51
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Tan HW, Xu YM, Wu DD, Lau ATY. Recent insights into human bronchial proteomics - how are we progressing and what is next? Expert Rev Proteomics 2018; 15:113-130. [PMID: 29260600 DOI: 10.1080/14789450.2017.1417847] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The human respiratory system is highly prone to diseases and complications. Many lung diseases, including lung cancer (LC), tuberculosis (TB), and chronic obstructive pulmonary disease (COPD) have been among the most common causes of death worldwide. Cystic fibrosis (CF), the most common genetic disease in Caucasians, has adverse impacts on the lungs. Bronchial proteomics plays a significant role in understanding the underlying mechanisms and pathogenicity of lung diseases and provides insights for biomarker and therapeutic target discoveries. Areas covered: We overview the recent achievements and discoveries in human bronchial proteomics by outlining how some of the different proteomic techniques/strategies are developed and applied in LC, TB, COPD, and CF. Also, the future roles of bronchial proteomics in predictive proteomics and precision medicine are discussed. Expert commentary: Much progress has been made in bronchial proteomics. Owing to the advances in proteomics, we now have better ability to isolate proteins from desired cellular compartments, greater protein separation methods, more powerful protein detection technologies, and more sophisticated bioinformatic techniques. These all contributed to our further understanding of lung diseases and for biomarker and therapeutic target discoveries.
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Affiliation(s)
- Heng Wee Tan
- a Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics , Shantou University Medical College , Shantou , People's Republic of China
| | - Yan-Ming Xu
- a Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics , Shantou University Medical College , Shantou , People's Republic of China
| | - Dan-Dan Wu
- a Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics , Shantou University Medical College , Shantou , People's Republic of China
| | - Andy T Y Lau
- a Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics , Shantou University Medical College , Shantou , People's Republic of China
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52
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Ajona D, Ortiz-Espinosa S, Pio R. Complement anaphylatoxins C3a and C5a: Emerging roles in cancer progression and treatment. Semin Cell Dev Biol 2017; 85:153-163. [PMID: 29155219 DOI: 10.1016/j.semcdb.2017.11.023] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/07/2017] [Accepted: 11/15/2017] [Indexed: 02/06/2023]
Abstract
Recent insights into the role of complement anaphylatoxins C3a and C5a in cancer provide new opportunities for the development of innovative biomarkers and therapeutic strategies. These two complement activation products can maintain chronic inflammation, promote an immunosuppressive microenvironment, induce angiogenesis, and increase the motility and metastatic potential of cancer cells. Still, the diverse heterogeneity of responses mediated by these peptides poses a challenge both to our understanding of the role played by these molecules in cancer progression and to the development of effective treatments. This review attempts to summarize the evidence surrounding the involvement of anaphylatoxins in the biological contexts associated with tumor progression. We also describe the recent developments that support the inhibition of anaphylatoxins, or their cognate receptors C3aR and C5aR1, as a treatment option for maximizing the clinical efficacy of current immunotherapies that target the PD-1/PD-L1 immune checkpoint.
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Affiliation(s)
- Daniel Ajona
- University of Navarra, Center for Applied Medical Research (CIMA), Program in Solid Tumors and Biomarkers, Pamplona, Spain; Navarra's Health Research Institute (IdiSNA), Pamplona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain; University of Navarra, School of Sciences, Department of Biochemistry and Genetics, Pamplona, Spain
| | - Sergio Ortiz-Espinosa
- University of Navarra, Center for Applied Medical Research (CIMA), Program in Solid Tumors and Biomarkers, Pamplona, Spain; University of Navarra, School of Sciences, Department of Biochemistry and Genetics, Pamplona, Spain
| | - Ruben Pio
- University of Navarra, Center for Applied Medical Research (CIMA), Program in Solid Tumors and Biomarkers, Pamplona, Spain; Navarra's Health Research Institute (IdiSNA), Pamplona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain; University of Navarra, School of Sciences, Department of Biochemistry and Genetics, Pamplona, Spain.
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53
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Li F, Zhu D, Yang Y, Wu K, Zhao S. Overexpression of calcyphosine is associated with poor prognosis in esophageal squamous cell carcinoma. Oncol Lett 2017; 14:6231-6237. [PMID: 29113272 DOI: 10.3892/ol.2017.6973] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 07/27/2017] [Indexed: 12/19/2022] Open
Abstract
Calcyphosine (CAPS), a calcium-binding protein, has been identified as a potential diagnostic and prognostic biomarker in several human carcinomas. However, little is known about CAPS in esophageal squamous cell carcinoma (ESCC). The present study aimed to investigate the expression levels of CAPS in ESCC tissues and evaluate its clinicopathological significance. Reverse transcription-quantitative polymerase chain reaction and immunohistochemical staining were conducted to detect the expression of CAPS in ESCC tissues and adjacent non-cancerous tissues. ESCC samples exhibited higher levels of CAPS mRNA than paired non-cancerous samples (P=0.0015), and the mRNA level of CAPS was positively associated with histological grade (P=0.0013) and tumor invasion depth (P=0.0206). In addition, Kaplan-Meier survival analysis revealed that patients with high CAPS expression experienced significantly shorter 5-year overall survival times than those with low CAPS expression (P=0.0112). Multivariate analysis demonstrated that CAPS protein expression was an independent prognostic biomarker for patients with ESCC. In conclusion, the findings of the present study demonstrated that CAPS may represent a novel diagnostic indicator and an independent prognostic biomarker in ESCC.
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Affiliation(s)
- Feng Li
- Department of Thoracic Surgery, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Dengyan Zhu
- Department of Thoracic Surgery, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Yang Yang
- Department of Thoracic Surgery, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Kai Wu
- Department of Thoracic Surgery, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Song Zhao
- Department of Thoracic Surgery, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
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54
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Endo S, Xia S, Suyama M, Morikawa Y, Oguri H, Hu D, Ao Y, Takahara S, Horino Y, Hayakawa Y, Watanabe Y, Gouda H, Hara A, Kuwata K, Toyooka N, Matsunaga T, Ikari A. Synthesis of Potent and Selective Inhibitors of Aldo-Keto Reductase 1B10 and Their Efficacy against Proliferation, Metastasis, and Cisplatin Resistance of Lung Cancer Cells. J Med Chem 2017; 60:8441-8455. [PMID: 28976752 DOI: 10.1021/acs.jmedchem.7b00830] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Aldo-keto reductase 1B10 (AKR1B10) is overexpressed in several extraintestinal cancers, particularly in non-small-cell lung cancer, where AKR1B10 is a potential diagnostic marker and therapeutic target. Selective AKR1B10 inhibitors are required because compounds should not inhibit the highly related aldose reductase that is involved in monosaccharide and prostaglandin metabolism. Currently, 7-hydroxy-2-(4-methoxyphenylimino)-2H-chromene-3-carboxylic acid benzylamide (HMPC) is known to be the most potent competitive inhibitor of AKR1B10, but it is nonselective. In this study, derivatives of HMPC were synthesized by removing the 4-methoxyphenylimino moiety and replacing the benzylamide with phenylpropylamide. Among them, 4c and 4e showed higher AKR1B10 inhibitory potency (IC50 4.2 and 3.5 nM, respectively) and selectivity than HMPC. The treatments with the two compounds significantly suppressed not only migration, proliferation, and metastasis of lung cancer A549 cells but also metastatic and invasive potentials of cisplatin-resistant A549 cells.
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Affiliation(s)
- Satoshi Endo
- Laboratory of Biochemistry, Gifu Pharmaceutical University , Gifu 501-1196, Japan
| | - Shuang Xia
- Graduate School of Innovative Life Science, University of Toyama , Toyama 930-8555, Japan
| | - Miho Suyama
- Laboratory of Biochemistry, Gifu Pharmaceutical University , Gifu 501-1196, Japan
| | - Yoshifumi Morikawa
- Laboratory of Biochemistry, Gifu Pharmaceutical University , Gifu 501-1196, Japan
| | - Hiroaki Oguri
- Laboratory of Biochemistry, Gifu Pharmaceutical University , Gifu 501-1196, Japan
| | - Dawei Hu
- Graduate School of Innovative Life Science, University of Toyama , Toyama 930-8555, Japan
| | - Yoshinori Ao
- Graduate School of Science and Engineering, University of Toyama , Toyama 930-8555, Japan
| | - Satoyuki Takahara
- Graduate School of Innovative Life Science, University of Toyama , Toyama 930-8555, Japan
| | - Yoshikazu Horino
- Graduate School of Science and Engineering, University of Toyama , Toyama 930-8555, Japan
| | - Yoshihiro Hayakawa
- Division of Pathogenic Biochemistry, Institute of Natural Medicine, University of Toyama , Toyama 930-0194, Japan
| | - Yurie Watanabe
- School of Pharmacy, Showa University , Tokyo 142-8555, Japan
| | - Hiroaki Gouda
- School of Pharmacy, Showa University , Tokyo 142-8555, Japan
| | - Akira Hara
- Faculty of Engineering, Gifu University , Gifu 501-1193, Japan
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University , Gifu 501-1193, Japan
| | - Naoki Toyooka
- Graduate School of Innovative Life Science, University of Toyama , Toyama 930-8555, Japan.,Graduate School of Science and Engineering, University of Toyama , Toyama 930-8555, Japan
| | - Toshiyuki Matsunaga
- Laboratory of Biochemistry, Gifu Pharmaceutical University , Gifu 501-1196, Japan
| | - Akira Ikari
- Laboratory of Biochemistry, Gifu Pharmaceutical University , Gifu 501-1196, Japan
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55
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Fujii K, Nakamura H, Nishimura T. Recent mass spectrometry-based proteomics for biomarker discovery in lung cancer, COPD, and asthma. Expert Rev Proteomics 2017; 14:373-386. [PMID: 28271730 DOI: 10.1080/14789450.2017.1304215] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
INTRODUCTION Lung cancer and related diseases have been one of the most common causes of deaths worldwide. Genomic-based biomarkers may hardly reflect the underlying dynamic molecular mechanism of functional protein interactions, which is the center of a disease. Recent developments in mass spectrometry (MS) have made it possible to analyze disease-relevant proteins expressed in clinical specimens by proteomic challenges. Areas covered: To understand the molecular mechanisms of lung cancer and its subtypes, chronic obstructive pulmonary disease (COPD), asthma and others, great efforts have been taken to identify numerous relevant proteins by MS-based clinical proteomic approaches. Since lung cancer is a multifactorial disease that is biologically associated with asthma and COPD among various lung diseases, this study focused on proteomic studies on biomarker discovery using various clinical specimens for lung cancer, COPD, and asthma. Expert commentary: MS-based exploratory proteomics utilizing clinical specimens, which can incorporate both experimental and bioinformatic analysis of protein-protein interaction and also can adopt proteogenomic approaches, makes it possible to reveal molecular networks that are relevant to a disease subgroup and that could differentiate between drug responders and non-responders, good and poor prognoses, drug resistance, and so on.
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Affiliation(s)
- Kiyonaga Fujii
- a Department of Translational Medicine Informatics , St. Marianna University School of Medicine, Miyamae-ku , Kawasaki , Japan
| | - Haruhiko Nakamura
- a Department of Translational Medicine Informatics , St. Marianna University School of Medicine, Miyamae-ku , Kawasaki , Japan.,b Department of Chest Surgery , St. Marianna University School of Medicine, Miyamae-ku , Kawasaki , Japan
| | - Toshihide Nishimura
- a Department of Translational Medicine Informatics , St. Marianna University School of Medicine, Miyamae-ku , Kawasaki , Japan
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56
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Carvalho AS, Cuco CM, Lavareda C, Miguel F, Ventura M, Almeida S, Pinto P, de Abreu TT, Rodrigues LV, Seixas S, Bárbara C, Azkargorta M, Elortza F, Semedo J, Field JK, Mota L, Matthiesen R. Bronchoalveolar Lavage Proteomics in Patients with Suspected Lung Cancer. Sci Rep 2017; 7:42190. [PMID: 28169345 PMCID: PMC5294405 DOI: 10.1038/srep42190] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 01/03/2017] [Indexed: 12/21/2022] Open
Abstract
Lung cancer configures as one of the deadliest types of cancer. The future implementation of early screening methods such as exhaled breath condensate analysis and low dose computed tomography (CT) as an alternative to current chest imaging based screening will lead to an increased burden on bronchoscopy units. New approaches for improvement of diagnosis in bronchoscopy units, regarding patient management, are likely to have clinical impact in the future. Diagnostic approaches to address mortality of lung cancer include improved early detection and stratification of the cancers according to its prognosis and further response to drug treatment. In this study, we performed a detailed mass spectrometry based proteome analysis of acellular bronchoalveolar lavage (BAL) fluid samples on an observational prospective cohort consisting of 90 suspected lung cancer cases which were followed during two years. The thirteen new lung cancer cases diagnosed during the follow up time period clustered, based on liquid chromatography-mass spectrometry (LC-MS) data, with lung cancer cases at the time of BAL collection. Hundred and thirty-tree potential biomarkers were identified showing significantly differential expression when comparing lung cancer versus non-lung cancer. The regulated biomarkers showed a large overlap with biomarkers detected in tissue samples.
