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Kartsova LA, Bessonova EA, Deev VA, Kolobova EA. Current Role of Modern Chromatography with Mass Spectrometry and Nuclear Magnetic Resonance Spectroscopy in the Investigation of Biomarkers of Endometriosis. Crit Rev Anal Chem 2023:1-24. [PMID: 36625278 DOI: 10.1080/10408347.2022.2156770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Endometriosis has a wide range of clinical manifestations, and the disease course is unpredictable, making the diagnosis a challenging task. Despite significant advances in the pathophysiology of endometriosis and various proposed theories, the exact etiology is not fully understood and is still unknown. The most commonly used biomarker of endometriosis is CA-125, however, it is nonspecific and is applied for cancers diagnosis. Therefore, the development of reliable noninvasive diagnostic tests for the early diagnosis of endometriosis remains one of the top priorities. Omics technologies are very promising approaches for constructing diagnostic models and biomarker discovery. Their use can greatly facilitate the study of such a complex disease as endometriosis. Nowadays, powerful analytical platforms commonly used in omics, such as gas and liquid chromatography with mass spectrometry and nuclear magnetic resonance (NMR) spectroscopy, have proven to be a promising tools for biomarker discovery. The aim of this review is to summarize the various features of the analytical approaches, practical challenges and features of gas and liquid chromatography with MS and NMR spectroscopy (including sample processing protocols, technological advancements, and methodology) used for profiling of metabolites, lipids, peptides and proteins in physiological fluids and tissues from patients with endometriosis. In addition, this report devotes special attention to the issue of how comprehensive analyses of these profiles can effectively contribute to the study of endometriosis. The search query included reports published between 2012 and 2022 years in PubMed, Web-of-Science, SCOPUS, Science Direct.
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Affiliation(s)
| | | | | | - Ekaterina Alekseevna Kolobova
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
- The Federal State Institute of Public Health 'The Nikiforov Russian Center of Emergency and Radiation Medicine', The Ministry of Russian Federation for Civil Defence, Emergencies and Elimination of Consequences of Natural Disasters, St. Petersburg, Russia
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Husain U, Verma P, Suvirya S, Priyadarshi K, Gupta P. An overview of mycetoma and its diagnostic dilemma: Time to move on to advanced techniques. Indian J Dermatol Venereol Leprol 2023; 89:12-17. [PMID: 36331840 DOI: 10.25259/ijdvl_615_2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 06/01/2022] [Indexed: 02/01/2023]
Abstract
The neglected tropical disease mycetoma can become extremely devastating, and can be caused both by fungi and bacteria; these are popularly known as eumycetoma and actinomycetoma respectively. The classical triad of the disease is subcutaneous swelling, multiple discharging sinuses and the presence of macroscopic granules. The present study aims to highlight the existing diagnostic modalities and the need to incorporate newer and more advanced laboratory techniques like pan fungal/pan bacterial 16S rRNA gene polymerase chain reaction (PCR) and sequencing, Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), rolling circle amplification (RCA), loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA). It is important for the medical team to be aware of the various diagnostic options (both existing and future), so that diagnosis of such a debilitating disease is never missed, both by clinicians and microbiologists/pathologists. The newer diagnostic methods discussed in this article will help in rapid, accurate diagnosis thus facilitating early treatment initiation, and decreasing the overall morbidity of the disease. In the Indian context, newer technologies need to be made available more widely. Making clinicians aware and promoting research and development in mycetoma diagnostics is the need of the hour.
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Affiliation(s)
- Uneza Husain
- Department of Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Parul Verma
- Department of Dermatology, Venereology, and Leprosy, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Swastika Suvirya
- Department of Dermatology, Venereology, and Leprosy, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Ketan Priyadarshi
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research, Pondicherry, India
| | - Prashant Gupta
- Department of Microbiology, King George's Medical University, Lucknow, Uttar Pradesh, India
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Establishment of a Potential Serum Biomarker Panel for the Diagnosis and Prognosis of Cholangiocarcinoma Using Decision Tree Algorithms. Diagnostics (Basel) 2021; 11:diagnostics11040589. [PMID: 33806004 PMCID: PMC8064492 DOI: 10.3390/diagnostics11040589] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 12/17/2022] Open
Abstract
Potential biomarkers which include S100 calcium binding protein A9 (S100A9), mucin 5AC (MUC5AC), transforming growth factor β1 (TGF-β1), and angiopoietin-2 have previously been shown to be effective for cholangiocarcinoma (CCA) diagnosis. This study attempted to measure the sera levels of these biomarkers compared with carbohydrate antigen 19-9 (CA19-9). A total of 40 serum cases of CCA, gastrointestinal cancers (non-CCA), and healthy subjects were examined by using an enzyme-linked immunosorbent assay. The panel of biomarkers was evaluated for their accuracy in diagnosing CCA and subsequently used as inputs to construct the decision tree (DT) model as a basis for binary classification. The findings showed that serum levels of S100A9, MUC5AC, and TGF-β1 were dramatically enhanced in CCA patients. In addition, 95% sensitivity and 90% specificity for CCA differentiation from healthy cases, and 70% sensitivity and 83% specificity for CCA versus non-CCA cases was obtained by a panel incorporating all five candidate biomarkers. In CCA patients with low CA19-9 levels, S100A9 might well be a complementary marker for improved diagnostic accuracy. The high levels of TGF-β1 and angiopoietin-2 were both associated with severe tumor stages and metastasis, indicating that they could be used as a reliable prognostic biomarkers panel for CCA patients. Furthermore, the outcome of the CCA burden from the Classification and Regression Tree (CART) algorithm using serial CA19-9 and S100A9 showed high diagnostic efficiency. In conclusion, results have shown the efficacy of CCA diagnosis and prognosis of the novel CCA-biomarkers panel examined herein, which may prove be useful in clinical settings.
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Implementation of MALDI Mass Spectrometry Imaging in Cancer Proteomics Research: Applications and Challenges. J Pers Med 2020; 10:jpm10020054. [PMID: 32580362 PMCID: PMC7354689 DOI: 10.3390/jpm10020054] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/12/2020] [Accepted: 06/19/2020] [Indexed: 02/07/2023] Open
Abstract
Studying the proteome–the entire set of proteins in cells, tissues, organs and body fluids—is of great relevance in cancer research, as differential forms of proteins are expressed in response to specific intrinsic and extrinsic signals. Discovering protein signatures/pathways responsible for cancer transformation may lead to a better understanding of tumor biology and to a more effective diagnosis, prognosis, recurrence and response to therapy. Moreover, proteins can act as a biomarker or potential drug targets. Hence, it is of major importance to implement proteomic, particularly mass spectrometric, approaches in cancer research, to provide new crucial insights into tumor biology. Recently, mass spectrometry imaging (MSI) approaches were implemented in cancer research, to provide individual molecular characteristics of each individual tumor while retaining molecular spatial distribution, essential in the context of personalized disease management and medicine.
