, and CD137L/TNFSF9 reduced liver colonization capacity of KM12SM cells. Finally, the panel of six proteins involved in invasion showed association with poor prognosis and overall survival after dataset analysis of gene alterations. In summary, we have defined a collection of proteins that are relevant for understanding the mechanisms underlying adhesion, migration, invasion, and metastasis in colorectal cancer.
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Affiliation(s)
- Rodrigo Barderas
- Functional Proteomics Laboratory, Centro de Investigaciones Biológicas, 28040 Madrid, Spain
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18
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Tan HT, Lee YH, Chung MCM. Cancer proteomics. MASS SPECTROMETRY REVIEWS 2012; 31:583-605. [PMID: 22422534 DOI: 10.1002/mas.20356] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 11/16/2011] [Accepted: 11/16/2011] [Indexed: 05/31/2023]
Abstract
Cancer presents high mortality and morbidity globally, largely due to its complex and heterogenous nature, and lack of biomarkers for early diagnosis. A proteomics study of cancer aims to identify and characterize functional proteins that drive the transformation of malignancy, and to discover biomarkers to detect early-stage cancer, predict prognosis, determine therapy efficacy, identify novel drug targets, and ultimately develop personalized medicine. The various sources of human samples such as cell lines, tissues, and plasma/serum are probed by a plethora of proteomics tools to discover novel biomarkers and elucidate mechanisms of tumorigenesis. Innovative proteomics technologies and strategies have been designed for protein identification, quantitation, fractionation, and enrichment to delve deeper into the oncoproteome. In addition, there is the need for high-throughput methods for biomarker validation, and integration of the various platforms of oncoproteome data to fully comprehend cancer biology.
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Affiliation(s)
- Hwee Tong Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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Kowdley G, Srikantan S, Abdelmohsen K, Gorospe M, Khan J. Molecular biology techniques for the surgeon. World J Surg Proced 2012; 2:5-15. [DOI: 10.5412/wjsp.v2.i2.5] [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
New technologies are constantly being introduced into the medical and surgical fields. These technologies come in the form of newer medicines, imaging methods and prognostic tools, among others, and allow clinicians to make more rational and informed decisions on the care of their patients. Many of these technologies utilize advanced techniques which are at the forefront of many research fields and represent a transition of bench advances into the clinical realm. This review will highlight four technologies that are at the forefront in the treatment of oncology patients treated by surgeons on a daily basis. Circulating tumor cells, microarray analysis, proteomic studies and rapid sequencing technologies will be highlighted. These technologies will be reviewed and their potential use in the care of surgical patients will be discussed.
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Hoekman B, Breitling R, Suits F, Bischoff R, Horvatovich P. msCompare: a framework for quantitative analysis of label-free LC-MS data for comparative candidate biomarker studies. Mol Cell Proteomics 2012; 11:M111.015974. [PMID: 22318370 DOI: 10.1074/mcp.m111.015974] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Data processing forms an integral part of biomarker discovery and contributes significantly to the ultimate result. To compare and evaluate various publicly available open source label-free data processing workflows, we developed msCompare, a modular framework that allows the arbitrary combination of different feature detection/quantification and alignment/matching algorithms in conjunction with a novel scoring method to evaluate their overall performance. We used msCompare to assess the performance of workflows built from modules of publicly available data processing packages such as SuperHirn, OpenMS, and MZmine and our in-house developed modules on peptide-spiked urine and trypsin-digested cerebrospinal fluid (CSF) samples. We found that the quality of results varied greatly among workflows, and interestingly, heterogeneous combinations of algorithms often performed better than the homogenous workflows. Our scoring method showed that the union of feature matrices of different workflows outperformed the original homogenous workflows in some cases. msCompare is open source software (https://trac.nbic.nl/mscompare), and we provide a web-based data processing service for our framework by integration into the Galaxy server of the Netherlands Bioinformatics Center (http://galaxy.nbic.nl/galaxy) to allow scientists to determine which combination of modules provides the most accurate processing for their particular LC-MS data sets.