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Affiliation(s)
- Ana Sofia Carvalho
- Computational and Experimental Biology Group, Health Promotion and Chronic Diseases Department, National Institute of Health Dr Ricardo Jorge, Lisbon, Portugal.,Computational and Experimental Biology Group, CEDOC, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Célia Marina Cuco
- Unidade de Técnicas Invasivas Pneumológicas, Pneumologia II, Hospital Pulido Valente, Centro Hospitalar Lisboa Norte, Lisbon, Portugal
| | - Carla Lavareda
- Unidade de Técnicas Invasivas Pneumológicas, Pneumologia II, Hospital Pulido Valente, Centro Hospitalar Lisboa Norte, Lisbon, Portugal
| | - Francisco Miguel
- Unidade de Técnicas Invasivas Pneumológicas, Pneumologia II, Hospital Pulido Valente, Centro Hospitalar Lisboa Norte, Lisbon, Portugal
| | - Mafalda Ventura
- Unidade de Técnicas Invasivas Pneumológicas, Pneumologia II, Hospital Pulido Valente, Centro Hospitalar Lisboa Norte, Lisbon, Portugal
| | - Sónia Almeida
- Unidade de Técnicas Invasivas Pneumológicas, Pneumologia II, Hospital Pulido Valente, Centro Hospitalar Lisboa Norte, Lisbon, Portugal
| | - Paula Pinto
- Unidade de Técnicas Invasivas Pneumológicas, Pneumologia II, Hospital Pulido Valente, Centro Hospitalar Lisboa Norte, Lisbon, Portugal.,Instituto de Saúde Ambiental, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Tiago Tavares de Abreu
- Unidade de Técnicas Invasivas Pneumológicas, Pneumologia II, Hospital Pulido Valente, Centro Hospitalar Lisboa Norte, Lisbon, Portugal
| | - Luís Vaz Rodrigues
- Department of Pulmonology, Unidade Local de Saúde da Guarda, Faculty of Health Sciences, University of Beira Interior, Portugal
| | - Susana Seixas
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Cristina Bárbara
- Unidade de Técnicas Invasivas Pneumológicas, Pneumologia II, Hospital Pulido Valente, Centro Hospitalar Lisboa Norte, Lisbon, Portugal.,Instituto de Saúde Ambiental, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, Derio, Spain
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, Derio, Spain
| | - Júlio Semedo
- Unidade de Técnicas Invasivas Pneumológicas, Pneumologia II, Hospital Pulido Valente, Centro Hospitalar Lisboa Norte, Lisbon, Portugal
| | - John K Field
- Roy Castle Lung Cancer Research Programme, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, William Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK
| | - Leonor Mota
- Unidade de Técnicas Invasivas Pneumológicas, Pneumologia II, Hospital Pulido Valente, Centro Hospitalar Lisboa Norte, Lisbon, Portugal
| | - Rune Matthiesen
- Computational and Experimental Biology Group, Health Promotion and Chronic Diseases Department, National Institute of Health Dr Ricardo Jorge, Lisbon, Portugal.,Computational and Experimental Biology Group, CEDOC, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
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57
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Willmes C, Kumar R, Becker JC, Fried I, Rachakonda PS, Poppe LM, Hesbacher S, Schadendorf D, Sucker A, Schrama D, Ugurel S. SERPINB1 expression is predictive for sensitivity and outcome of cisplatin-based chemotherapy in melanoma. Oncotarget 2017; 7:10117-32. [PMID: 26799424 PMCID: PMC4891108 DOI: 10.18632/oncotarget.6956] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 12/26/2015] [Indexed: 12/02/2022] Open
Abstract
Despite of highly effective new therapeutic strategies, chemotherapy still is an important treatment option in metastatic melanoma. Since predictors of chemotherapy response are rare, drugs and regimens are currently chosen arbitrarily. The present study was aimed at the identification of molecular markers predicting the outcome of chemotherapy in melanoma. Tumor biopsies from metastatic lesions were collected from 203 stage IV melanoma patients prior to chemotherapy onset and used for gene expression profiling (n = 6; marker identification set), quantitative real-time PCR (n = 127; validation set 1), and immunohistochemistry on tissue microarrays (n = 70; validation set 2). The results were correlated to the tumors' in-vitro chemosensitivity and to the patients' in-vivo chemotherapy outcome. SERPINB1 was found to correlate to the in-vitro sensitivity to cisplatin-containing chemotherapy regimens (p = 0.005). High SERPINB1 gene expression was associated with favorable tumor response (p = 0.012) and prolonged survival (p = 0.081) under cisplatin-based chemotherapy. High SERPINB1 protein expression in tumor tissue from cisplatin-treated patients was associated with a favorable survival (p = 0.011), and proved as an independent predictor of survival (p = 0.008) by multivariate analysis. We conclude, that SERPINB1 expression, although not functionally involved, is predictive for the outcome of cisplatin-based chemotherapy in melanoma, and thus may be useful to personalize melanoma chemotherapy.
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Affiliation(s)
- Christoph Willmes
- Department of Dermatology, University Hospital Würzburg, Würzburg, Germany
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Jürgen C Becker
- Translational Skin Cancer Research, Deutsches Konsortium für Translationale Krebsforschung (DKTK), Essen, Germany.,Department of Dermatology, University Duisburg-Essen, Essen, Germany
| | - Isabella Fried
- Department of Dermatology, Medical University of Graz, Graz, Austria
| | | | - Lidia M Poppe
- Department of Dermatology, University Hospital Würzburg, Würzburg, Germany
| | - Sonja Hesbacher
- Department of Dermatology, University Hospital Würzburg, Würzburg, Germany
| | - Dirk Schadendorf
- Department of Dermatology, University Duisburg-Essen, Essen, Germany
| | - Antje Sucker
- Department of Dermatology, University Duisburg-Essen, Essen, Germany
| | - David Schrama
- Department of Dermatology, University Hospital Würzburg, Würzburg, Germany
| | - Selma Ugurel
- Department of Dermatology, University Hospital Würzburg, Würzburg, Germany.,Department of Dermatology, University Duisburg-Essen, Essen, Germany
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58
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Wang Q, Zhu L, Jiang Y, Xu J, Wang F, He Z. miR-219-5p suppresses the proliferation and invasion of colorectal cancer cells by targeting calcyphosin. Oncol Lett 2017; 13:1319-1324. [PMID: 28454255 DOI: 10.3892/ol.2017.5570] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 10/27/2016] [Indexed: 11/06/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs involved in an array of biological processes, and their dysregulation is associated with tumor development and progression. One such miRNA, miR-219-5p, is abnormally expressed in patients with colorectal cancer (CRC). In the present study, reverse transcription-quantitative polymerase chain reaction was performed to measure miR-219-5p expression in cells from both CRC tumors, and surrounding healthy tissue. MTT and invasion assays were used to determine the role of miR-219-5p in regulating CRC cell proliferation and invasion, respectively. A luciferase assay was then performed to assess the binding of miR-219-5p to the CAPS gene that encodes calcyphosin protein. The present study confirmed that miR-219-5p expression is significantly downregulated in CRC tissue. miR-219-5p knockdown promoted the growth of HCT-8 cells and increased the expression of calcyphosin protein (CAPS). On the other hand, overexpressing miR-219-5p inhibited HCT-8 cell growth and invasion, and downregulated CAPS expression. In addition, CAPS was identified as the functional downstream target of miR-219-5p by directly targeting its 3'-untranslated region. Therefore, miR-219-5p may function as a tumor suppressor by decreasing CAPS expression, and subsequently inhibit tumor proliferation and invasion. These results indicate that novel therapeutic strategies that increase miR-219-5p expression may be developed to treat CRC.
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Affiliation(s)
- Quhui Wang
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Lirong Zhu
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Yasu Jiang
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Junfei Xu
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Feiran Wang
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Zhixian He
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
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59
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Kriegsmann M, Longuespée R, Wandernoth P, Mohanu C, Lisenko K, Weichert W, Warth A, Dienemann H, De Pauw E, Katzenberger T, Aust D, Baretton G, Kriegsmann J, Casadonte R. Typing of colon and lung adenocarcinoma by high throughput imaging mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:858-864. [PMID: 27939606 DOI: 10.1016/j.bbapap.2016.11.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 11/21/2016] [Accepted: 11/23/2016] [Indexed: 10/20/2022]
Abstract
In advanced tumor stages, diagnosis is frequently made from metastatic tumor tissue. In some cases, the identification of the tumor of origin may be difficult by histology alone. In this setting, immunohistochemical and molecular biological methods are often required. In a subset of tumors definite diagnosis cannot be achieved. Thus, additional new diagnostic methods are required for precise tumor subtyping. Mass spectrometric methods are of special interest for the discrimination of different tumor types. We investigated whether it is possible to discern adenocarcinomas of colon and lung using high-throughput imaging mass spectrometry on formalin-fixed paraffin-embedded tissue microarrays. 101 primary adenocarcinoma of the colon and 91 primary adenocarcinoma of the lung were used to train a Linear Discriminant Analysis model. Results were validated on an independent set of 116 colonic and 75 lung adenocarcinomas. In the validation cohort 109 of 116 patients with colonic and 67 of 75 patients with lung adenocarcinomas were correctly classified. The ability to define proteomic profiles capable to discern different tumor types promises a valuable tool in cancer diagnostics and might complement current approaches. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
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Affiliation(s)
- Mark Kriegsmann
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.
| | | | | | | | - Katharina Lisenko
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany.
| | | | - Arne Warth
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany; Translational Lung Research Center Heidelberg, Member of the German Center for Lung Research, Germany.
| | - Hendrik Dienemann
- Department of Thoracic Surgery, Thoraxklinik at Heidelberg University, Heidelberg, Germany.
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, Systems Biology and Chemical Biology, GIGA-Research, University of Liège, Belgium.
| | | | - Daniela Aust
- Institute of Pathology, University Hospital Carl Gustav Carus, Dresden, Germany.
| | - Gustavo Baretton
- Institute of Pathology, University Hospital Carl Gustav Carus, Dresden, Germany.
| | - Joerg Kriegsmann
- Proteopath GmbH, Trier, Germany; Center for Histology, Cytology and Molecular Diagnostics Trier, Trier, Germany.
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60
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Identification of actin beta-like 2 (ACTBL2) as novel, upregulated protein in colorectal cancer. J Proteomics 2016; 152:33-40. [PMID: 27989943 DOI: 10.1016/j.jprot.2016.10.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 10/20/2016] [Accepted: 10/23/2016] [Indexed: 12/11/2022]
Abstract
Early diagnosis of colorectal cancer (CRC) can be of value for increasing the survival rate of patients. Recently, proteomic strategies to identify markers for the diagnosis of cancer at an early stage have been employed with noteworthy results. To extend these studies, we utilized two dimensional gel electrophoresis and mass spectrometry for expression profiling of proteins extracted from the freshly frozen human colorectal cancer tissue specimens and the comparable regions of adjacent normal mucosa (serving as controls). Four gel spots were determined to be differentially stained between the tumor and the control samples on a consistent basis. Following mass spectrometric analysis of these spots, six proteins were identified; five of these had previously been reported to be associated with colorectal cancer. One protein actin beta-like 2 (ACTBL2), not linked with colorectal cancer in the earlier reports, was however found to be at higher abundance in colorectal tumor samples both by proteomics and immunohistochemistry analysis. Thus ACTBL2 association and differential upregulation in colorectal cancer is novel, and as such may contribute to our understanding of the colorectal carcinogenesis and potentially serve a function in developing markers for colorectal cancer. BIOLOGICAL SIGNIFICANCE Colorectal cancer (CRC) is a major cause of death world-wide and good markers for early detection are lacking. In this study we conducted a proteomic analysis of tumor vs. normal tissue. We corroborated the finding of a number of previously identified proteins associated with CRC and more importantly identified a novel protein, ACTBL2, which we demonstrated to be upregulated in CRC. As additional proteins associated with CRC are identified the potential for developing panels of markers may be realized with better outcomes in early cancer detection.
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61
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Terayama H, Hirai S, Naito M, Qu N, Katagiri C, Nagahori K, Hayashi S, Sasaki H, Moriya S, Hiramoto M, Miyazawa K, Hatayama N, Li ZL, Sakabe K, Matsushita M, Itoh M. Specific autoantigens identified by sera obtained from mice that are immunized with testicular germ cells alone. Sci Rep 2016; 6:35599. [PMID: 27752123 PMCID: PMC5067510 DOI: 10.1038/srep35599] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 10/04/2016] [Indexed: 02/08/2023] Open
Abstract
There are various autoimmunogenic antigens (AIs) in testicular germ cells (TGCs) recognized as foreign by the body's immune system. However, there is little information of TGC-specific AIs being available. The aim of this study is to identify TGC-specific AIs. We have previously established that immunization using viable syngeneic TGC can also induce murine experimental autoimmune orchitis (EAO) without using any adjuvant. This study is to identify TGC-specific AIs by TGC liquid chromatography-tandem mass spectrometry analysis, followed by two-dimensional gel electrophoresis that reacted with serum IgG from EAO mice. In this study, we identified 11 TGC-specific AIs that reacted with serum from EAO mice. Real-time RT-PCR analysis showed that the mRNA expressions of seven TGC-specific AIs were significantly higher in only mature testis compared to other organs. Moreover, the recombinant proteins of identified 10 (except unnamed protein) TGC-specific AIs were created by using human embryonic kidney 293 (HEK293) cells and these antigencities were reconfirmed by Western blot using EAO serum reaction. These results indicated Atp6v1a, Hsc70t, Fbp1 and Dazap1 were candidates for TGC-specific AIs. Identification of these AIs will facilitate new approaches for understanding infertility and cancer pathogenesis and may provide a basis for the development of novel therapies.
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Affiliation(s)
- Hayato Terayama
- Department of Anatomy, Division of Basic Medical Science, Tokai University School of Medicine, Kanagawa, Japan.,Department of Anatomy, Tokyo Medical University, Tokyo, Japan
| | - Shuichi Hirai
- Department of Anatomy, Tokyo Medical University, Tokyo, Japan.,Department of Anatomy, Aichi Medical University, Aichi, Japan
| | - Munekazu Naito
- Department of Anatomy, Tokyo Medical University, Tokyo, Japan.,Department of Anatomy, Aichi Medical University, Aichi, Japan
| | - Ning Qu
- Department of Anatomy, Tokyo Medical University, Tokyo, Japan
| | - Chiaki Katagiri
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Kenta Nagahori
- Department of Anatomy, Tokyo Medical University, Tokyo, Japan
| | - Shogo Hayashi
- Department of Anatomy, Tokyo Medical University, Tokyo, Japan
| | - Hiraku Sasaki
- Department of Health Science, School of Health and Sports Science, Juntendo University, Chiba, Japan
| | - Shota Moriya
- Department of Biochemistry, Tokyo Medical University, Tokyo, Japan
| | - Masaki Hiramoto
- Department of Biochemistry, Tokyo Medical University, Tokyo, Japan
| | - Keisuke Miyazawa
- Department of Biochemistry, Tokyo Medical University, Tokyo, Japan
| | - Naoyuki Hatayama
- Department of Anatomy, Tokyo Medical University, Tokyo, Japan.,Department of Anatomy, Aichi Medical University, Aichi, Japan
| | - Zhong-Lian Li
- Department of Anatomy, Tokyo Medical University, Tokyo, Japan
| | - Kou Sakabe
- Department of Anatomy, Division of Basic Medical Science, Tokai University School of Medicine, Kanagawa, Japan
| | - Masayuki Matsushita
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Masahiro Itoh
- Department of Anatomy, Tokyo Medical University, Tokyo, Japan
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Licier R, Miranda E, Serrano H. A Quantitative Proteomics Approach to Clinical Research with Non-Traditional Samples. Proteomes 2016; 4:proteomes4040031. [PMID: 28248241 PMCID: PMC5260964 DOI: 10.3390/proteomes4040031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/19/2016] [Accepted: 09/21/2016] [Indexed: 01/13/2023] Open
Abstract
The proper handling of samples to be analyzed by mass spectrometry (MS) can guarantee excellent results and a greater depth of analysis when working in quantitative proteomics. This is critical when trying to assess non-traditional sources such as ear wax, saliva, vitreous humor, aqueous humor, tears, nipple aspirate fluid, breast milk/colostrum, cervical-vaginal fluid, nasal secretions, bronco-alveolar lavage fluid, and stools. We intend to provide the investigator with relevant aspects of quantitative proteomics and to recognize the most recent clinical research work conducted with atypical samples and analyzed by quantitative proteomics. Having as reference the most recent and different approaches used with non-traditional sources allows us to compare new strategies in the development of novel experimental models. On the other hand, these references help us to contribute significantly to the understanding of the proportions of proteins in different proteomes of clinical interest and may lead to potential advances in the emerging field of precision medicine.