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Billatos E, Duan F, Moses E, Marques H, Mahon I, Dymond L, Apgar C, Aberle D, Washko G, Spira A. Detection of early lung cancer among military personnel (DECAMP) consortium: study protocols. BMC Pulm Med 2019; 19:59. [PMID: 30845938 PMCID: PMC6407252 DOI: 10.1186/s12890-019-0825-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 02/26/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Lung cancer is the leading cause of cancer-related death due in large part to our inability to diagnose it at an early and potentially curable stage. Screening for lung cancer via low dose computed tomographic (LDCT) imaging has been demonstrated to improve mortality but also results in a high rate of false positive tests. The identification and application of non-invasive molecular biomarkers that improve the performance of CT imaging for the detection of lung cancer in high risk individuals would aid in clinical decision-making, eliminate the need for unnecessary LDCT follow-up, and further refine the screening criteria for an already large high-risk population. METHODS The Detection of Early Lung Cancer Among Military Personnel (DECAMP) consortium is conducting two multicenter prospective studies with the goals of developing an integrated panel of both airway and blood-based molecular biomarkers that discriminate benign and malignant indeterminate nodules detected on CT scan as well as predict the future development of lung cancer in high-risk individuals. To achieve these goals, DECAMP is compiling an extensive array of biospecimens including nasal brushings, serum, plasma and intrathoracic airway samples (bronchial brushings and bronchial biopsies) from normal-appearing airway epithelium. DISCUSSION This bank of samples is the foundation for multiple DECAMP efforts focused on the identification of those at greatest risk of developing lung cancer as well as the discrimination of benign and malignant pulmonary nodules. The clinical, imaging and biospecimen repositories will serve as a resource for the biomedical community and their investigation of the molecular basis of chronic respiratory disease. TRIAL REGISTRATION Retrospectively registered as NCT01785342 - DECAMP-1: Diagnosis and Surveillance of Indeterminate Pulmonary Nodules (DECAMP-1). Date of Registration: February 7, 2013. Retrospectively registered as NCT02504697 - DECAMP-2: Screening of Patients With Early Stage Lung Cancer or at High Risk for Developing Lung Cancer (DECAMP-2). Date of Registration: July 22, 2015.
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Affiliation(s)
- Ehab Billatos
- Division of Pulmonary, Allergy, and Critical Care Medicine, Boston University School of Medicine, Boston, MA 02118 USA
| | - Fenghai Duan
- Department of Biostatistics, Brown University, Providence, RI 02912 USA
| | - Elizabeth Moses
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA 02118 USA
| | - Helga Marques
- Department of Biostatistics, Brown University, Providence, RI 02912 USA
| | - Irene Mahon
- American College of Radiology Imaging Network, Philadelphia, PA 19103 USA
| | - Lindsey Dymond
- American College of Radiology Imaging Network, Philadelphia, PA 19103 USA
| | - Charles Apgar
- American College of Radiology Imaging Network, Philadelphia, PA 19103 USA
| | - Denise Aberle
- Department of Radiological Sciences, University of California at Los Angeles, Los Angeles, CA 90024 USA
| | - George Washko
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s University, Boston, MA 02115 USA
| | - Avrum Spira
- Division of Pulmonary, Allergy, and Critical Care Medicine, Boston University School of Medicine, Boston, MA 02118 USA
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA 02118 USA
| | - on behalf of the DECAMP investigators
- Division of Pulmonary, Allergy, and Critical Care Medicine, Boston University School of Medicine, Boston, MA 02118 USA
- Department of Biostatistics, Brown University, Providence, RI 02912 USA
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA 02118 USA
- American College of Radiology Imaging Network, Philadelphia, PA 19103 USA
- Department of Radiological Sciences, University of California at Los Angeles, Los Angeles, CA 90024 USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s University, Boston, MA 02115 USA
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Belczacka I, Latosinska A, Metzger J, Marx D, Vlahou A, Mischak H, Frantzi M. Proteomics biomarkers for solid tumors: Current status and future prospects. MASS SPECTROMETRY REVIEWS 2019; 38:49-78. [PMID: 29889308 DOI: 10.1002/mas.21572] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 05/08/2018] [Indexed: 06/08/2023]
Abstract
Cancer is a heterogeneous multifactorial disease, which continues to be one of the main causes of death worldwide. Despite the extensive efforts for establishing accurate diagnostic assays and efficient therapeutic schemes, disease prevalence is on the rise, in part, however, also due to improved early detection. For years, studies were focused on genomics and transcriptomics, aiming at the discovery of new tests with diagnostic or prognostic potential. However, cancer phenotypic characteristics seem most likely to be a direct reflection of changes in protein metabolism and function, which are also the targets of most drugs. Investigations at the protein level are therefore advantageous particularly in the case of in-depth characterization of tumor progression and invasiveness. Innovative high-throughput proteomic technologies are available to accurately evaluate cancer formation and progression and to investigate the functional role of key proteins in cancer. Employing these new highly sensitive proteomic technologies, cancer biomarkers may be detectable that contribute to diagnosis and guide curative treatment when still possible. In this review, the recent advances in proteomic biomarker research in cancer are outlined, with special emphasis placed on the identification of diagnostic and prognostic biomarkers for solid tumors. In view of the increasing number of screening programs and clinical trials investigating new treatment options, we discuss the molecular connections of the biomarkers as well as their potential as clinically useful tools for diagnosis, risk stratification and therapy monitoring of solid tumors.