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Affiliation(s)
- Berend Hoekman
- Department of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands
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21
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Zheng J, Sugrue RJ, Tang K. Mass spectrometry based proteomic studies on viruses and hosts--a review. Anal Chim Acta 2011; 702:149-59. [PMID: 21839192 PMCID: PMC7094357 DOI: 10.1016/j.aca.2011.06.045] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 06/20/2011] [Accepted: 06/21/2011] [Indexed: 02/07/2023]
Abstract
In terms of proteomic research in the 21st century, the realm of virology is still regarded as an enormous challenge mainly brought by three aspects, namely, studying on the complex proteome of the virus with unexpected variations, developing more accurate analytical techniques as well as understanding viral pathogenesis and virus-host interaction dynamics. Progresses in these areas will be helpful to vaccine design and antiviral drugs discovery. Mass spectrometry based proteomics have shown exceptional display of capabilities, not only precisely identifying viral and cellular proteins that are functionally, structurally, and dynamically changed upon virus infection, but also enabling us to detect important pathway proteins. In addition, many isolation and purification techniques and quantitative strategies in conjunction with MS can significantly improve the sensitivity of mass spectrometry for detecting low-abundant proteins, replenishing the stock of virus proteome and enlarging the protein-protein interaction maps. Nevertheless, only a small proportion of the infectious viruses in both of animal and plant have been studied using this approach. As more virus and host genomes are being sequenced, MS-based proteomics is becoming an indispensable tool for virology. In this paper, we provide a brief review of the current technologies and their applications in studying selected viruses and hosts.
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Affiliation(s)
- Jie Zheng
- Division of Chemical Biology and Biotechnology, School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Richard J. Sugrue
- Division of Molecular and Cell Biology, School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Kai Tang
- Division of Chemical Biology and Biotechnology, School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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Current World Literature. Curr Opin Oncol 2011; 23:303-10. [DOI: 10.1097/cco.0b013e328346cbfa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Yang W, Chung YG, Kim Y, Kim TK, Keay SK, Zhang CO, Ji M, Hwang D, Kim KP, Steen H, Freeman MR, Kim J. Quantitative proteomics identifies a beta-catenin network as an element of the signaling response to Frizzled-8 protein-related antiproliferative factor. Mol Cell Proteomics 2011; 10:M110.007492. [PMID: 21422242 DOI: 10.1074/mcp.m110.007492] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Antiproliferative factor (APF), a Frizzled-8 protein-related sialoglycopeptide involved in the pathogenesis of interstitial cystitis, potently inhibits proliferation of normal urothelial cells as well as certain cancer cells. To elucidate the molecular mechanisms of the growth-inhibitory effect of APF, we performed stable isotope labeling by amino acids in cell culture analysis of T24 bladder cancer cells treated with and without APF. Among over 2000 proteins identified, 54 were significantly up-regulated and 48 were down-regulated by APF treatment. Bioinformatic analysis revealed that a protein network involved in cell adhesion was substantially altered by APF and that β-catenin was a prominent node in this network. Functional assays demonstrated that APF down-regulated β-catenin, at least in part, via proteasomal and lysosomal degradation. Moreover, silencing of β-catenin mimicked the antiproliferative effect of APF whereas ectopic expression of nondegradable β-catenin rescued growth inhibition in response to APF, confirming that β-catenin is a key mediator of APF signaling. Notably, the key role of β-catenin in APF signaling is not restricted to T24 cells, but was also observed in an hTERT-immortalized human bladder epithelial cell line, TRT-HU1. In addition, the network model suggested that β-catenin is linked to cyclooxygenase-2 (COX-2), implying a potential connection between APF and inflammation. Functional assays verified that APF increased the production of prostaglandin E(2) and that down-modulation of β-catenin elevated COX-2 expression, whereas forced expression of nondegradable β-catenin inhibited APF-induced up-regulation of COX-2. Furthermore, we confirmed that β-catenin was down-regulated whereas COX-2 was up-regulated in epithelial cells explanted from IC bladder biopsies compared with control tissues. In summary, our quantitative proteomics study describes the first provisional APF-regulated protein network, within which β-catenin is a key node, and provides new insight that targeting the β-catenin signaling pathway may be a rational approach toward treating interstitial cystitis.
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Affiliation(s)
- Wei Yang
- Urological Diseases Research Center, Children's Hospital Boston, Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
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