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Affiliation(s)
- Rígel Licier
- Department of Medicine, San Juan Bautista School of Medicine, Caguas 00727, Puerto Rico.
- Quantitative Proteomics Laboratory, Comprehensive Cancer Center of Puerto Rico, San Juan 00936, Puerto Rico.
| | - Eric Miranda
- Quantitative Proteomics Laboratory, Comprehensive Cancer Center of Puerto Rico, San Juan 00936, Puerto Rico.
- Department of Internal Medicine, University of Puerto Rico, Medical Sciences Campus, San Juan 00936, Puerto Rico.
| | - Horacio Serrano
- Quantitative Proteomics Laboratory, Comprehensive Cancer Center of Puerto Rico, San Juan 00936, Puerto Rico.
- Department of Internal Medicine, University of Puerto Rico, Medical Sciences Campus, San Juan 00936, Puerto Rico.
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63
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Diao WQ, Shen N, Du YP, Liu BB, Sun XY, Xu M, He B. Fetuin-B (FETUB): a Plasma Biomarker Candidate Related to the Severity of Lung Function in COPD. Sci Rep 2016; 6:30045. [PMID: 27443820 PMCID: PMC4957096 DOI: 10.1038/srep30045] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/29/2016] [Indexed: 12/03/2022] Open
Abstract
Biomarkers for the progression of lung function in COPD are currently scarce. Plasma fetuin-B (FETUB) was identified by iTRAQ-based proteomics and was verified by ELISA in another group. Information regarding acute exacerbation (AE) was collected in a one-year follow-up programme. FETUB concentrations (1652 ± 427 ng/ml) were greater in COPD patients than in controls (1237 ± 77 ng/ml). The concentrations of FETUB in GOLD II (1762 ± 427 ng/ml), III (1650 ± 375 ng/ml) and IV (1800 ± 451 ng/ml) groups were greater than those in the controls (1257 ± 414 ng/ml) and the GOLD I (1345 ± 391 ng/ml) group. ROCs indicated that FETUB distinguished COPD patients from controls (AUC 0.747, 95% CI: 0.642–0.834) and also GOLD II, III and IV from GOLD I COPD patients (AUC: 0.770, 95% CI: 0.634–0.874). The combination of FETUB and fibrinogen performed better (AUC: 0.804, 95% CI: 0.705–0.881). FETUB also predicted the occurrence of AE (AUC: 0.707, 95% CI: 0.566–0.824) or frequent AE (AUC: 0.727, 95% CI: 0.587–0.840). FETUB concentrations were negatively correlated with FEV1%pred (r = −0.446, p = 0.000) and positively correlated with RV%pred (r = 0.317, p = 0.004), RV/TLC% (r = 0.360, p = 0.004), CT emphysema% (r = 0.322, p = 0.008) and grades of lung function (r = 0.437, p = 0.000). In conclusion, FETUB is likely to assist the diagnosis and management of COPD as a complement for other markers.
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Affiliation(s)
- Wen-Qi Diao
- Department of Respiratory Medicine, Peking University Third Hospital, Beijing 100191, China
| | - Ning Shen
- Department of Respiratory Medicine, Peking University Third Hospital, Beijing 100191, China
| | - Yi-Peng Du
- Department of Respiratory Medicine, Peking University Third Hospital, Beijing 100191, China
| | - Bei-Bei Liu
- Department of Respiratory Medicine, Peking University Third Hospital, Beijing 100191, China
| | - Xiao-Yan Sun
- Department of Respiratory Medicine, Peking University Third Hospital, Beijing 100191, China
| | - Ming Xu
- Department of Cardiology, Institute of Vascular Medicine, Peking University Third Hospital, Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, Beijing 100191, China
| | - Bei He
- Department of Respiratory Medicine, Peking University Third Hospital, Beijing 100191, China
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64
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Proteomic-Based Approaches for the Study of Cytokines in Lung Cancer. DISEASE MARKERS 2016; 2016:2138627. [PMID: 27445423 PMCID: PMC4944034 DOI: 10.1155/2016/2138627] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/12/2016] [Indexed: 02/06/2023]
Abstract
Proteomic techniques are currently used to understand the biology of different human diseases, including studies of the cell signaling pathways implicated in cancer progression, which is important in knowing the roles of different proteins in tumor development. Due to its poor prognosis, proteomic approaches are focused on the identification of new biomarkers for the early diagnosis, prognosis, and targeted treatment of lung cancer. Cytokines are proteins involved in inflammatory processes and have been proposed as lung cancer biomarkers and therapeutic targets because it has been reported that some cytokines play important roles in tumor development, invasion, and metastasis. In this review, we aim to summarize the different proteomic techniques used to discover new lung cancer biomarkers and therapeutic targets. Several cytokines have been identified as important players in lung cancer using these techniques. We underline the most important cytokines that are useful as biomarkers and therapeutic targets. We also summarize some of the therapeutic strategies targeted for these cytokines in lung cancer.
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65
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Ghosh N, Dutta M, Singh B, Banerjee R, Bhattacharyya P, Chaudhury K. Transcriptomics, proteomics and metabolomics driven biomarker discovery in COPD: an update. Expert Rev Mol Diagn 2016; 16:897-913. [PMID: 27267972 DOI: 10.1080/14737159.2016.1198258] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Diagnosis of chronic obstructive pulmonary disease (COPD), characterized by progressive irreversible airflow limitation, remains a challenge. Lack of sensitive diagnostic markers and alternative treatments have limited patients' survival rate. Herein, we provide for clinicians and scientists a comprehensive review on the various omics platforms used to investigate COPD. AREAS COVERED This review consists of articles from PubMed (2009-2016) as well as views of the contributing authors. The review highlights the need for COPD biomarker identification and also provides an update on promising candidate markers identified in various biological fluids using omics technologies. Expert commentary: The multi-omics approach holds promise for the development of robust early stage COPD diagnostic markers, screening of high-risk population, and also improved prognosis which could lead to personalized medicine in future. Various factors regulating an omics study including sample size, control selection, disease phenotyping, usage of complementary techniques and result replication in omics-based research are outlined.
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Affiliation(s)
- Nilanjana Ghosh
- a School of Medical Science and Technology , Indian Institute of Technology Kharagpur , Kharagpur , India
| | - Mainak Dutta
- a School of Medical Science and Technology , Indian Institute of Technology Kharagpur , Kharagpur , India
| | - Brajesh Singh
- a School of Medical Science and Technology , Indian Institute of Technology Kharagpur , Kharagpur , India
| | - Rintu Banerjee
- b Department of Agricultural & Food Engineering , Indian Institute of Technology Kharagpur , Kharagpur , India
| | | | - Koel Chaudhury
- a School of Medical Science and Technology , Indian Institute of Technology Kharagpur , Kharagpur , India
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66
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Li Y, Xu Y, Ye K, Wu N, Li J, Liu N, He M, Lu B, Zhou W, Hu R. Knockdown of Tubulin Polymerization Promoting Protein Family Member 3 Suppresses Proliferation and Induces Apoptosis in Non-Small-Cell Lung Cancer. J Cancer 2016; 7:1189-96. [PMID: 27390593 PMCID: PMC4934026 DOI: 10.7150/jca.14790] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/26/2016] [Indexed: 12/22/2022] Open
Abstract
Our previous studies demonstrated that depletion of tubulin polymerization promoting protein family member 3 (TPPP3) inhibits proliferation and induces apoptosis of HeLa cells. However, the expression and roles of TPPP3 in cancers remain largely unknown. In this study, we investigated the expression of TPPP3 in clinicopathological correlations in non-small-cell lung cancer (NSCLC) samples by immunohistochemistry. TPPP3 expression was significantly upregulated in NSCLC tissues, and high TPPP3 expression was positively associated with tumor size, lymph node metastasis, clinical stage, and poor survival. Furthermore, knockdown of TPPP3 by shRNA significantly inhibited cell proliferation and induced cell apoptosis and cell cycle arrest in vitro. In addition, depletion of TPPP3 inhibited lung cancer growth in vivo in the xenografts of H1299 cells; this effect was accompanied by the suppression of Ki67 expression. Our data suggested that TPPP3 might act as an oncogene in NSCLC. TPPP3 warrants consideration as a therapeutic candidate with anti-tumor potential.
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Affiliation(s)
- Yintao Li
- 1. Department of Endocrinology and Metabolism, Institute of Endocrinology and Diabetology, Huashan Hospital, Fudan University, Shanghai, P.R. China; 2. Department of Medical Oncology, Shandong Cancer Hospital and Institute, Jinan, Shandong, P.R. China
| | - Yali Xu
- 3. Department of Pathology, Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, P.R. China
| | - Kuanping Ye
- 1. Department of Endocrinology and Metabolism, Institute of Endocrinology and Diabetology, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Nan Wu
- 4. Department of Geriatrics, Zhongshan Hospital, Fudan University, Shanghai, P.R. China
| | - Junfeng Li
- 5. Department of Endocrinology, Renmin Hospital of Wuhan University, Wuhan, Hubei, P.R. China
| | - Naijia Liu
- 1. Department of Endocrinology and Metabolism, Institute of Endocrinology and Diabetology, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Min He
- 1. Department of Endocrinology and Metabolism, Institute of Endocrinology and Diabetology, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Bin Lu
- 1. Department of Endocrinology and Metabolism, Institute of Endocrinology and Diabetology, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Wenbai Zhou
- 1. Department of Endocrinology and Metabolism, Institute of Endocrinology and Diabetology, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Renming Hu
- 1. Department of Endocrinology and Metabolism, Institute of Endocrinology and Diabetology, Huashan Hospital, Fudan University, Shanghai, P.R. China
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67
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Jin H, Cheng X, Pei Y, Fu J, Lyu Z, Peng H, Yao Q, Jiang Y, Luo L, Zhuo H. Data from a comparative proteomic analysis of tumor-derived lung-cancer CD105(+) endothelial cells. Data Brief 2016; 7:927-39. [PMID: 27081670 PMCID: PMC4818351 DOI: 10.1016/j.dib.2016.03.062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/25/2016] [Accepted: 03/16/2016] [Indexed: 01/16/2023] Open
Abstract
Increasing evidence indicates that tumor-derived endothelial cells (TECs) are more relevant for the study of tumor angiogenesis and for screening antiangiogenic drugs than normal ECs (NECs). In this data article, high-purity (>98%) primary CD105+ NECs and TECs purified from a mouse Lewis lung carcinoma model bearing 0.5 cm tumors were identified using 2D-PAGE and Matrix-assisted laser desorption/ionization tandem mass spectrometry (MALDI-MS/MS). All the identified proteins were categorized functionally by Gene Ontology (GO) analysis, and gene-pathway annotated by Kyoto Encyclopedia of Genes and Genomes (KEGG). Finally, protein–protein interaction networks were also built. The proteomics and bioinformatics data presented here provide novel insights into the molecular characteristics and the early modulation of the TEC proteome in the tumor microenvironment.
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Affiliation(s)
- Hongwei Jin
- Xiamen Center of Clinical Laboratory, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, China
| | - Xiao Cheng
- Respiratory Department, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, China
| | - Yihua Pei
- Central Laboratory, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, China
| | - Jianguo Fu
- Hospital Infection Control Office, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, China
| | - Zhi Lyu
- Respiratory Department, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, China
| | - Huifang Peng
- State Key Laboratory of Stress Cell Biology, School of Life Science, Xiamen University, Xiamen, Fujian 361004, China
| | - Qin Yao
- Central Laboratory, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, China
| | - Yu Jiang
- Central Laboratory, Xiamen Women׳s and Children׳s Hospital, Xiamen, Fujian 361004, China
| | - Lianzhong Luo
- Department of Pharmacy, Xiamen Medical College, Xiamen, Fujian 361004, China
| | - Huiqin Zhuo
- Central Laboratory, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, China
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Ohlmeier S, Nieminen P, Gao J, Kanerva T, Rönty M, Toljamo T, Bergmann U, Mazur W, Pulkkinen V. Lung tissue proteomics identifies elevated transglutaminase 2 levels in stable chronic obstructive pulmonary disease. Am J Physiol Lung Cell Mol Physiol 2016; 310:L1155-65. [PMID: 27084846 DOI: 10.1152/ajplung.00021.2016] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 04/05/2016] [Indexed: 11/22/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease characterized by irreversible airflow limitation. Cigarette smoking represents the main risk factor, but the specific mechanisms of COPD are not completely understood. Our aim was to identify COPD-specific proteomic changes involved in disease onset and severity. A comparative proteomic analysis of 51 lung tissues from nonsmokers, smokers, smokers with mild to moderate (stage I-II) COPD, severe to very severe COPD (stage III-IV), and patients with α-1-antitrypsin deficiency (AATD) and idiopathic pulmonary fibrosis (IPF) was performed by cysteine-specific two-dimensional difference gel electrophoresis (2D-DIGE) coupled with mass spectrometry. Selected COPD-specific changes were validated by immunoblotting and further by ELISA in 120 induced sputum and plasma samples from nonsmokers, smokers, and patients with COPD (stage I-III). Altogether 82 altered proteins were identified comprising COPD-, AATD-, and IPF-specific, overlapping, and unspecific changes. Cathepsin D (CTSD), dihydropyrimidinase-related protein 2 (DPYSL2), transglutaminase 2 (TGM2), and tripeptidyl-peptidase 1 (TPP1) were validated as COPD-specific. TGM2 was not associated with smoking and correlated with COPD severity in lung tissue. TGM2 levels in sputum and plasma were elevated in patients with COPD (stage II-III) and correlated with lung function. In conclusion, new proteins related to COPD onset and severity could be identified with TGM2 being a novel potential diagnostic and therapeutic target for COPD. Further studies in carefully characterized cohorts are required to validate the identified changes.