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Affiliation(s)
- Iwona Belczacka
- Mosaiques-Diagnostics GmbH, Hannover, Germany
- University Hospital RWTH Aachen, Institute for Molecular Cardiovascular Research (IMCAR), Aachen, Germany
| | | | | | - David Marx
- Hôpitaux Universitaires de Strasbourg, Service de Transplantation Rénale, Strasbourg, France
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), University of Strasbourg, National Center for Scientific Research (CNRS), Institut Pluridisciplinaire Hubert Curien (IPHC) UMR 7178, Strasbourg, France
| | - Antonia Vlahou
- Biotechnology Division, Biomedical Research Foundation, Academy of Athens (BRFAA), Athens, Greece
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Wang Z, Zhang X. Single Cell Proteomics for Molecular Targets in Lung Cancer: High-Dimensional Data Acquisition and Analysis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1068:73-87. [PMID: 29943297 DOI: 10.1007/978-981-13-0502-3_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In the proteomic and genomic era, lung cancer researchers are increasingly under challenge with traditional protein analyzing tools. High output, multiplexed analytical procedures are in demand for disclosing the post-translational modification, molecular interactions and signaling pathways of proteins precisely, specifically, dynamically and systematically, as well as for identifying novel proteins and their functions. This could be better realized by single-cell proteomic methods than conventional proteomic methods. Using single-cell proteomic tools including flow cytometry, mass cytometry, microfluidics and chip technologies, chemical cytometry, single-cell western blotting, the quantity and functions of proteins are analyzed simultaneously. Aside from deciphering disease mechanisms, single-cell proteomic techniques facilitate the identification and screening of biomarkers, molecular targets and promising compounds as well. This review summarized single-cell proteomic tools and their use in lung cancer.
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Affiliation(s)
- Zheng Wang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Xiaoju Zhang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Zhengzhou, China. .,Biomedical Research Center, Zhengzhou University People's Hospital, Zhengzhou, China.
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Roointan A, Ahmad Mir T, Ibrahim Wani S, Mati-Ur-Rehman, Hussain KK, Ahmed B, Abrahim S, Savardashtaki A, Gandomani G, Gandomani M, Chinnappan R, Akhtar MH. Early detection of lung cancer biomarkers through biosensor technology: A review. J Pharm Biomed Anal 2018; 164:93-103. [PMID: 30366148 DOI: 10.1016/j.jpba.2018.10.017] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 10/05/2018] [Accepted: 10/07/2018] [Indexed: 02/07/2023]
Abstract
Lung cancer is undoubtedly one of the most serious health issues of the 21 st century. It is the second leading cause of cancer-related deaths in both men and women worldwide, accounting for about 1.5 million deaths annually. Despite advances in the treatment of lung cancer with new pharmaceutical products and technological improvements, morbidity and mortality rates remains a significant challenge for the cancer biologists and oncologists. The vast majority of lung cancer patients present with advanced-stage of pathological process that ultimately leads to poor prognosis and a five-year survival rate less than 20%. Early and accurate screening and analysis using cost-effective means are urgently needed to effectively diagnose the disease, improve the survival rate or to reduce mortality and morbidity associated with lung cancer patients. Thus, the only hope for early recognition of risk factors and timely diagnosis and treatment of lung cancer is biosensors technology. Novel biosensing based diagnostics approaches for predicting metastatic risks are likely to have significant therapeutic and clinical impact in the near future. This article systematically provides a brief overview of various biosensing platforms for identification of lung cancer disease biomarkers, with a specific focus on recent advancements in electrochemical and optical biosensors, analytical performances of different biosensors, challenges and further research opportunities for routine clinical analysis.
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Affiliation(s)
- Amir Roointan
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Tanveer Ahmad Mir
- Division of Biomedical System Engineering, Graduate School of Science and Engineering for Education, University of Toyama, Toyama, Japan; Department of Chemistry and Institute of BioPhysio Sensor Technology (IBST), Pusan National University, Busan, 46241, South Korea; Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, Al Takhassusi Road, Riyadh, 11533, Saudi Arabia; Toyama Nanotechnology Manufacturing Cluster, Toyama, Japan.
| | - Shadil Ibrahim Wani
- Department of Immunology and Molecular Medicine,Sher-i-Kashmir Institute of Medical Sciences, Srinagar, India
| | - Mati-Ur-Rehman
- Department of Radiological Sciences, Graduate school of Medicine and Pharmaceutical Sciences, University of Toyama, Japan
| | - Khalil Khadim Hussain
- Department of Chemistry and Institute of BioPhysio Sensor Technology (IBST), Pusan National University, Busan, 46241, South Korea; Department of pharmacy, University of central Punjab 1-Khayaban-e-Jinnah, Johar Town, Lahore, Pakistan
| | - Bilal Ahmed
- Department of Intellectual Information Engineering, Graduate School of Science and Engineering for Education, University of Toyama, Toyama, Japan
| | - Shugufta Abrahim
- Department of Intellectual Information Engineering, Graduate School of Science and Engineering for Education, University of Toyama, Toyama, Japan
| | - Amir Savardashtaki
- Department of Environmental Sciences, Cyprus International University, Nicosia, Cyprus
| | - Ghazaal Gandomani
- Department of Bioengineering, Biotechnology Research Center, Cyprus International University, Nicosia, Cyprus
| | - Molood Gandomani
- Department of pharmacy, University of central Punjab 1-Khayaban-e-Jinnah, Johar Town, Lahore, Pakistan
| | - Raja Chinnappan
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, Al Takhassusi Road, Riyadh, 11533, Saudi Arabia
| | - Mahmood H Akhtar
- Department of Chemistry and Institute of BioPhysio Sensor Technology (IBST), Pusan National University, Busan, 46241, South Korea
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Billatos E, Vick JL, Lenburg ME, Spira AE. The Airway Transcriptome as a Biomarker for Early Lung Cancer Detection. Clin Cancer Res 2018; 24:2984-2992. [PMID: 29463557 DOI: 10.1158/1078-0432.ccr-16-3187] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/06/2017] [Accepted: 02/16/2018] [Indexed: 12/17/2022]
Abstract
Lung cancer remains the leading cause of cancer-related death due to its advanced stage at diagnosis. Early detection of lung cancer can be improved by better defining who should be screened radiographically and determining which imaging-detected pulmonary nodules are malignant. Gene expression biomarkers measured in normal-appearing airway epithelium provide an opportunity to use lung cancer-associated molecular changes in this tissue for early detection of lung cancer. Molecular changes in the airway may result from an etiologic field of injury and/or field cancerization. The etiologic field of injury reflects the aberrant physiologic response to carcinogen exposure that creates a susceptible microenvironment for cancer initiation. In contrast, field cancerization reflects effects of "first-hit" mutations in a clone of cells from which the tumor ultimately arises or the effects of the tumor on the surrounding tissue. These fields might have value both for assessing lung cancer risk and diagnosis. Cancer-associated gene expression changes in the bronchial airway have recently been used to develop and validate a 23-gene classifier that improves the diagnostic yield of bronchoscopy for lung cancer among intermediate-risk patients. Recent studies have demonstrated that these lung cancer-related gene expression changes extend to nasal epithelial cells that can be sampled noninvasively. While the bronchial gene expression biomarker is being adopted clinically, further work is necessary to explore the potential clinical utility of gene expression profiling in the nasal epithelium for lung cancer diagnosis, lung cancer risk assessment, and precision medicine for lung cancer treatment and chemoprevention. Clin Cancer Res; 24(13); 2984-92. ©2018 AACR.