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Affiliation(s)
- Steffen Ohlmeier
- Proteomics Core Facility, Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu
| | - Pentti Nieminen
- Medical Informatics and Statistics Group, University of Oulu, Oulu
| | - Jing Gao
- Heart and Lung Center, Division of Pulmonary Medicine, University of Helsinki and Helsinki University Hospital, Helsinki
| | - Tinja Kanerva
- Heart and Lung Center, Division of Pulmonary Medicine, University of Helsinki and Helsinki University Hospital, Helsinki
| | - Mikko Rönty
- HUSLAB, University of Helsinki and Helsinki University Hospital, Helsinki; and
| | - Tuula Toljamo
- Department of Pulmonary Medicine, Lapland Central Hospital, Rovaniemi, Finland
| | - Ulrich Bergmann
- Proteomics Core Facility, Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu
| | - Witold Mazur
- Heart and Lung Center, Division of Pulmonary Medicine, University of Helsinki and Helsinki University Hospital, Helsinki
| | - Ville Pulkkinen
- Heart and Lung Center, Division of Pulmonary Medicine, University of Helsinki and Helsinki University Hospital, Helsinki;
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69
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Jones JT, Qian X, van der Velden JLJ, Chia SB, McMillan DH, Flemer S, Hoffman SM, Lahue KG, Schneider RW, Nolin JD, Anathy V, van der Vliet A, Townsend DM, Tew KD, Janssen-Heininger YMW. Glutathione S-transferase pi modulates NF-κB activation and pro-inflammatory responses in lung epithelial cells. Redox Biol 2016; 8:375-82. [PMID: 27058114 PMCID: PMC4827796 DOI: 10.1016/j.redox.2016.03.005] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 03/22/2016] [Indexed: 01/30/2023] Open
Abstract
Nuclear Factor kappa B (NF-κB) is a transcription factor family critical in the activation of pro- inflammatory responses. The NF-κB pathway is regulated by oxidant-induced post-translational modifications. Protein S-glutathionylation, or the conjugation of the antioxidant molecule, glutathione to reactive cysteines inhibits the activity of inhibitory kappa B kinase beta (IKKβ), among other NF-κB proteins. Glutathione S-transferase Pi (GSTP) is an enzyme that has been shown to catalyze protein S-glutathionylation (PSSG) under conditions of oxidative stress. The objective of the present study was to determine whether GSTP regulates NF-κB signaling, S-glutathionylation of IKK, and subsequent pro-inflammatory signaling. We demonstrated that, in unstimulated cells, GSTP associated with the inhibitor of NF-κB, IκBα. However, exposure to LPS resulted in a rapid loss of association between IκBα and GSTP, and instead led to a protracted association between IKKβ and GSTP. LPS exposure also led to increases in the S-glutathionylation of IKKβ. SiRNA-mediated knockdown of GSTP decreased IKKβ-SSG, and enhanced NF-κB nuclear translocation, transcriptional activity, and pro-inflammatory cytokine production in response to lipopolysaccharide (LPS). TLK117, an isotype-selective inhibitor of GSTP, also enhanced LPS-induced NF-κB transcriptional activity and pro-inflammatory cytokine production, suggesting that the catalytic activity of GSTP is important in repressing NF-κB activation. Expression of both wild-type and catalytically-inactive Y7F mutant GSTP significantly attenuated LPS- or IKKβ-induced production of GM-CSF. These studies indicate a complex role for GSTP in modulating NF-κB, which may involve S-glutathionylation of IKK proteins, and interaction with NF-κB family members. Our findings suggest that targeting GSTP is a potential avenue for regulating the activity of this prominent pro-inflammatory and immunomodulatory transcription factor.
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Affiliation(s)
- Jane T Jones
- Department of Pathology and Laboratory Medicine, The University of Vermont, Burlington, VT, United States
| | - Xi Qian
- Department of Pathology and Laboratory Medicine, The University of Vermont, Burlington, VT, United States
| | - Jos L J van der Velden
- Department of Pathology and Laboratory Medicine, The University of Vermont, Burlington, VT, United States
| | - Shi Biao Chia
- Department of Pathology and Laboratory Medicine, The University of Vermont, Burlington, VT, United States
| | - David H McMillan
- Department of Pathology and Laboratory Medicine, The University of Vermont, Burlington, VT, United States
| | - Stevenson Flemer
- Department of Chemistry, The University of Vermont, Burlington, VT, United States
| | - Sidra M Hoffman
- Department of Pathology and Laboratory Medicine, The University of Vermont, Burlington, VT, United States
| | - Karolyn G Lahue
- Department of Pathology and Laboratory Medicine, The University of Vermont, Burlington, VT, United States
| | - Robert W Schneider
- Department of Pathology and Laboratory Medicine, The University of Vermont, Burlington, VT, United States
| | - James D Nolin
- Department of Pathology and Laboratory Medicine, The University of Vermont, Burlington, VT, United States
| | - Vikas Anathy
- Department of Pathology and Laboratory Medicine, The University of Vermont, Burlington, VT, United States
| | - Albert van der Vliet
- Department of Pathology and Laboratory Medicine, The University of Vermont, Burlington, VT, United States
| | - Danyelle M Townsend
- Department of Pharmaceutical and Biomedical Sciences, Medical University of South Carolina, Charleston, SC, United States
| | - Kenneth D Tew
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States
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70
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Fang Y, Guan X, Cai T, Long J, Wang H, Xie X, Zhang Y. Knockdown of ANXA1 suppresses the biological behavior of human NSCLC cells in vitro. Mol Med Rep 2016; 13:3858-66. [PMID: 27035116 PMCID: PMC4838122 DOI: 10.3892/mmr.2016.5022] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 01/14/2016] [Indexed: 12/20/2022] Open
Abstract
Annexin A1 (ANXA1) is a member of the annexin superfamily. Previous studies have reported that ANXA1 is highly expressed in various types of malignant tumor; however, its role in the progression of non‑small cell lung cancer (NSCLC) remains to be fully clarified. The present study aimed to investigate the oncogenic role of ANXA1 in NSCLC cells in vitro. RNA interference was used to downregulate ANXA1 expression in A549 and H1299 cells using a small interfering RNA lentiviral vector. Subsequently, cell proliferation and migration were detected using Cell Counting kit‑8, clone formation, wound healing and Transwell chamber assays. Successful transfection was confirmed using fluorescence microscopy, which demonstrated that ANXA1 had been efficiently inhibited. ANXA1 knockdown suppressed the proliferation, migration and invasion of NSCLC cells. In conclusion, the present study provided evidence suggesting that ANXA1 may contribute to the growth and invasion of NSCLC cell lines, and ANXA1 may be exploited as an in vitro therapeutic target for the treatment of NSCLC.
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Affiliation(s)
- Ying Fang
- Department of Pathology, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Xiaoying Guan
- Department of Pathology, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Tonghui Cai
- Department of Pathology, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Jie Long
- Department of Pathology, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Hongyan Wang
- Department of Pathology, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Xiaobin Xie
- Department of Pathology, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Yajie Zhang
- Department of Pathology, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
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71
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Immunoproteasome deficiency is a feature of non-small cell lung cancer with a mesenchymal phenotype and is associated with a poor outcome. Proc Natl Acad Sci U S A 2016; 113:E1555-64. [PMID: 26929325 DOI: 10.1073/pnas.1521812113] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The immunoproteasome plays a key role in generation of HLA peptides for T cell-mediated immunity. Integrative genomic and proteomic analysis of non-small cell lung carcinoma (NSCLC) cell lines revealed significantly reduced expression of immunoproteasome components and their regulators associated with epithelial to mesenchymal transition. Low expression of immunoproteasome subunits in early stage NSCLC patients was associated with recurrence and metastasis. Depleted repertoire of HLA class I-bound peptides in mesenchymal cells deficient in immunoproteasome components was restored with either IFNγ or 5-aza-2'-deoxycytidine (5-aza-dC) treatment. Our findings point to a mechanism of immune evasion of cells with a mesenchymal phenotype and suggest a strategy to overcome immune evasion through induction of the immunoproteasome to increase the cellular repertoire of HLA class I-bound peptides.
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72
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Whole exome sequencing of rare aggressive breast cancer histologies. Breast Cancer Res Treat 2016; 156:21-32. [DOI: 10.1007/s10549-016-3718-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/11/2016] [Indexed: 01/14/2023]
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73
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Ortea I, Rodríguez-Ariza A, Chicano-Gálvez E, Arenas Vacas MS, Jurado Gámez B. Discovery of potential protein biomarkers of lung adenocarcinoma in bronchoalveolar lavage fluid by SWATH MS data-independent acquisition and targeted data extraction. J Proteomics 2016; 138:106-14. [PMID: 26917472 DOI: 10.1016/j.jprot.2016.02.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 02/01/2016] [Accepted: 02/13/2016] [Indexed: 12/11/2022]
Abstract
UNLABELLED Lung cancer currently ranks as the neoplasia with the highest global mortality rate. Although some improvements have been introduced in recent years, new advances in diagnosis are required in order to increase survival rates. New mildly invasive endoscopy-based diagnostic techniques include the collection of bronchoalveolar lavage fluid (BALF), which is discarded after using a portion of the fluid for standard pathological procedures. BALF proteomic analysis can contribute to clinical practice with more sensitive biomarkers, and can complement cytohistological studies by aiding in the diagnosis, prognosis, and subtyping of lung cancer, as well as the monitoring of treatment response. The range of quantitative proteomics methodologies used for biomarker discovery is currently being broadened with the introduction of data-independent acquisition (DIA) analysis-related approaches that address the massive quantitation of the components of a proteome. Here we report for the first time a DIA-based quantitative proteomics study using BALF as the source for the discovery of potential lung cancer biomarkers. The results have been encouraging in terms of the number of identified and quantified proteins. A panel of candidate protein biomarkers for adenocarcinoma in BALF is reported; this points to the activation of the complement network as being strongly over-represented and suggests this pathway as a potential target for lung cancer research. In addition, the results reported for haptoglobin, complement C4-A, and glutathione S-transferase pi are consistent with previous studies, which indicates that these proteins deserve further consideration as potential lung cancer biomarkers in BALF. Our study demonstrates that the analysis of BALF proteins by liquid chromatography-tandem mass spectrometry (LC-MS/MS), combining a simple sample pre-treatment and SWATH DIA MS, is a useful method for the discovery of potential lung cancer biomarkers. SIGNIFICANCE Bronchoalveolar lavage fluid (BALF) analysis can contribute to clinical practice with more sensitive biomarkers, thus complementing cytohistological studies in order to aid in the diagnosis, prognosis, and subtyping of lung cancer, as well as the monitoring of treatment response. Here we report a panel of candidate protein biomarkers for adenocarcinoma in BALF. Forty-four proteins showed a fold-change higher than 3.75 among adenocarcinoma patients compared with controls. This report is the first DIA-based quantitative proteomics study to use bronchoalveolar lavage fluid (BALF) as a matrix for discovering potential biomarkers. The results are encouraging in terms of the number of identified and quantified proteins, demonstrating that the analysis of BALF proteins by a SWATH approach is a useful method for the discovery of potential biomarkers of pulmonary diseases.
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Affiliation(s)
- I Ortea
- Proteomics Unit, IMIBIC, Maimonides Institute for Biomedical Research, Córdoba, Spain.
| | - A Rodríguez-Ariza
- Medical Oncology Department, Reina Sofia University Hospital and IMIBIC, Maimonides Institute for Biomedical Research, Córdoba, Spain
| | - E Chicano-Gálvez
- Proteomics Unit, IMIBIC, Maimonides Institute for Biomedical Research, Córdoba, Spain
| | - M S Arenas Vacas
- Department of Respiratory Medicine, Reina Sofia University Hospital and IMIBIC, Maimonides Institute for Biomedical Research, Córdoba, Spain
| | - B Jurado Gámez
- Department of Respiratory Medicine, Reina Sofia University Hospital and IMIBIC, Maimonides Institute for Biomedical Research, Córdoba, Spain
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Shao W, Wang Q, Wang F, Jiang Y, Xu M, Xu J. Abnormal expression of calcyphosine is associated with poor prognosis and cell biology function in colorectal cancer. Onco Targets Ther 2016; 9:477-87. [PMID: 26889086 PMCID: PMC4741367 DOI: 10.2147/ott.s92226] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The aim of this study was to investigate the calcyphosine (CAPS) expression in human colorectal cancer (CRC) and to explore its clinical and prognostic significances. CAPS expression was measured by Western blot, real-time polymerase chain reaction analysis, and immunohistochemistry. The relationships between the CAPS expression levels and the clinicopathological factors were investigated. The Kaplan–Meier method and log-rank test were used to investigate the overall survival of the patients. Moreover, the effects of CAPS on biological roles of CRC cells were also evaluated by MTT assay, colony formation assay, and transwell assay. CAPS was significantly overexpressed in cancerous tissue and CRC cell lines compared with adjacent nontumor tissue and a normal human intestinal epithelial cell line. Overexpression of CAPS was significantly associated with histological grade (P=0.004), invasive depth (P<0.001), lymph node metastasis (P=0.003), tumor node metastasis stage (P=0.017), and distant metastasis (P=0.042). Furthermore, silencing of CAPS expression in CRC cells inhibited their proliferation, colony formation, migration, and invasion. Kaplan–Meier survival analysis showed that high CAPS expression might demonstrate poor prognosis in CRC patients. Cox regression analysis revealed that CAPS expression was an independent prognostic factor of CRC. Our data suggested that the upregulation of CAPS might play a role in the carcinogenesis and progression of CRC. CAPS could be used as a potential diagnostic factor and be an independent good prognostic indicator for CRC patients.
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Affiliation(s)
- Weiwei Shao
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, People's Republic of China
| | - Quhui Wang
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, People's Republic of China
| | - Feiran Wang
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, People's Republic of China
| | - Yasu Jiang
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, People's Republic of China
| | - Meirong Xu
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, People's Republic of China
| | - Junfei Xu
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, People's Republic of China
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Takebayashi K, Hara K, Terasawa T, Naruse R, Suetsugu M, Tsuchiya T, Inukai T. Circulating SerpinB1 levels and clinical features in patients with type 2 diabetes. BMJ Open Diabetes Res Care 2016; 4:e000274. [PMID: 27933185 PMCID: PMC5128937 DOI: 10.1136/bmjdrc-2016-000274] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 10/05/2016] [Accepted: 10/12/2016] [Indexed: 12/29/2022] Open
Abstract
OBJECTIVE The main purpose of this study was to investigate the association of serum SerpinB1 levels and various parameters in patients with type 2 diabetes. The effect of canagliflozin (a sodium glucose cotransporter 2 (SGLT2) inhibitor), which can decrease circulating insulin levels, on serum SerpinB1 levels was also investigated. A recent study suggests that the serum levels of SerpinB1, also known as monocyte neutrophil elastase inhibitor, increase with insulin resistance, may have a protective effect for pancreatic β cells, and may decrease insulin resistance. RESEARCH DESIGN AND METHODS The study included 30 patients with type 2 diabetes hospitalized for glycemic control and 10 control subjects. RESULTS SerpinB1 levels were significantly higher in patients with type 2 diabetes, compared with that in heathy control subjects (10.01±3.59 vs 5.69±1.64 ng/mL, p<0.0001). Serum SerpinB1 levels had a significant negative correlation with low-density lipoprotein cholesterol (LDL-C) (p=0.0123). Serum SerpinB1 levels had a significant positive association or trend toward a positive association with age and with hemoglobin A1c (HbA1c), and significant negative association with LDL-C levels in some multiple regression analysis models. Patients treated with statins had a tendency toward higher serum SerpinB1 levels, compared with those patients not treated with statins. During a 3-day observation period both with and without canagliflozin treatment, the serum SerpinB1 levels did not change. CONCLUSIONS Serum SerpinB1 levels are elevated in patients with type 2 diabetes compared with that in healthy subjects and are negatively correlated with serum LDL-C.
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Affiliation(s)
- Kohzo Takebayashi
- Department of Internal Medicine , Dokkyo Medical University Koshigaya Hospital , Koshigaya, Saitama , Japan
| | - Kenji Hara
- Department of Internal Medicine , Dokkyo Medical University Koshigaya Hospital , Koshigaya, Saitama , Japan
| | - Tomoko Terasawa
- Department of Internal Medicine , Dokkyo Medical University Koshigaya Hospital , Koshigaya, Saitama , Japan
| | - Rika Naruse
- Department of Internal Medicine , Dokkyo Medical University Koshigaya Hospital , Koshigaya, Saitama , Japan
| | - Mariko Suetsugu
- Department of Internal Medicine , Dokkyo Medical University Koshigaya Hospital , Koshigaya, Saitama , Japan
| | - Takafumi Tsuchiya
- Department of Internal Medicine , Dokkyo Medical University Koshigaya Hospital , Koshigaya, Saitama , Japan
| | - Toshihiko Inukai
- Department of Internal Medicine , Dokkyo Medical University Koshigaya Hospital , Koshigaya, Saitama , Japan
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Personalized Medicine in Respiratory Disease: Role of Proteomics. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2015; 102:115-46. [PMID: 26827604 DOI: 10.1016/bs.apcsb.2015.11.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Respiratory diseases affect humanity globally, with chronic lung diseases (e.g., asthma, chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, among others) and lung cancer causing extensive morbidity and mortality. These conditions are highly heterogeneous and require an early diagnosis. However, initial symptoms are nonspecific, and the clinical diagnosis is made late frequently. Over the last few years, personalized medicine has emerged as a medical care approach that uses novel technology aiming to personalize treatments according to the particular patient's medical needs. This review highlights the contributions of proteomics toward the understanding of personalized medicine in respiratory disease and its potential applications in the clinic.
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Jin H, Cheng X, Pei Y, Fu J, Lyu Z, Peng H, Yao Q, Jiang Y, Luo L, Zhuo H. Identification and verification of transgelin-2 as a potential biomarker of tumor-derived lung-cancer endothelial cells by comparative proteomics. J Proteomics 2015; 136:77-88. [PMID: 26721444 DOI: 10.1016/j.jprot.2015.12.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 12/02/2015] [Accepted: 12/09/2015] [Indexed: 12/16/2022]
Abstract
UNLABELLED To investigate heterogeneity of endothelial cells (ECs) in the tumor microenvironment and biomarkers for antitumor angiogenesis therapy, high-purity (>98%) normal (NECs) and tumor-derived CD105(+) ECs (TECs) were purified from a mouse Lewis lung carcinoma model bearing 0.5 cm tumors by immunomagnetic separation. Proteomics analysis revealed that 48 proteins (28 upregulated and 20 downregulated) were differentially regulated by at least 1.5-fold in TECs, and that these proteins were involved in metabolism, energy pathways, protein folding, cell growth and/or functioned as structural constituents of the cytoskeleton. Upregulation of heat shock protein 60 (Hspd1) and transgelin-2 (Tagln2) was revealed in TECs, and by immunohistochemistry (IHC) in paired tissues from 30 consecutive lung cancer (LC) patients. Higher expression levels of Hspd1, Tagln2 were detected in microvascular ECs of paratumor and tumor tissues than in paired normal counterparts. Stronger Tagln2 staining was associated with clinical stage, tumor size, and histological neural invasion. Higher Hspd1 (area under the curve [AUC], 0.82) and lower Tagln2 (AUC, 0.90) levels were detected in LC patient sera. Pearson correlation analysis revealed a positive correlation between serum Hspd1 and Tagln2 levels. In conclusion, higher Tagln2 levels were associated with tumor development, lymph node metastasis, and neural invasion in LC and may thus serve as a potential biomarker of tumor angiogenesis. SIGNIFICANCE High-purity endothelial cells (normal and tumor derived) were prepared to characterize ECs heterogeneity in the tumor microenvironment and to explore biomarkers of early stages of tumor development by proteomics. Candidate proteins Hspd1 and Tagln2, were further verification in the sera and tumor tissues of lung cancer patients. Moreover, higher Tagln2 was significantly associated with clinical tumor development, metastasis, and neural invasion. All these results indicated a crucial role for Tagln2 in TECs for tumor development and metastasis.
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Affiliation(s)
- Hongwei Jin
- Xiamen Center of Clinical Laboratory, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, China
| | - Xiao Cheng
- Respiratory Department, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, China
| | - Yihua Pei
- Central Laboratory, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, China
| | - Jianguo Fu
- Hospital Infection Control Office, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, China
| | - Zhi Lyu
- Respiratory Department, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, China
| | - Huifang Peng
- State Key Laboratory of Stress Cell Biology, School of Life Science, Xiamen University, Xiamen, Fujian 361004, China
| | - Qin Yao
- Central Laboratory, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, China
| | - Yu Jiang
- Central Laboratory, Xiamen Women's and Children's Hospital, Xiamen, Fujian 361004, China.
| | - Lianzhong Luo
- Department of Pharmacy, Xiamen Medical College, Xiamen, Fujian 361004, China.
| | - Huiqin Zhuo
- Central Laboratory, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, China.
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Yu G, Yu W, Jin G, Xu D, Chen Y, Xia T, Yu A, Fang W, Zhang X, Li Z, Xie K. PKM2 regulates neural invasion of and predicts poor prognosis for human hilar cholangiocarcinoma. Mol Cancer 2015; 14:193. [PMID: 26576639 PMCID: PMC4650283 DOI: 10.1186/s12943-015-0462-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 10/22/2015] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The therapeutic and prognostic value of the glycolytic enzymes hexokinase, phosphofructokinase, and pyruvate kinase (PK) has been implicated in a variety of cancers, while their roles in treatment of and prognosis for hilar cholangiocarcinoma (HC) remain unclear. In this study, we determined the expression of PKM2 in and its impact on biology and clinical outcome of human HC. METHODS The regulation and function of PKM2 in HC pathogenesis was evaluated using human tissues, molecular and cell biology, and animal models, and its prognostic significance was determined according to its impact on patient survival. RESULTS We found that expression of hexokinase 1 and the M2 splice isoform of PK (PKM2) was upregulated in HC tissues and that this expression correlated with tumor recurrence and outcome. PKM2 expression was increased in HC cases with chronic cholangitis as demonstrated by isobaric tags for relative and absolute quantification. High PKM2 expression was highly correlated with high syndecan 2 (SDC2) expression and neural invasion. PKM2 downregulation led to a decrease in SDC2 expression. Treatment with metformin markedly suppressed PKM2 and SDC2 expression at both the transcriptional and posttranscriptional levels and inhibited HC cell proliferation and tumor growth. CONCLUSIONS PKM2 regulates neural invasion of HC cells at least in part via regulation of SDC2. Inhibition of PKM2 and SDC2 expression contributes to the therapeutic effect of metformin on HC. Therefore, PKM2 is an independent prognostic factor and potential therapeutic target for human HC.
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Affiliation(s)
- Guanzhen Yu
- Department of Oncology, East Hospital, Tongji University School of Medicine, Shanghai, 200120, People's Republic of China.
- Department of Gastroenterology, Hepatology and Nutrition, Unit 1466, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA.
| | - Wenlong Yu
- Department of Surgery, Eastern Hepatobiliary Hospital, Shanghai, People's Republic of China
| | - Guangzhi Jin
- Department of Pathology, Eastern Hepatobiliary Hospital, Shanghai, People's Republic of China
| | - Dongyun Xu
- Department of Oncology, East Hospital, Tongji University School of Medicine, Shanghai, 200120, People's Republic of China
| | - Ying Chen
- Department of Pathology, Changhai Hospital, Shanghai, People's Republic of China
| | - Tian Xia
- Department of Gastroenterology, Changhai Hospital, Shanghai, 200433, People's Republic of China
- Department of Gastroenterology, Hepatology and Nutrition, Unit 1466, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Allan Yu
- Department of Gastroenterology, Hepatology and Nutrition, Unit 1466, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Wenzheng Fang
- Department of Oncology, East Hospital, Tongji University School of Medicine, Shanghai, 200120, People's Republic of China
| | - Xiaoli Zhang
- Department of Pathology, Chinese People's Liberation Army, No 411 Hospital, Shanghai, People's Republic of China
| | - Zhaosheng Li
- Department of Gastroenterology, Changhai Hospital, Shanghai, 200433, People's Republic of China.
| | - Keping Xie
- Department of Gastroenterology, Hepatology and Nutrition, Unit 1466, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA.
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Mining for Candidate Genes Related to Pancreatic Cancer Using Protein-Protein Interactions and a Shortest Path Approach. BIOMED RESEARCH INTERNATIONAL 2015; 2015:623121. [PMID: 26613085 PMCID: PMC4647023 DOI: 10.1155/2015/623121] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 10/15/2015] [Indexed: 12/13/2022]
Abstract
Pancreatic cancer (PC) is a highly malignant tumor derived from pancreas tissue and is one of the leading causes of death from cancer. Its molecular mechanism has been partially revealed by validating its oncogenes and tumor suppressor genes; however, the available data remain insufficient for medical workers to design effective treatments. Large-scale identification of PC-related genes can promote studies on PC. In this study, we propose a computational method for mining new candidate PC-related genes. A large network was constructed using protein-protein interaction information, and a shortest path approach was applied to mine new candidate genes based on validated PC-related genes. In addition, a permutation test was adopted to further select key candidate genes. Finally, for all discovered candidate genes, the likelihood that the genes are novel PC-related genes is discussed based on their currently known functions.
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Fong JJ, Sreedhara K, Deng L, Varki NM, Angata T, Liu Q, Nizet V, Varki A. Immunomodulatory activity of extracellular Hsp70 mediated via paired receptors Siglec-5 and Siglec-14. EMBO J 2015; 34:2775-88. [PMID: 26459514 DOI: 10.15252/embj.201591407] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 09/18/2015] [Indexed: 12/16/2022] Open
Abstract
The intracellular chaperone heat-shock protein 70 (Hsp70) can be secreted from cells, but its extracellular role is unclear, as the protein has been reported to both activate and suppress the innate immune response. Potential immunomodulatory receptors on myelomonocytic lineage cells that bind extracellular Hsp70 are not well defined. Siglecs are Ig-superfamily lectins on mammalian leukocytes that recognize sialic acid-bearing glycans and thereby modulate immune responses. Siglec-5 and Siglec-14, expressed on monocytes and neutrophils, share identical ligand-binding domains but have opposing signaling functions. Based on phylogenetic analyses of these receptors, we predicted that endogenous sialic acid-independent ligands should exist. An unbiased screen revealed Hsp70 as a ligand for Siglec-5 and Siglec-14. Hsp70 stimulation through Siglec-5 delivers an anti-inflammatory signal, while stimulation through Siglec-14 is pro-inflammatory. The functional consequences of this interaction are also addressed in relation to a SIGLEC14 polymorphism found in humans. Our results demonstrate that an endogenous non-sialic acid-bearing molecule can be either a danger-associated or self-associated signal through paired Siglecs, and may explain seemingly contradictory prior reports on extracellular Hsp70 action.
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Affiliation(s)
- Jerry J Fong
- Glycobiology Research and Training Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA, USA Department of Cellular and Molecular Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA, USA
| | - Karthik Sreedhara
- Glycobiology Research and Training Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA, USA Department of Cellular and Molecular Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA, USA
| | - Liwen Deng
- Glycobiology Research and Training Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA, USA Department of Pathology, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA, USA
| | - Nissi M Varki
- Glycobiology Research and Training Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA, USA Department of Pathology, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA, USA Department of Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA, USA
| | - Takashi Angata
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Qinglian Liu
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Victor Nizet
- Glycobiology Research and Training Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA, USA Department of Pediatrics, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA, USA UC San Diego School of Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA, USA Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA, USA
| | - Ajit Varki
- Glycobiology Research and Training Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA, USA Department of Cellular and Molecular Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA, USA Department of Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA, USA UC San Diego School of Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA, USA
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Davalieva K, Kostovska IM, Kiprijanovska S, Markoska K, Kubelka-Sabit K, Filipovski V, Stavridis S, Stankov O, Komina S, Petrusevska G, Polenakovic M. Proteomics analysis of malignant and benign prostate tissue by 2D DIGE/MS reveals new insights into proteins involved in prostate cancer. Prostate 2015; 75:1586-600. [PMID: 26074449 DOI: 10.1002/pros.23034] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/18/2015] [Indexed: 12/25/2022]
Abstract
BACKGROUND The key to a more effective diagnosis, prognosis, and therapeutic management of prostate cancer (PCa) could lie in the direct analysis of cancer tissue. In this study, by comparative proteomics analysis of PCa and benign prostate hyperplasia (BPH) tissues we attempted to elucidate the proteins and regulatory pathways involved in this disease. METHODS The samples used in this study were fresh surgical tissues with clinically and histologically confirmed PCa (n = 19) and BPH (n = 33). We used two dimensional difference in gel electrophoresis (2D DIGE) coupled with mass spectrometry (MS) and bioinformatics analysis. RESULTS Thirty-nine spots with statistically significant 1.8-fold variation or more in abundance, corresponding to 28 proteins were identified. The IPA analysis pointed out to 3 possible networks regulated within MAPK, ERK, TGFB1, and ubiquitin pathways. Thirteen of the identified proteins, namely, constituents of the intermediate filaments (KRT8, KRT18, DES), potential tumor suppressors (ARHGAP1, AZGP1, GSTM2, and MFAP4), transport and membrane organization proteins (FABP5, GC, and EHD2), chaperons (FKBP4 and HSPD1) and known cancer marker (NME1) have been associated with prostate and other cancers by numerous proteomics, genomics or functional studies. We evidenced for the first time the dysregulation of 9 proteins (CSNK1A1, ARID5B, LYPLA1, PSMB6, RABEP1, TALDO1, UBE2N, PPP1CB, and SERPINB1) that may have role in PCa. The UBE2N, PSMB6, and PPP1CB, involved in cell cycle regulation and progression were evaluated by Western blot analysis which confirmed significantly higher abundances of UBE2N and PSMB6 and significantly lower abundance of PPP1CB in PCa. CONCLUSION In addition to the identification of substantial number of proteins with known association with PCa, the proteomic approach in this study revealed proteins not previously clearly related to PCa, providing a starting point for further elucidation of their function in disease initiation and progression.