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Affiliation(s)
- Ehab Billatos
- Section of Computational Biomedicine, Department of Medicine and BU-BMC Cancer Center, Boston University, Boston, Massachusetts
| | - Jessica L Vick
- Section of Computational Biomedicine, Department of Medicine and BU-BMC Cancer Center, Boston University, Boston, Massachusetts
| | - Marc E Lenburg
- Section of Computational Biomedicine, Department of Medicine and BU-BMC Cancer Center, Boston University, Boston, Massachusetts
| | - Avrum E Spira
- Section of Computational Biomedicine, Department of Medicine and BU-BMC Cancer Center, Boston University, Boston, Massachusetts.
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Serum lipid profile discriminates patients with early lung cancer from healthy controls. Lung Cancer 2017; 112:69-74. [DOI: 10.1016/j.lungcan.2017.07.036] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 07/11/2017] [Accepted: 07/31/2017] [Indexed: 01/09/2023]
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Lobb RJ, Hastie ML, Norris EL, van Amerongen R, Gorman JJ, Möller A. Oncogenic transformation of lung cells results in distinct exosome protein profile similar to the cell of origin. Proteomics 2017; 17. [DOI: 10.1002/pmic.201600432] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 06/09/2017] [Indexed: 01/01/2023]
Affiliation(s)
- Richard J. Lobb
- Tumour Microenvironment Laboratory; QIMR Berghofer Medical Research Institute; Herston Australia
| | - Marcus L. Hastie
- Protein Discovery Centre; QIMR Berghofer Medical Research Institute; Herston Australia
| | - Emma L. Norris
- Protein Discovery Centre; QIMR Berghofer Medical Research Institute; Herston Australia
| | - Rosa van Amerongen
- Tumour Microenvironment Laboratory; QIMR Berghofer Medical Research Institute; Herston Australia
| | - Jeffrey J. Gorman
- Protein Discovery Centre; QIMR Berghofer Medical Research Institute; Herston Australia
- Institute for Molecular Bioscience; University of Queensland; Brisbane Australia
| | - Andreas Möller
- Tumour Microenvironment Laboratory; QIMR Berghofer Medical Research Institute; Herston Australia
- School of Medicine; University of Queensland; Brisbane Australia
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Identification of protein biomarkers and signaling pathways associated with prostate cancer radioresistance using label-free LC-MS/MS proteomic approach. Sci Rep 2017; 7:41834. [PMID: 28225015 PMCID: PMC5320484 DOI: 10.1038/srep41834] [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: 09/06/2016] [Accepted: 12/28/2016] [Indexed: 12/20/2022] Open
Abstract
Identifying biomarkers and signaling pathways are important for the management of prostate cancer (CaP) radioresistance. In this study, we identified differential proteins and signaling pathways from parental CaP cell lines and CaP radioresistant (RR) sublines using a label-free LC-MS/MS proteomics approach. A total of 309 signaling pathway proteins were identified to be significantly altered between CaP and CaP-RR cells (p ≤ 0.05, fold differences >1.5, ≥80% power). Among these proteins, nineteen are common among three paired CaP cell lines and associated with metastasis, progression and radioresistance. The PI3K/Akt, VEGF and glucose metabolism pathways were identified as the main pathways associated with CaP radioresistance. In addition, the identified potential protein markers were further validated in CaP-RR cell lines and subcutaneous (s.c) animal xenografts by western blotting and immunohistochemistry, respectively and protein aldolase A (ALDOA) was selected for a radiosensitivity study. We found the depletion of ALDOA combined with radiotherapy effectively reduced colony formation, induced more apoptosis and increased radiosensitivity in CaP-RR cells. Our findings indicate that CaP radioresistance is caused by multifactorial traits and downregulation of ALDOA increases radiosensitivity in CaP-RR cells, suggesting that controlling these identified proteins or signaling pathways in combination with radiotherapy may hold promise to overcome CaP radioresistance.
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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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Widlak P, Pietrowska M, Polanska J, Marczyk M, Ros-Mazurczyk M, Dziadziuszko R, Jassem J, Rzyman W. Serum mass profile signature as a biomarker of early lung cancer. Lung Cancer 2016; 99:46-52. [PMID: 27565913 DOI: 10.1016/j.lungcan.2016.06.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 05/12/2016] [Accepted: 06/11/2016] [Indexed: 01/10/2023]
Abstract
OBJECTIVES Circulating molecular biomarkers of lung cancer may allow the pre-selection of candidates for computed tomography screening or increase its efficacy. We aimed to identify features of serum mass profile distinguishing individuals with early lung cancer from healthy participants of the lung cancer screening program. METHODS Blood samples were collected during a low-dose computed tomography (LD-CT) screening program performed by one institution (Medical University of Gdansk, Poland). MALDI-ToF mass spectrometry was used to characterize the low-molecular-weight (1000-14,000Da) serum fraction. The analysis comprised 95 patients with early stage lung cancer (including 30 screen-detected cases) and a matched group of 285 healthy controls. The cases were split into two independent cohorts (discovery and validation), analyzed separately 6 months apart. RESULTS Several molecular components of serum (putatively components of endogenous peptidome) discriminating patients with early lung cancer from controls were identified in a discovery cohort. This allowed building an effective cancer classifier as a model tuned to maximize negative predictive value, with an area under the curve (AUC) of 0.88, a negative predictive value of 100%, and a positive predictive value of 48%. However, the classifier performed worse in a validation cohort including independent sample sets (AUC 0.73, NPV 88% and PPV 30%). CONCLUSIONS We developed a serum mass profile-based signature identifying patients with early lung cancer. Although this marker has insufficient value as a stand-alone preselecting tool for LD-CT screening, its potential clinical usefulness in evaluation of indeterminate pulmonary nodules deserves further investigation.