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Affiliation(s)
- Katarina Davalieva
- Research Centre for Genetic Engineering and Biotechnology "Georgi D Efremov", Macedonian Academy of Sciences and Arts, Skopje, Republic of Macedonia
| | - Ivana Maleva Kostovska
- Research Centre for Genetic Engineering and Biotechnology "Georgi D Efremov", Macedonian Academy of Sciences and Arts, Skopje, Republic of Macedonia
| | - Sanja Kiprijanovska
- Research Centre for Genetic Engineering and Biotechnology "Georgi D Efremov", Macedonian Academy of Sciences and Arts, Skopje, Republic of Macedonia
| | - Katerina Markoska
- Research Centre for Genetic Engineering and Biotechnology "Georgi D Efremov", Macedonian Academy of Sciences and Arts, Skopje, Republic of Macedonia
| | - Katerina Kubelka-Sabit
- Labaratory for Histopathology, Clinical Hospital "Sistina", Skopje, Republic of Macedonia
| | - Vanja Filipovski
- Labaratory for Histopathology, Clinical Hospital "Sistina", Skopje, Republic of Macedonia
| | - Sotir Stavridis
- University Clinic for Urology, University Clinical Centre "Mother Theresa", Skopje, Republic of Macedonia
| | - Oliver Stankov
- University Clinic for Urology, University Clinical Centre "Mother Theresa", Skopje, Republic of Macedonia
| | - Selim Komina
- Institute of Pathology, Medical Faculty, University "St. Cyril and Methodius", Skopje, Republic of Macedonia
| | - Gordana Petrusevska
- Institute of Pathology, Medical Faculty, University "St. Cyril and Methodius", Skopje, Republic of Macedonia
| | - Momir Polenakovic
- Research Centre for Genetic Engineering and Biotechnology "Georgi D Efremov", Macedonian Academy of Sciences and Arts, Skopje, Republic of Macedonia
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Zinke M, Hanff E, Böhmer A, Supuran CT, Tsikas D. Discovery and microassay of a nitrite-dependent carbonic anhydrase activity by stable-isotope dilution gas chromatography-mass spectrometry. Amino Acids 2015; 48:245-55. [PMID: 26334347 DOI: 10.1007/s00726-015-2081-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 08/20/2015] [Indexed: 12/21/2022]
Abstract
The intrinsic activity of carbonic anhydrase (CA) is the hydration of CO2 to carbonic acid and its dehydration to CO2. CA may also function as esterase and phosphatase. Recently, we demonstrated that renal CA is mainly responsible for the reabsorption of nitrite (NO2(-)) which is the most abundant reservoir of the biologically highly potent nitric oxide (NO). By means of a stable-isotope dilution GC-MS method, we discovered a novel CA activity which strictly depends upon nitrite. We found that bovine erythrocytic CAII (beCAII) catalyses the incorporation of (18)O from H2 (18)O into nitrite at pH 7.4. After derivatization with pentafluorobenzyl bromide, gas chromatographic separation and mass spectrometric analysis, we detected ions at m/z 48 for singly (18)O-labelled nitrite ((16)O=N-(18)O(-)/(18)O=N-(16)O(-)) and at m/z 50 for doubly (18)O-labelled nitrite ((18)O=N-(18)O(-)) in addition to m/z 46 for unlabelled nitrite. Using (15)N-labelled nitrite ((15)NO2 (-), m/z 47) as an internal standard and selected-ion monitoring of m/z 46, m/z 48, m/z 50 and m/z 47, we developed a GC-MS microassay for the quantitative determination of the nitrite-dependent beCAII activity. The CA inhibitors acetazolamide and FC5 207A did not alter beCAII-catalysed formation of singly and doubly (18)O-labelled nitrite. Cysteine and the experimental CA inhibitor DIDS (a diisothiocyanate) increased several fold the beCAII-catalysed formation of the (18)O-labelled nitrite species. Cysteine, acetazolamide, FC5 207A, and DIDS by themselves had no effect on the incorporation of (18)O from H2 (18)O into nitrite. We conclude that erythrocytic CA possesses a nitrite-dependent activity which can only be detected when nitrite is used as the substrate and the reaction is performed in buffers of neutral pH values prepared in H2 (18)O. This novel CA activity, i.e., the nitrous acid anhydrase activity, represents a bioactivation of nitrite and may have both beneficial (via S-nitrosylation and subsequent NO release) and possibly adverse (via C- and N-nitrosylation) effects in living organisms.
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Affiliation(s)
- Maximilian Zinke
- Bioanalytical Research Laboratory for NO, Oxidative Stress and Eicosanoids (BIOFORNOX20), Centre of Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Erik Hanff
- Bioanalytical Research Laboratory for NO, Oxidative Stress and Eicosanoids (BIOFORNOX20), Centre of Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Anke Böhmer
- Bioanalytical Research Laboratory for NO, Oxidative Stress and Eicosanoids (BIOFORNOX20), Centre of Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Claudiu T Supuran
- Dipartmento di Chimica Ugo Schiff, Università degli Studi di Firenze, Sesto Fiorentino, Florence, Italy
| | - Dimitrios Tsikas
- Bioanalytical Research Laboratory for NO, Oxidative Stress and Eicosanoids (BIOFORNOX20), Centre of Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany.
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83
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Abstract
INTRODUCTION The enormous biological complexity and high mortality rate of lung cancer highlights the need for new global approaches for the discovery of reliable early diagnostic biomarkers. The study of bronchoalveolar lavage samples by proteomic techniques could identify new lung cancer biomarkers and may provide promising noninvasive diagnostic tools able to enhance the sensitivity of current methods. METHODS First, an observational prospective study was designed to assess protein expression differences in bronchoalveolar lavages from patients with (n = 139) and without (n = 49) lung cancer, using two-dimensional gel electrophoresis and subsequent protein identification by mass spectrometry. Second, validation of candidate biomarkers was performed by bead-based immunoassays with a different patient cohort (204 patients, 48 controls). RESULTS Thirty-two differentially expressed proteins were identified in bronchoalveolar lavages, 10 of which were confirmed by immunoassays. The expression levels of APOA1, CO4A, CRP, GSTP1, and SAMP led to a lung cancer diagnostic panel that reached 95% sensitivity and 81% specificity, and the quantification of STMN1 and GSTP1 proteins allowed the two main lung cancer subtypes to be discriminated with 90% sensitivity and 57% specificity. CONCLUSIONS Bronchoalveolar lavage represents a promising noninvasive source of lung cancer specific protein biomarkers with high diagnostic accuracy. Measurement of APOA1, CO4A, CRP, GSTP1, SAMP, and STMN1 in this fluid may be a useful tool for lung cancer diagnosis, although a further validation in a larger clinical set is required for early stages.
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84
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Birse CE, Lagier RJ, FitzHugh W, Pass HI, Rom WN, Edell ES, Bungum AO, Maldonado F, Jett JR, Mesri M, Sult E, Joseloff E, Li A, Heidbrink J, Dhariwal G, Danis C, Tomic JL, Bruce RJ, Moore PA, He T, Lewis ME, Ruben SM. Blood-based lung cancer biomarkers identified through proteomic discovery in cancer tissues, cell lines and conditioned medium. Clin Proteomics 2015; 12:18. [PMID: 26279647 PMCID: PMC4537594 DOI: 10.1186/s12014-015-9090-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 07/07/2015] [Indexed: 12/18/2022] Open
Abstract
Background Support for early detection of lung cancer has emerged from the National Lung Screening Trial (NLST), in which low-dose computed tomography (LDCT) screening reduced lung cancer mortality by 20 % relative to chest x-ray. The US Preventive Services Task Force (USPSTF) recently recommended annual screening for the high-risk population, concluding that the benefits (life years gained) outweighed harms (false positive findings, abortive biopsy/surgery, radiation exposure). In making their recommendation, the USPSTF noted that the moderate net benefit of screening was dependent on the resolution of most false-positive results without invasive procedures. Circulating biomarkers may serve as a valuable adjunctive tool to imaging. Results We developed a broad-based proteomics discovery program, integrating liquid chromatography/mass spectrometry (LC/MS) analyses of freshly resected lung tumor specimens (n = 13), lung cancer cell lines (n = 17), and conditioned media collected from tumor cell lines (n = 7). To enrich for biomarkers likely to be found at elevated levels in the peripheral circulation of lung cancer patients, proteins were prioritized based on predicted subcellular localization (secreted, cell-membrane associated) and differential expression in disease samples. 179 candidate biomarkers were identified. Several markers selected for further validation showed elevated levels in serum collected from subjects with stage I NSCLC (n = 94), relative to healthy smoker controls (n = 189). An 8-marker model was developed (TFPI, MDK, OPN, MMP2, TIMP1, CEA, CYFRA 21–1, SCC) which accurately distinguished subjects with lung cancer (n = 50) from high risk smokers (n = 50) in an independent validation study (AUC = 0.775). Conclusions Integrating biomarker discovery from multiple sample types (fresh tissue, cell lines and conditioned medium) has resulted in a diverse repertoire of candidate biomarkers. This unique collection of biomarkers may have clinical utility in lung cancer detection and diagnoses. Electronic supplementary material The online version of this article (doi:10.1186/s12014-015-9090-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Charles E Birse
- Celera employees during the course of these studies, Celera, 1311 Harbor Bay Parkway, Alameda, CA 94502 USA
| | - Robert J Lagier
- Celera employees during the course of these studies, Celera, 1311 Harbor Bay Parkway, Alameda, CA 94502 USA
| | - William FitzHugh
- Celera employees during the course of these studies, Celera, 1311 Harbor Bay Parkway, Alameda, CA 94502 USA
| | - Harvey I Pass
- Department of Cardiothoracic Surgery, NYU Langone Medical Center, 530 First Avenue, New York, NY USA
| | - William N Rom
- Division of Pulmonary, Critical Care, and Sleep Medicine, NYU School of Medicine, New York, NY USA
| | - Eric S Edell
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN USA
| | - Aaron O Bungum
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN USA
| | - Fabien Maldonado
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN USA
| | - James R Jett
- Division of Oncology, National Jewish Health, Denver, CO USA
| | - Mehdi Mesri
- Celera employees during the course of these studies, Celera, 1311 Harbor Bay Parkway, Alameda, CA 94502 USA
| | - Erin Sult
- Celera employees during the course of these studies, Celera, 1311 Harbor Bay Parkway, Alameda, CA 94502 USA
| | - Elizabeth Joseloff
- Celera employees during the course of these studies, Celera, 1311 Harbor Bay Parkway, Alameda, CA 94502 USA
| | - Aiqun Li
- Celera employees during the course of these studies, Celera, 1311 Harbor Bay Parkway, Alameda, CA 94502 USA
| | - Jenny Heidbrink
- Celera employees during the course of these studies, Celera, 1311 Harbor Bay Parkway, Alameda, CA 94502 USA
| | - Gulshan Dhariwal
- Celera employees during the course of these studies, Celera, 1311 Harbor Bay Parkway, Alameda, CA 94502 USA
| | - Chad Danis
- Celera employees during the course of these studies, Celera, 1311 Harbor Bay Parkway, Alameda, CA 94502 USA
| | - Jennifer L Tomic
- Celera employees during the course of these studies, Celera, 1311 Harbor Bay Parkway, Alameda, CA 94502 USA
| | - Robert J Bruce
- Celera employees during the course of these studies, Celera, 1311 Harbor Bay Parkway, Alameda, CA 94502 USA
| | - Paul A Moore
- Celera employees during the course of these studies, Celera, 1311 Harbor Bay Parkway, Alameda, CA 94502 USA
| | - Tao He
- Celera employees during the course of these studies, Celera, 1311 Harbor Bay Parkway, Alameda, CA 94502 USA
| | - Marcia E Lewis
- Celera employees during the course of these studies, Celera, 1311 Harbor Bay Parkway, Alameda, CA 94502 USA
| | - Steve M Ruben
- Celera employees during the course of these studies, Celera, 1311 Harbor Bay Parkway, Alameda, CA 94502 USA
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85
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Nigro E, Imperlini E, Scudiero O, Monaco ML, Polito R, Mazzarella G, Orrù S, Bianco A, Daniele A. Differentially expressed and activated proteins associated with non small cell lung cancer tissues. Respir Res 2015; 16:74. [PMID: 26104294 PMCID: PMC4487583 DOI: 10.1186/s12931-015-0234-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 06/09/2015] [Indexed: 12/26/2022] Open
Abstract
Background Lung cancer is a leading cause of mortality. The most common cancer subtype, non small cell lung cancer (NSCLC), accounts for 85-90 % all cases and is mainly caused by environmental and genetic factors. Mechanisms involved in lung carcinogenesis include deregulation of several kinases and molecular pathways affecting cell proliferation, apoptosis and differentiation. Despite advances in lung cancer detection, diagnosis and staging, survival rate still remains poor and novel biomarkers for both diagnosis and therapy need to be identified. In the present study, we have explored the potential of novel specific biomarkers in the diagnosis of NSCLC, and the over-expression/activation of several kinases involved in disease development and progression. Method Lung tumor tissue specimens and adjacent cancer-free tissues from 8 NSCLC patients undergoing surgery were collected. The differential activation status of ERK1/2, AKT and IKBα/NF-κβ was analyzed. Subsequently, protein expression profile of NSCLC vs normal surrounding tissue was compared by a proteomic approach using LC-MS MS. Subsequently, MS/MS outputs were analyzed by the Protein Discoverer platform for label-free quantitation analysis. Finally, results were confirmed by western blotting analysis. Results This study confirms the involvement of ERK1/2, AKT, IKBα and NF-κβ proteins in NSCLC demonstrating a significant over-activation of all tested proteins. Furthermore, we found significant differential expression of 20 proteins (Rsc ≥ 1.50 or ≤ −1.50) of which 7 are under-expressed and 13 over-expressed in NSCLC lung tissues. Finally, we validated, by western blotting, the two most under-expressed NSCLC tissue proteins, carbonic anhydrase I and II isoforms. Conclusion Our data further support the possibility of developing both diagnostic tests and innovative targeted therapy in NSCLC. In addition to selective inhibitors of ERK1/2, AKT, IKBα and NF-κβ, as therapeutic options, our data, for the first time, indicates carbonic anhydrase I and II as attractive targets for development of diagnostic tools enabling selection of patients for a more specific therapy in NSCLC.