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Affiliation(s)
- Piotr Widlak
- Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, ul. Wybrzeże Armii Krajowej 15, 44-100 Gliwice, Poland.
| | - Monika Pietrowska
- Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, ul. Wybrzeże Armii Krajowej 15, 44-100 Gliwice, Poland.
| | - Joanna Polanska
- Silesian University of Technology, ul. Akademicka 16, 44-100 Gliwice, Poland.
| | - Michal Marczyk
- Silesian University of Technology, ul. Akademicka 16, 44-100 Gliwice, Poland.
| | - Malgorzata Ros-Mazurczyk
- Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, ul. Wybrzeże Armii Krajowej 15, 44-100 Gliwice, Poland.
| | | | - Jacek Jassem
- Medical University of Gdańsk, ul. Dębinki 7, 80-211 Gdańsk, Poland.
| | - Witold Rzyman
- Medical University of Gdańsk, ul. Dębinki 7, 80-211 Gdańsk, Poland.
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15
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Gebretsadik G, Menon MKC. Proteomics and Its Applications in Diagnosis of Auto Immune Diseases. ACTA ACUST UNITED AC 2016. [DOI: 10.4236/oji.2016.61003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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16
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Kim YJ, Sertamo K, Pierrard MA, Mesmin C, Kim SY, Schlesser M, Berchem G, Domon B. Verification of the biomarker candidates for non-small-cell lung cancer using a targeted proteomics approach. J Proteome Res 2015; 14:1412-9. [PMID: 25597550 DOI: 10.1021/pr5010828] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Lung cancer, with its high metastatic potential and high mortality rate, is the worldwide leading cause of cancer-related deaths. High-throughput "omics"-based platforms have accelerated the discovery of biomarkers for lung cancer, and the resulting candidates are to be evaluated for their diagnostic potential as noninvasive biomarkers. The evaluation of the biomarker candidates involves the quantitative measurement of large numbers of proteins in bodily fluids using advanced mass spectrometric techniques. In this study, a robust pipeline based on targeted proteomics was developed for biomarker verification in plasma samples and applied to verifying lung cancer biomarker candidates. Highly multiplexed liquid chromatrography-selected reaction monitoring (LC-SRM) assays for 95 potential tumor markers for non-small-cell lung cancer (NSCLC) were generated to screen plasma samples obtained from 72, early to late stage, patients. A total of 17 proteins were verified as potent tumor markers detectable in plasma and, where available, verified by enzyme-linked immunosorbent assays (ELISAs). A novel plasma-based biomarker, zyxin, fulfilled the criteria for a potential early diagnostic marker for NSCLC.
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Affiliation(s)
- Yeoun Jin Kim
- Luxembourg Clinical Proteomics Center, Luxembourg Institute of Health , Strassen L-1445, Luxembourg
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17
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Abstract
Enriched by a decade of remarkable developments, matrix-assisted laser desorption ionization imaging mass spectrometry (MALDI IMS) has witnessed a phenomenal expansion. Initially introduced for the mapping of peptides and intact proteins from mammalian tissue sections, MALDI IMS applications now extend to a wide range of molecules including peptides, lipids, metabolites and xenobiotics. Technology and methodology are quickly evolving to push the limits of the technique forward. Within a short period of time, numerous protocols and concepts have been developed and introduced in tissue section preparation, nonexhaustively including in situ tissue chemistries and solvent-free matrix depositions. Considering the past progress and current capabilities, this Review aims to cover the different aspects and challenges of tissue section preparation for MALDI IMS.
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Abstract
INTRODUCTION Small-cell lung cancer (SCLC) is the most aggressive subtype of lung cancer, with no early detection strategy or targeted therapy currently available. We hypothesized that difference gel electrophoresis (DIGE) may identify membrane-associated proteins (MAPs) specific to SCLC, advance our understanding of SCLC biology, and discover new biomarkers of SCLC. METHODS MAP lysates were prepared from three SCLCs, three non-small-cell lung cancers, and three immortalized normal bronchial epithelial cell lines and coanalyzed by DIGE. Subsequent protein identification was performed by mass spectrometry. Proteins were submitted to Ingenuity Pathway Analysis. Candidate biomarkers were validated by Western blotting (WB) and immunohistochemistry (IHC). RESULTS Principal component analysis on the global DIGE data set demonstrated that the four replicates derived from each of the nine cell lines clustered closely, as did samples within the same histological group. One hundred thirty-seven proteins were differentially expressed in SCLC compared with non-small-cell lung cancer and immortalized normal bronchial epithelial cells. These proteins were overrepresented in cellular/tissue morphology networks. Dihydropyrimidinase-related protein 2, guanine nucleotide-binding protein alpha-q, laminin receptor 1, pontin, and stathmin 1 were selected as candidate biomarkers among MAPs overexpressed in SCLC. Overexpression of all candidates but RSSA in SCLC was verified by WB and/or IHC on tissue microarrays. These proteins were significantly associated with SCLC histology and survival in univariables analyses. CONCLUSION DIGE analysis of a membrane-associated subproteome discovered overexpression of dihydropyrimidinase-related protein 2, guanine nucleotide-binding protein alpha-q, RUVB1, and stathmin 1 in SCLC. Results were verified by WB and/or IHC in primary tumors, suggesting that investigating their functional relevance in SCLC progression is warranted. Association with survival requires further validation in larger clinical data sets.
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Hirales Casillas CE, Flores Fernández JM, Camberos EP, Herrera López EJ, Pacheco GL, Velázquez MM. Current status of circulating protein biomarkers to aid the early detection of lung cancer. Future Oncol 2014; 10:1501-13. [DOI: 10.2217/fon.14.21] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
ABSTRACT: Considerable efforts have been undertaken to produce an effective screening method to reduce lung cancer mortality. Imaging tools such as low-dose computed tomography has shown an increase in the detection of early disease and a reduction in the rate of death. This screening modality has, however, several limitations, such as overdiagnosis and a high rate of false positives. Therefore, new screening methods, such as the use of circulating protein biomarkers, have emerged as an option that could complement imaging studies. In this review, current imaging techniques applied to lung cancer screening protocols are presented, as well as up-to-date status of circulating protein biomarker panels that may improve lung cancer diagnosis. Additionally, diverse statistical and artificial intelligence tools applied to the design and optimization of these panels are discussed along with the presentation of two commercially available blood tests recently developed to help detect lung cancer early.
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Affiliation(s)
- Carlos Enrique Hirales Casillas
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco Avenida Normalistas 800, Colonia Colinas de la Normal, 44270, Guadalajara, Jalisco, México
| | - José Miguel Flores Fernández
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco Avenida Normalistas 800, Colonia Colinas de la Normal, 44270, Guadalajara, Jalisco, México
| | - Eduardo Padilla Camberos
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco Avenida Normalistas 800, Colonia Colinas de la Normal, 44270, Guadalajara, Jalisco, México
| | - Enrique J Herrera López
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco Avenida Normalistas 800, Colonia Colinas de la Normal, 44270, Guadalajara, Jalisco, México
| | - Gisela Leal Pacheco
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco Avenida Normalistas 800, Colonia Colinas de la Normal, 44270, Guadalajara, Jalisco, México
| | - Moisés Martínez Velázquez
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco Avenida Normalistas 800, Colonia Colinas de la Normal, 44270, Guadalajara, Jalisco, México
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Hassanein M, Carbone DP. Serum Proteomic Biomarkers. Lung Cancer 2014. [DOI: 10.1002/9781118468791.ch5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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21
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Yu H, Huang X, Zhu Z, Hu Y, Ou W, Zhang L, Zhou N. Significance of combined detection of LunX mRNA and tumor markers in diagnosis of lung carcinoma. Chin J Cancer Res 2014; 26:89-94. [PMID: 24653630 DOI: 10.3978/j.issn.1000-9604.2014.02.04] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 02/07/2014] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVE To evaluate the significance of combined detection of LunX mRNA, carcinoembryonic antigen (CEA), neuron-specific enolase (NSE), and cytokeratin 21-1 fragment (CYFRA21-1) in clinical diagnosis of lung carcinoma. METHODS Based on the quantitative RT-PCR and chemiluminescence immunoassay, the expression levels of LunX mRNA, CEA, NSE, and CYFRA21-1 in 113 patients with lung carcinoma (case group) and 30 healthy participants (control group) were detected. Meantime, the sensitivity, specificity, and accuracy of the combination detection were also explored. RESULTS The positive rates of LunX mRNA in peripheral blood and CEA, NSE, and CYFRA21-1 in serum were significantly higher in case group than those in control group ((χ) (2)=17.295, 16.825, 19.148, and 17.450; P<0.05). There was no statistical significance when positive rate of LunX mRNA was evaluated among different pathological types ((χ) (2)=0.047, P>0.05). The positive rate of LunX mRNA in stage I + II, III, and IV had a significantly increasing tendency ((χ) (2)=10.565, 32.462, P<0.05). The positive rate of CYFRA21-1 was highest in squamous carcinoma (78.5%), the positive rate of NSE was highest in small cell carcinoma (86.7%), and the positive rate of CEA wag highest in lung adenocarcinoma (80.4%). The sensitivity and accuracy of the combination detection were 91.1% and 88.1%, respectively. CONCLUSIONS The combined detection of LunX mRNA and tumor markers (TMs) including CEA, NSE, and CYFRA21-1 in peripheral blood is helpful to increase the diagnostic accuracy of lung cancer. Also, it can inform the pathological typing of lung carcinoma.
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Affiliation(s)
- Hui Yu
- 1 Department of Thoracic Surgery, Sun Yat-Sen University Cancer Center; State Key Laboratory of Oncology in South China ; Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China ; 2 Department of Medical Oncology, Sun Yat-Sen University Cancer Center; State Key Laboratory of Oncology in South China ; Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China
| | - Xiuying Huang
- 1 Department of Thoracic Surgery, Sun Yat-Sen University Cancer Center; State Key Laboratory of Oncology in South China ; Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China ; 2 Department of Medical Oncology, Sun Yat-Sen University Cancer Center; State Key Laboratory of Oncology in South China ; Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China
| | - Zhihua Zhu
- 1 Department of Thoracic Surgery, Sun Yat-Sen University Cancer Center; State Key Laboratory of Oncology in South China ; Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China ; 2 Department of Medical Oncology, Sun Yat-Sen University Cancer Center; State Key Laboratory of Oncology in South China ; Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China
| | - Yi Hu
- 1 Department of Thoracic Surgery, Sun Yat-Sen University Cancer Center; State Key Laboratory of Oncology in South China ; Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China ; 2 Department of Medical Oncology, Sun Yat-Sen University Cancer Center; State Key Laboratory of Oncology in South China ; Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China
| | - Wei Ou
- 1 Department of Thoracic Surgery, Sun Yat-Sen University Cancer Center; State Key Laboratory of Oncology in South China ; Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China ; 2 Department of Medical Oncology, Sun Yat-Sen University Cancer Center; State Key Laboratory of Oncology in South China ; Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China
| | - Lanjun Zhang
- 1 Department of Thoracic Surgery, Sun Yat-Sen University Cancer Center; State Key Laboratory of Oncology in South China ; Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China ; 2 Department of Medical Oncology, Sun Yat-Sen University Cancer Center; State Key Laboratory of Oncology in South China ; Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China
| | - Ningning Zhou
- 1 Department of Thoracic Surgery, Sun Yat-Sen University Cancer Center; State Key Laboratory of Oncology in South China ; Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China ; 2 Department of Medical Oncology, Sun Yat-Sen University Cancer Center; State Key Laboratory of Oncology in South China ; Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China
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Hudler P, Kocevar N, Komel R. Proteomic approaches in biomarker discovery: new perspectives in cancer diagnostics. ScientificWorldJournal 2014; 2014:260348. [PMID: 24550697 PMCID: PMC3914447 DOI: 10.1155/2014/260348] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 10/08/2013] [Indexed: 12/14/2022] Open
Abstract
Despite remarkable progress in proteomic methods, including improved detection limits and sensitivity, these methods have not yet been established in routine clinical practice. The main limitations, which prevent their integration into clinics, are high cost of equipment, the need for highly trained personnel, and last, but not least, the establishment of reliable and accurate protein biomarkers or panels of protein biomarkers for detection of neoplasms. Furthermore, the complexity and heterogeneity of most solid tumours present obstacles in the discovery of specific protein signatures, which could be used for early detection of cancers, for prediction of disease outcome, and for determining the response to specific therapies. However, cancer proteome, as the end-point of pathological processes that underlie cancer development and progression, could represent an important source for the discovery of new biomarkers and molecular targets for tailored therapies.