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Affiliation(s)
- E Nigro
- CEINGE-Biotecnologie Avanzate Scarl, Via G. Salvatore 486, 80145, Naples, Italy
| | - E Imperlini
- IRCCS SDN, Via E. Gianturco 113, 80142, Naples, Italy.,Present address: CEINGE-Biotecnologie Avanzate Scarl, Via G. Salvatore 486, 80145, Naples, Italy
| | - O Scudiero
- CEINGE-Biotecnologie Avanzate Scarl, Via G. Salvatore 486, 80145, Naples, Italy.,Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Via S. Pansini 5, 80131, Naples, Italy
| | - M L Monaco
- CEINGE-Biotecnologie Avanzate Scarl, Via G. Salvatore 486, 80145, Naples, Italy
| | - R Polito
- CEINGE-Biotecnologie Avanzate Scarl, Via G. Salvatore 486, 80145, Naples, Italy
| | - G Mazzarella
- Dipartimento di Scienze Cardio-Toraciche e Respiratorie, Seconda Università degli Studi di Napoli, Via L. Bianchi, 80131, Naples, Italy
| | - S Orrù
- CEINGE-Biotecnologie Avanzate Scarl, Via G. Salvatore 486, 80145, Naples, Italy.,Dipartimento di Scienze Motorie e del Benessere, Università di Napoli Parthenope, Via Amm. F. Acton 38, 80133, Naples, Italy
| | - A Bianco
- Cattedra di Malattie dell'Apparato Respiratorio, Dipartimento di Medicina e Scienze per la Salute "V Tiberio", Università del Molise, Via De Sanctis, 86100, Campobasso, Italy
| | - A Daniele
- CEINGE-Biotecnologie Avanzate Scarl, Via G. Salvatore 486, 80145, Naples, Italy. .,Dipartimento di Scienze e Tecnologie Ambientali Biologiche Farmaceutiche, Seconda Università degli Studi di Napoli, Via G. Vivaldi 42, 81100, Caserta, Italy.
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86
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Justet C, Evans F, Torriglia A, Chifflet S. Increase in the expression of leukocyte elastase inhibitor during wound healing in corneal endothelial cells. Cell Tissue Res 2015; 362:557-68. [DOI: 10.1007/s00441-015-2223-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Accepted: 05/22/2015] [Indexed: 11/29/2022]
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87
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Gao J, Ohlmeier S, Nieminen P, Toljamo T, Tiitinen S, Kanerva T, Bingle L, Araujo B, Rönty M, Höyhtyä M, Bingle CD, Mazur W, Pulkkinen V. Elevated sputum BPIFB1 levels in smokers with chronic obstructive pulmonary disease: a longitudinal study. Am J Physiol Lung Cell Mol Physiol 2015; 309:L17-26. [PMID: 25979078 DOI: 10.1152/ajplung.00082.2015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/12/2015] [Indexed: 01/22/2023] Open
Abstract
A previous study involving a proteomic screen of induced sputum from smokers and patients with chronic obstructive pulmonary disease (COPD) demonstrated elevated levels of bactericidal/permeability-increasing fold-containing protein B1 (BPIFB1). The aim of the present study was to further evaluate the association of sputum BPIFB1 levels with smoking and longitudinal changes in lung function in smokers with COPD. Sputum BPIFB1 was characterized by two-dimensional gel electrophoresis and mass spectrometry. The expression of BPIFB1 in COPD was investigated by immunoblotting and immunohistochemistry using sputum and lung tissue samples. BPIFB1 levels were also assessed in induced sputum from nonsmokers (n = 31), smokers (n = 169), and patients with COPD (n = 52) via an ELISA-based method. The longitudinal changes in lung function during the 4-year follow-up period were compared with the baseline sputum BPIFB1 levels. In lung tissue samples, BPIFB1 was localized to regions of goblet cell metaplasia. Secreted and glycosylated BPIFB1 was significantly elevated in the sputum of patients with COPD compared with that of smokers and nonsmokers. Sputum BPIFB1 levels correlated with pack-years and lung function as measured by forced expiratory volume in 1 s (FEV1) % predicted and FEV1/FVC (forced vital capacity) at baseline and after the 4-year follow-up in all participants. The changes in lung function over 4 years were significantly associated with BPIFB1 levels in current smokers with COPD. In conclusion, higher sputum concentrations of BPIFB1 were associated with changes of lung function over time, especially in current smokers with COPD. BPIFB1 may be involved in the pathogenesis of smoking-related lung diseases.
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Affiliation(s)
- J Gao
- HUCH Heart and Lung Center, Department of Pulmonary Medicine, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - S Ohlmeier
- Proteomics Core Facility, Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - P Nieminen
- Medical Informatics and Statistics Group, University of Oulu, Oulu, Finland
| | - T Toljamo
- Department of Pulmonary Medicine, Lapland Central Hospital, Rovaniemi, Finland
| | | | - T Kanerva
- HUCH Heart and Lung Center, Department of Pulmonary Medicine, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - L Bingle
- Academic Unit of Respiratory Medicine, Department of Infection and Immunity, University of Sheffield, Sheffield, UK; and
| | - B Araujo
- Academic Unit of Respiratory Medicine, Department of Infection and Immunity, University of Sheffield, Sheffield, UK; and
| | - M Rönty
- HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - M Höyhtyä
- Medix Biochemica, Kauniainen, Finland
| | - C D Bingle
- Academic Unit of Respiratory Medicine, Department of Infection and Immunity, University of Sheffield, Sheffield, UK; and
| | - W Mazur
- HUCH Heart and Lung Center, Department of Pulmonary Medicine, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - V Pulkkinen
- HUCH Heart and Lung Center, Department of Pulmonary Medicine, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland;
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88
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Kültz D, Li J, Sacchi R, Morin D, Buckpitt A, Van Winkle L. Alterations in the proteome of the respiratory tract in response to single and multiple exposures to naphthalene. Proteomics 2015; 15:2655-68. [PMID: 25825134 DOI: 10.1002/pmic.201400445] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 01/16/2015] [Accepted: 03/25/2015] [Indexed: 12/12/2022]
Abstract
Protein adduction is considered to be critical to the loss of cellular homeostasis associated with environmental chemicals undergoing metabolic activation. Despite considerable effort, our understanding of the key proteins mediating the pathologic consequences from protein modification by electrophiles is incomplete. This work focused on naphthalene (NA) induced acute injury of respiratory epithelial cells and tolerance which arises after multiple toxicant doses to define the initial cellular proteomic response and later protective actions related to tolerance. Airways and nasal olfactory epithelium from mice exposed to 15 ppm NA either for 4 h (acute) or for 4 h/day × 7 days (tolerant) were used for label-free protein quantitation by LC/MS/MS. Cytochrome P450 2F2 and secretoglobin 1A1 are decreased dramatically in airways of mice exposed for 4 h, a finding consistent with the fact that CYPs are localized primarily in Clara cells. A number of heat shock proteins and protein disulfide isomerases, which had previously been identified as adduct targets for reactive metabolites from several lung toxicants, were upregulated in airways but not olfactory epithelium of tolerant mice. Protein targets that are upregulated in tolerance may be key players in the pathophysiology associated with reactive metabolite protein adduction. All MS data have been deposited in the ProteomeXchange with identifier PXD000846 (http://proteomecentral.proteomexchange.org/dataset/PXD000846).
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Affiliation(s)
- Dietmar Kültz
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California, Davis, CA, USA
| | - Johnathon Li
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California, Davis, CA, USA
| | - Romina Sacchi
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California, Davis, CA, USA
| | - Dexter Morin
- Depatment of Molecular Biosciences, University of California, Davis, CA, USA
| | - Alan Buckpitt
- Depatment of Molecular Biosciences, University of California, Davis, CA, USA
| | - Laura Van Winkle
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis, CA, USA
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Sheng H, Ying L, Zheng L, Zhang D, Zhu C, Wu J, Feng J, Su D. Down Expression of FBP1 Is a Negative Prognostic Factor for Non-Small-Cell Lung Cancer. Cancer Invest 2015; 33:197-204. [PMID: 25844935 DOI: 10.3109/07357907.2015.1020385] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Downregulation of fructose-1,6-bisphosphatse-1 (FBP1) was observed in several cancers but its role in the lung cancer still remains unknown. We examined the cancer tissues from 140 patients with nonsmall cell lung cancer patients and found that the relative gene expression of FBP1 was significantly lower in lung cancer tissues as compared to incisal marginal tissues and normal tissues. The patients with higher level of FBP1 RNA expression have significantly longer disease free survival and overall survival as compared to the lower expression groups. There was a negative correlation with the level of FBP1 and recurrence of the lung cancer.
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Affiliation(s)
- Huaying Sheng
- 1Cancer Research Institute, Zhejiang Cancer Hospital , Hangzhou, Zhejiang , China
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90
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Vachani A, Pass HI, Rom WN, Midthun DE, Edell ES, Laviolette M, Li XJ, Fong PY, Hunsucker SW, Hayward C, Mazzone PJ, Madtes DK, Miller YE, Walker MG, Shi J, Kearney P, Fang KC, Massion PP. Validation of a multiprotein plasma classifier to identify benign lung nodules. J Thorac Oncol 2015; 10:629-37. [PMID: 25590604 PMCID: PMC4382127 DOI: 10.1097/jto.0000000000000447] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Indeterminate pulmonary nodules (IPNs) lack clinical or radiographic features of benign etiologies and often undergo invasive procedures unnecessarily, suggesting potential roles for diagnostic adjuncts using molecular biomarkers. The primary objective was to validate a multivariate classifier that identifies likely benign lung nodules by assaying plasma protein expression levels, yielding a range of probability estimates based on high negative predictive values (NPVs) for patients with 8 to 30 mm IPNs. METHODS A retrospective, multicenter, case-control study was performed using multiple reaction monitoring mass spectrometry, a classifier comprising five diagnostic and six normalization proteins, and blinded analysis of an independent validation set of plasma samples. RESULTS The classifier achieved validation on 141 lung nodule-associated plasma samples based on predefined statistical goals to optimize sensitivity. Using a population based nonsmall-cell lung cancer prevalence estimate of 23% for 8 to 30 mm IPNs, the classifier identified likely benign lung nodules with 90% negative predictive value and 26% positive predictive value, as shown in our prior work, at 92% sensitivity and 20% specificity, with the lower bound of the classifier's performance at 70% sensitivity and 48% specificity. Classifier scores for the overall cohort were statistically independent of patient age, tobacco use, nodule size, and chronic obstructive pulmonary disease diagnosis. The classifier also demonstrated incremental diagnostic performance in combination with a four-parameter clinical model. CONCLUSIONS This proteomic classifier provides a range of probability estimates for the likelihood of a benign etiology that may serve as a noninvasive, diagnostic adjunct for clinical assessments of patients with IPNs.
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Affiliation(s)
- Anil Vachani
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - Harvey I. Pass
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - William N. Rom
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - David E. Midthun
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - Eric S. Edell
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - Michel Laviolette
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - Xiao-Jun Li
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - Pui-Yee Fong
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - Stephen W. Hunsucker
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - Clive Hayward
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - Peter J. Mazzone
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - David K. Madtes
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - York E. Miller
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - Michael G. Walker
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - Jing Shi
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - Paul Kearney
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - Kenneth C. Fang
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - Pierre P. Massion
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
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91
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Whitsett TG, Inge LJ, Tran NL. The use of quantitative proteomics towards biomarker discovery in lung squamous cell carcinoma. Transl Lung Cancer Res 2015; 2:457-60. [PMID: 25806270 DOI: 10.3978/j.issn.2218-6751.2013.10.17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 10/30/2013] [Indexed: 11/14/2022]
Abstract
The high mortality rate in advanced lung cancer, due to a preponderance of tumors discovered at advanced stage, demands the discovery and clinical validation of biomarkers for diagnosing early stage disease. Quantitative proteomics technologies are capable of identifying protein biomarkers with diagnostic, prognostic, and predictive value. Recent works have demonstrated the utility in using quantitative proteomics across normal, pre-cancerous, and cancerous lesions towards the discovery of biomarkers for early stage lung cancer, as well as discovering novel mechanisms of lung carcinogenesis.
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Affiliation(s)
- Timothy G Whitsett
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Landon J Inge
- Center for Thoracic Disease and Transplantation, Heart and Lung Institute, St. Joseph's Hospital and Medical Center, Phoenix, AZ, USA
| | - Nhan L Tran
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
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92
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Terracciano R, Pelaia G, Preianò M, Savino R. Asthma and COPD proteomics: current approaches and future directions. Proteomics Clin Appl 2015; 9:203-20. [PMID: 25504544 DOI: 10.1002/prca.201400099] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 11/26/2014] [Accepted: 12/08/2014] [Indexed: 12/25/2022]
Abstract
Although asthma and chronic obstructive pulmonary disease COPD represent the two most common chronic respiratory diseases worldwide, the mechanisms underlying their pathobiology need to be further elucidated. Presently, differentiation of asthma and COPD are largely based on clinical and lung function parameters. However, the complexity of these multifactorial diseases may lead to misclassification and to inappropriate management strategies. Recently, tremendous progress in MS has extended the sensitivity, accuracy, and speed of analysis, enabling the identification of thousands of proteins per experiment. Beyond identification, MS has also greatly implemented quantitation issues allowing to assess qualitative-quantitative differences in protein profiles of different samples, in particular diseased versus normal. Herein, we provide a summary of recent proteomics-based investigations in the field of asthma/COPD, highlighting major issues related to sampling and processing procedures for proteomic analyses of specific airway and parenchymal specimens (induced sputum, exhaled breath condensate, epithelial lining fluid, bronchoalveolar and nasal lavage fluid), as well as blood-derived specimen (plasma and serum). Within such a context, together with current difficulties and limitations mainly due to lack of general standardization in preanalytical sampling procedure, our discussion will focus on the challenges and possible benefits of proteomic studies in phenotypic stratification of asthma and COPD.