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Affiliation(s)
- Petra Hudler
- Medical Centre for Molecular Biology, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Nina Kocevar
- Medical Centre for Molecular Biology, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Radovan Komel
- Medical Centre for Molecular Biology, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
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23
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Kinnula VL, Ishikawa N, Bergmann U, Ohlmeier S. Proteomic approaches for studying human parenchymal lung diseases. Expert Rev Proteomics 2014; 6:619-29. [DOI: 10.1586/epr.09.80] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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24
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Pastor MD, Nogal A, Molina-Pinelo S, Carnero A, Paz-Ares L. Proteomic biomarkers in lung cancer. Clin Transl Oncol 2013; 15:671-82. [DOI: 10.1007/s12094-013-1034-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 03/25/2013] [Indexed: 12/12/2022]
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25
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Indovina P, Marcelli E, Pentimalli F, Tanganelli P, Tarro G, Giordano A. Mass spectrometry-based proteomics: the road to lung cancer biomarker discovery. MASS SPECTROMETRY REVIEWS 2013; 32:129-142. [PMID: 22829143 DOI: 10.1002/mas.21355] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2011] [Revised: 04/18/2012] [Accepted: 04/18/2012] [Indexed: 06/01/2023]
Abstract
Lung cancer is the leading cause of cancer death in men and women in Western nations, and is among the deadliest cancers with a 5-year survival rate of 15%. The high mortality caused by lung cancer is attributable to a late-stage diagnosis and the lack of effective treatments. So, it is crucial to identify new biomarkers that could function not only to detect lung cancer at an early stage but also to shed light on the molecular mechanisms that underlie cancer development and serve as the basis for the development of novel therapeutic strategies. Considering that DNA-based biomarkers for lung cancer showed inadequate sensitivity, specificity, and reproducibility, proteomics could represent a better tool for the identification of useful biomarkers and therapeutic targets for this cancer type. Among the proteomics technologies, the most powerful tool is mass spectrometry. In this review, we describe studies that use mass spectrometry-based proteomics technologies to analyze tumor proteins and peptides, which might represent new diagnostic, prognostic, and predictive markers for lung cancer. We focus in particular on those findings that hold promise to impact significantly on the clinical management of this disease.
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MESH Headings
- Animals
- Antineoplastic Agents/therapeutic use
- Biomarkers/blood
- Biomarkers/metabolism
- Biomarkers, Tumor/blood
- Biomarkers, Tumor/chemistry
- Biomarkers, Tumor/metabolism
- Chromatography, High Pressure Liquid
- Glycosylation/drug effects
- Humans
- Lung Neoplasms/blood
- Lung Neoplasms/diagnosis
- Lung Neoplasms/drug therapy
- Lung Neoplasms/metabolism
- Pleural Effusion, Malignant/blood
- Pleural Effusion, Malignant/drug therapy
- Pleural Effusion, Malignant/metabolism
- Prognosis
- Protein Processing, Post-Translational/drug effects
- Proteomics/methods
- Saliva/chemistry
- Saliva/drug effects
- Spectrometry, Mass, Electrospray Ionization
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Tandem Mass Spectrometry
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Affiliation(s)
- Paola Indovina
- Department of Human Pathology and Oncology, University of Siena, Siena, Italy
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Thomas A, Patterson NH, Laveaux Charbonneau J, Chaurand P. Orthogonal organic and aqueous-based washes of tissue sections to enhance protein sensitivity by MALDI imaging mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:42-48. [PMID: 23303746 DOI: 10.1002/jms.3114] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 09/26/2012] [Accepted: 09/27/2012] [Indexed: 06/01/2023]
Abstract
Imaging mass spectrometry (IMS) is an emergent and innovative approach for measuring the composition, abundance and regioselectivity of molecules within an investigated area of fixed dimension. Although providing unprecedented molecular information compared with conventional MS techniques, enhancement of protein signature by IMS is still necessary and challenging. This paper demonstrates the combination of conventional organic washes with an optimized aqueous-based buffer for tissue section preparation before matrix-assisted laser desorption/ionization (MALDI) IMS of proteins. Based on a 500 mM ammonium formate in water-acetonitrile (9:1; v/v, 0.1% trifluororacetic acid, 0.1% Triton) solution, this buffer wash has shown to significantly enhance protein signature by profiling and IMS (~fourfold) when used after organic washes (70% EtOH followed by 90% EtOH), improving the quality and number of ion images obtained from mouse kidney and a 14-day mouse fetus whole-body tissue sections, while maintaining a similar reproducibility with conventional tissue rinsing. Even if some protein losses were observed, the data mining has demonstrated that it was primarily low abundant signals and that the number of new peaks found is greater with the described procedure. The proposed buffer has thus demonstrated to be of high efficiency for tissue section preparation providing novel and complementary information for direct on-tissue MALDI analysis compared with solely conventional organic rinsing.
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Affiliation(s)
- Aurélien Thomas
- Department of Chemistry, University of Montreal, Montreal, Quebec, Canada
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27
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Lai JH, She TF, Juang YM, Tsay YG, Huang AH, Yu SL, Chen JJW, Lai CC. Comparative proteomic profiling of human lung adenocarcinoma cells (CL 1-0) expressing miR-372. Electrophoresis 2012; 33:675-88. [PMID: 22451061 DOI: 10.1002/elps.201100329] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Lung cancer is a common malignancy and has a poor overall prognosis. Widespread metastasis is a common phenomenon in non-small cell lung cancer (NSCLC). It has been demonstrated that cancer relapse and survival can be predicted by the presence of a five-microRNA (miRNA) signature independent of stage or histologic type in NSCLC patients. Among the five miRNAs in the signature, miR-372 has been shown to play a significant role in metastasis and in the development of human testicular germ cell tumors. In addition, there is evidence that miR-372 posttranscriptionally downregulates large tumor suppressor, homolog 2 (Lats2), resulting in tumorigenesis and proliferation. To further investigate the cellular mechanisms involved in miR-372-induced silencing, we conducted a comparative proteomic analysis of NSCLC CL 1-0 cells expressing miRNA-372 and/or vector only by using two-dimensional gel electrophoresis (2DE), two-dimensional difference gel electrophoresis (2D-DIGE), and LC/MS/MS. Proteins identified as being up- or downregulated were further classified according to their biological functions. Many of the proteins identified in our study may be potential diagnostic biomarkers of NSCLC, particularly phosphorylated eIF4A-I.