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Affiliation(s)
- Rosa Terracciano
- Department of Health Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
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93
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Phaniendra A, Jestadi DB, Periyasamy L. Free radicals: properties, sources, targets, and their implication in various diseases. Indian J Clin Biochem 2015; 30:11-26. [PMID: 25646037 PMCID: PMC4310837 DOI: 10.1007/s12291-014-0446-0] [Citation(s) in RCA: 1227] [Impact Index Per Article: 136.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 05/14/2014] [Indexed: 02/07/2023]
Abstract
Free radicals and other oxidants have gained importance in the field of biology due to their central role in various physiological conditions as well as their implication in a diverse range of diseases. The free radicals, both the reactive oxygen species (ROS) and reactive nitrogen species (RNS), are derived from both endogenous sources (mitochondria, peroxisomes, endoplasmic reticulum, phagocytic cells etc.) and exogenous sources (pollution, alcohol, tobacco smoke, heavy metals, transition metals, industrial solvents, pesticides, certain drugs like halothane, paracetamol, and radiation). Free radicals can adversely affect various important classes of biological molecules such as nucleic acids, lipids, and proteins, thereby altering the normal redox status leading to increased oxidative stress. The free radicals induced oxidative stress has been reported to be involved in several diseased conditions such as diabetes mellitus, neurodegenerative disorders (Parkinson's disease-PD, Alzheimer's disease-AD and Multiple sclerosis-MS), cardiovascular diseases (atherosclerosis and hypertension), respiratory diseases (asthma), cataract development, rheumatoid arthritis and in various cancers (colorectal, prostate, breast, lung, bladder cancers). This review deals with chemistry, formation and sources, and molecular targets of free radicals and it provides a brief overview on the pathogenesis of various diseased conditions caused by ROS/RNS.
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Affiliation(s)
- Alugoju Phaniendra
- Department of Biochemistry and Molecular Biology, Pondicherry University, Pondicherry, 605 014 India
| | - Dinesh Babu Jestadi
- Department of Biochemistry and Molecular Biology, Pondicherry University, Pondicherry, 605 014 India
| | - Latha Periyasamy
- Department of Biochemistry and Molecular Biology, Pondicherry University, Pondicherry, 605 014 India
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94
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Lygirou V, Makridakis M, Vlahou A. Biological sample collection for clinical proteomics: existing SOPs. Methods Mol Biol 2015; 1243:3-27. [PMID: 25384737 DOI: 10.1007/978-1-4939-1872-0_1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Proteomic study of clinical samples aims at the better understanding of physiological and pathological conditions, as well as the discovery of diagnostic and prognostic markers for the latter. Quantitative and/or qualitative variations of body fluid proteome may reflect health- or disease-associated events connected to the adjacent or distant body regions of the fluid production/secretion/excretion and/or systemic reactions to the presence of disease. Sample collection and preparation is a critical step in order to obtain useful and valid information in clinical proteomics analysis. In this chapter, we present the current protocols and guidelines for human body fluid collection and storage, prior to proteomic analysis. A variety of body fluids that are currently being used in proteomic analysis and have potential interest in clinical practice are presented including blood plasma and serum, urine, cerebrospinal fluid, cerumen, nasal secretions, saliva, tears, breast milk, bronchoalveolar fluid, nipple aspirate fluid, amniotic fluid, bile, cervico-vaginal fluid, and seminal plasma. With no doubt these body fluids differ in the extent of their application in clinical proteomics investigations, hence in some cases the presented SOPs are established following more extensive testing (e.g., plasma, serum, urine, CSF) than others (nasal secretions, saliva, tears, breast milk, bronchoalveolar fluid, nipple aspirate fluid, amniotic fluid, bile, cervico-vaginal fluid, and seminal plasma). However, even in these latter cases, the presented protocols were reported by at least two independent groups according to the literature. We hope they can thus serve as a reliable guide for sample collection based on our current knowledge in the field and excellent starting points for proteomics investigators. It should also be pointed that variations to these protocols exist and their further refinement in the future is foreseen following the evolution of the proteomics technologies.
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Affiliation(s)
- Vasiliki Lygirou
- Biotechnology Division, Biomedical Research Foundation, Academy of Athens, Athens, 11527, Greece
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95
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Teran LM, Montes-Vizuet R, Li X, Franz T. Respiratory proteomics: from descriptive studies to personalized medicine. J Proteome Res 2014; 14:38-50. [PMID: 25382407 DOI: 10.1021/pr500935s] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Respiratory diseases are highly prevalent and affect humankind worldwide, causing extensive morbidity and mortality with the environment playing an important role. Given the complex structure of the airways, sophisticated tools are required for early diagnosis; initial symptoms are nonspecific, and the clinical diagnosis is made frequently late. Over the past few years, proteomics has made high technological progress in mass-spectrometry-based protein identification and has allowed us to gain new insights into disease mechanisms and identify potential novel therapeutic targets. This review will highlight the contributions of proteomics toward the understanding of the respiratory proteome listing potential biomarkers and its potential application to the clinic. We also outline the contributions of proteomics to creating a personalized approach in respiratory medicine.
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Affiliation(s)
- Luis M Teran
- Instituto Nacional de Enfermedades Respiratorias , Calz. de Tlalpan 4502, Distrito Federal 14080, Mexico
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96
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Xu J, Wang L, Li J. Biological network module-based model for the analysis of differential expression in shotgun proteomics. J Proteome Res 2014; 13:5743-50. [PMID: 25327611 DOI: 10.1021/pr5007203] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Protein differential expression analysis plays an important role in the understanding of molecular mechanisms as well as the pathogenesis of complex diseases. With the rapid development of mass spectrometry, shotgun proteomics using spectral counts has become a prevailing method for the quantitative analysis of complex protein mixtures. Existing methods in differential proteomics expression typically carry out analysis at the single-protein level. However, it is well-known that proteins interact with each other when they function in biological processes. In this study, focusing on biological network modules, we proposed a negative binomial generalized linear model for differential expression analysis of spectral count data in shotgun proteomics. In order to show the efficacy of the model in protein expression analysis at the level of protein modules, we conducted two simulation studies using synthetic data sets generated from theoretical distribution of count data and a real data set with shuffled counts. Then, we applied our method to a colorectal cancer data set and a nonsmall cell lung cancer data set. When compared with single-protein analysis methods, the results showed that module-based statistical model which takes account of the interactions among proteins led to more effective identification of subtle but coordinated changes at the systems level.
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Affiliation(s)
- Jia Xu
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai 200240, People's Republic of China
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97
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Rossi R, De Palma A, Benazzi L, Riccio AM, Canonica GW, Mauri P. Biomarker discovery in asthma and COPD by proteomic approaches. Proteomics Clin Appl 2014; 8:901-15. [PMID: 25186471 DOI: 10.1002/prca.201300108] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 07/01/2014] [Accepted: 09/01/2014] [Indexed: 11/07/2022]
Abstract
Asthma and chronic obstructive pulmonary disease (COPD) are multifactorial respiratory diseases, characterized by reversible and irreversible airway obstruction, respectively. Even if the primary causes of these diseases remain unknown, inflammation is a central feature that leads to progressive and permanent pulmonary tissue damage (airway remodeling) up to the total loss of lung function. Therefore, the elucidation of the inflammation mechanisms and the characterization of the biological pathways, involved in asthma and COPD pathogenesis, are relevant in finding new possible diagnostic/prognostic biomarkers and for the validation of new drug targets. In this context, current advances in proteomic approaches, especially those based on MS, provide new tools to facilitate the discovery-driven studies of new biomarkers in respiratory diseases and improve the clinical reliability of the next generation of biomarkers for these diseases consisting of multiple phenotypes. This review will report an overview of the current proteomic methods applied to the discovery of candidate biomarkers for asthma and COPD, giving a special emphasis to emerging MS-based techniques.
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Affiliation(s)
- Rossana Rossi
- Institute for Biomedical Technologies (ITB-CNR), Proteomics and Metabolomics Unit, Segrate, MI, Italy
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98
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Huasong G, Zongmei D, Jianfeng H, Xiaojun Q, Jun G, Sun G, Donglin W, Jianhong Z. Serine protease inhibitor (SERPIN) B1 suppresses cell migration and invasion in glioma cells. Brain Res 2014; 1600:59-69. [PMID: 24968089 DOI: 10.1016/j.brainres.2014.06.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 06/07/2014] [Accepted: 06/13/2014] [Indexed: 02/07/2023]
Abstract
The serine protease inhibitor (SERPIN) B1 is expressed in numerous human tumors, but little is known regarding its role in the pathophysiology of glioma. In this paper, we report that SERPINB1 expression was down-regulated in high-grade human glioma tissue samples and glioblastoma cell lines. To investigate the role of SERPINB1 in glioma migration and invasion, we generated human glioma cell lines in which SERPINB1 was either overexpressed or depleted. Overexpression of SERPINB1 suppressed, while elimination of SERPINB1 promoted, the migration and invasion of glioma cells. SERPINB1 inhibited glioma migration and invasion probably by dampening the expression of matrix metalloproteinase-2 (MMP-2). Molecular data showed that the effect of SERPINB1 in glioma cells might be mediated via sustained inactivation of the phosphorylation of focal adhesion kinase (FAK) involved in the downregulation of the expressions of MMP-2. In a multivariate analysis, high SERPINB1 expression was showed to be associated with good prognosis in glioma. In conclusion, our data suggest that SERPINB1 negatively regulates glioma cell migration and invasion probably by abrogating the expression of MMP-2 and the activation of FAK. We suggest that SERPINB1 may offer the application in clinical medicine.
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Affiliation(s)
- Gao Huasong
- Department of Neurosurgery, Fudan University Huashan Hospital, National Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Shanghai Medical College, Fudan University, Shanghai 200000, China
| | - Ding Zongmei
- Department of Pathology, Subei People's Hospital, Yangzhou 225001, Jiangsu, China
| | - Huang Jianfeng
- Department of Pathology, Subei People's Hospital, Yangzhou 225001, Jiangsu, China
| | - Qiu Xiaojun
- Department of Pathology, Subei People's Hospital, Yangzhou 225001, Jiangsu, China
| | - Guo Jun
- Department of Pathology, Subei People's Hospital, Yangzhou 225001, Jiangsu, China
| | - Guan Sun
- Department of Pathology, Subei People's Hospital, Yangzhou 225001, Jiangsu, China
| | - Wang Donglin
- Department of Pathology, Medical College, Nantong University, Nantong 226001, Jiangsu, China.
| | - Zhu Jianhong
- Department of Neurosurgery, Fudan University Huashan Hospital, National Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Shanghai Medical College, Fudan University, Shanghai 200000, China.
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99
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Application of proteomics and peptidomics to COPD. BIOMED RESEARCH INTERNATIONAL 2014; 2014:764581. [PMID: 24895607 PMCID: PMC4026877 DOI: 10.1155/2014/764581] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Accepted: 03/24/2014] [Indexed: 11/24/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is a complex disorder involving both airways and lung parenchyma, usually associated with progressive and poorly reversible airflow limitation. In order to better characterize the phenotypic heterogeneity and the prognosis of patients with COPD, there is currently an urgent need for discovery and validation of reliable disease biomarkers. Within this context, proteomic and peptidomic techniques are emerging as very valuable tools that can be applied to both systemic and pulmonary samples, including peripheral blood, induced sputum, exhaled breath condensate, bronchoalveolar lavage fluid, and lung tissues. Identification of COPD biomarkers by means of proteomic and peptidomic approaches can thus also lead to discovery of new molecular targets potentially useful to improve and personalize the therapeutic management of this widespread respiratory disease.
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100
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Madak-Erdogan Z, Ventrella R, Petry L, Katzenellenbogen BS. Novel roles for ERK5 and cofilin as critical mediators linking ERα-driven transcription, actin reorganization, and invasiveness in breast cancer. Mol Cancer Res 2014; 12:714-27. [PMID: 24505128 DOI: 10.1158/1541-7786.mcr-13-0588] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
UNLABELLED Cancer cell motility and invasiveness are fundamental characteristics of the malignant phenotype and are regulated through diverse signaling networks involving kinases and transcription factors. This study establishes an estrogen receptor (ERα)/MAPK (ERK5)/cofilin (CFL1) network that specifies the degree of breast cancer cell aggressiveness through coupling of actin reorganization and hormone receptor-mediated transcription. Using dominant negative and constitutively active forms, as well as small-molecule inhibitors of extracellular signal-regulated kinase (ERK)5 and MAP-ERK kinase (MEK)5, it was revealed that hormone activation of ERα determined the subcellular localization of ERK5, which functions as a coregulator of ERα-dependent gene transcription. Notably, ERK5 acted in concert with the actin remodeling protein, CFL1, and upon hormone exposure, both localized to active nuclear transcriptional hubs as verified by immunofluorescence and proximity ligation assays. Both ERK5 and CFL1 facilitated PAF1 recruitment to the RNA Pol II complex and both were required for regulation of gene transcription. In contrast, in cells lacking ERα, ERK5 and CFL1 localized to cytoplasmic membrane regions of high actin remodeling, promoting cell motility and invasion, thereby revealing a mechanism likely contributing to the generally poorer prognosis of patients with ERα-negative breast cancer. Thus, this study uncovers the dynamic interplay of nuclear receptor-mediated transcription and actin reorganization in phenotypes of breast cancer aggressiveness. IMPLICATIONS Identification of the ER/ERK5/CFL1 axis suggests new prognostic biomarkers and novel therapeutic avenues to moderate cancer aggressiveness.
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Affiliation(s)
- Zeynep Madak-Erdogan
- Authors' Affiliation: Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, Illinois
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