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Affiliation(s)
- Juo-Hsin Lai
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
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28
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Hassanein M, Callison JC, Callaway-Lane C, Aldrich MC, Grogan EL, Massion PP. The state of molecular biomarkers for the early detection of lung cancer. Cancer Prev Res (Phila) 2012; 5:992-1006. [PMID: 22689914 DOI: 10.1158/1940-6207.capr-11-0441] [Citation(s) in RCA: 157] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Using biomarkers to select the most at-risk population, to detect the disease while measurable and yet not clinically apparent has been the goal of many investigations. Recent advances in molecular strategies and analytic platforms, including genomics, epigenomics, proteomics, and metabolomics, have identified increasing numbers of potential biomarkers in the blood, urine, exhaled breath condensate, bronchial specimens, saliva, and sputum, but none have yet moved to the clinical setting. Therefore, there is a recognized gap between the promise and the product delivery in the cancer biomarker field. In this review, we define clinical contexts where risk and diagnostic biomarkers may have use in the management of lung cancer, identify the most relevant candidate biomarkers of early detection, provide their state of development, and finally discuss critical aspects of study design in molecular biomarkers for early detection of lung cancer.
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Affiliation(s)
- Mohamed Hassanein
- Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt-Ingram Cancer Center, Nashville TN 37232, USA
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29
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Kowdley G, Srikantan S, Abdelmohsen K, Gorospe M, Khan J. Molecular biology techniques for the surgeon. World J Surg Proced 2012; 2:5-15. [DOI: 10.5412/wjsp.v2.i2.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
New technologies are constantly being introduced into the medical and surgical fields. These technologies come in the form of newer medicines, imaging methods and prognostic tools, among others, and allow clinicians to make more rational and informed decisions on the care of their patients. Many of these technologies utilize advanced techniques which are at the forefront of many research fields and represent a transition of bench advances into the clinical realm. This review will highlight four technologies that are at the forefront in the treatment of oncology patients treated by surgeons on a daily basis. Circulating tumor cells, microarray analysis, proteomic studies and rapid sequencing technologies will be highlighted. These technologies will be reviewed and their potential use in the care of surgical patients will be discussed.
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30
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Thomas A, Charbonneau JL, Fournaise E, Chaurand P. Sublimation of New Matrix Candidates for High Spatial Resolution Imaging Mass Spectrometry of Lipids: Enhanced Information in Both Positive and Negative Polarities after 1,5-Diaminonapthalene Deposition. Anal Chem 2012; 84:2048-54. [DOI: 10.1021/ac2033547] [Citation(s) in RCA: 250] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Aurélien Thomas
- Department of Chemistry, University of Montreal, Montreal, Quebec, Canada
| | | | - Erik Fournaise
- Department of Chemistry, University of Montreal, Montreal, Quebec, Canada
| | - Pierre Chaurand
- Department of Chemistry, University of Montreal, Montreal, Quebec, Canada
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31
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Zeng GQ, Zhang PF, Deng X, Yu FL, Li C, Xu Y, Yi H, Li MY, Hu R, Zuo JH, Li XH, Wan XX, Qu JQ, He QY, Li JH, Ye X, Chen Y, Li JY, Xiao ZQ. Identification of candidate biomarkers for early detection of human lung squamous cell cancer by quantitative proteomics. Mol Cell Proteomics 2012; 11:M111.013946. [PMID: 22298307 DOI: 10.1074/mcp.m111.013946] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
To discover novel biomarkers for early detection of human lung squamous cell cancer (LSCC) and explore possible mechanisms of LSCC carcinogenesis, iTRAQ-tagging combined with two dimensional liquid chromatography tandem MS analysis was used to identify differentially expressed proteins in human bronchial epithelial carcinogenic process using laser capture microdissection-purified normal bronchial epithelium (NBE), squamous metaplasia (SM), atypical hyperplasia (AH), carcinoma in situ (CIS) and invasive LSCC. As a result, 102 differentially expressed proteins were identified, and three differential proteins (GSTP1, HSPB1 and CKB) showing progressively expressional changes in the carcinogenic process were selectively validated by Western blotting. Immunohistochemistry was performed to detect the expression of the three proteins in an independent set of paraffin-embedded archival specimens including various stage tissues of bronchial epithelial carcinogenesis, and their ability for early detection of LSCC was evaluated by receiver operating characteristic analysis. The results showed that the combination of the three proteins could perfectly discriminate NBE from preneoplastic lesions (SM, AH and CIS) from invasive LSCC, achieving a sensitivity of 96% and a specificity of 92% in discriminating NBE from preneoplatic lesions, a sensitivity of 100% and a specificity of 98% in discriminating NBE from invasive LSCC, and a sensitivity of 92% and a specificity of 91% in discriminating preneoplastic lesions from invasive LSCC, respectively. Furthermore, we knocked down GSTP1 in immortalized human bronchial epithelial cell line 16HBE cells, and then measured their susceptibility to carcinogen benzo(a)pyrene-induced cell transformation. The results showed that GSTP1 knockdown significantly increased the efficiency of benzo(a)pyrene-induced 16HBE cell transformation. The present data first time show that GSTP1, HSPB1 and CKB are novel potential biomarkers for early detection of LSCC, and GSTP1 down-regulation is involved in human bronchial epithelial carcinogenesis.
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Affiliation(s)
- Gu-Qing Zeng
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha 410008, China
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Pyatnitskiy MA, Lisitsa AV, Moshkovskii SA, Arnotskaya NE, Akhmedov BB, Zaridze DG, Polotskii BE, Shevchenko VE. Identification of differential signs of squamous cell lung carcinoma by means of the mass spectrometry profiling of blood plasma. JOURNAL OF ANALYTICAL CHEMISTRY 2011. [DOI: 10.1134/s1061934811140139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Guergova-Kuras M, Kurucz I, Hempel W, Tardieu N, Kádas J, Malderez-Bloes C, Jullien A, Kieffer Y, Hincapie M, Guttman A, Csánky E, Dezso B, Karger BL, Takács L. Discovery of lung cancer biomarkers by profiling the plasma proteome with monoclonal antibody libraries. Mol Cell Proteomics 2011; 10:M111.010298. [PMID: 21947365 PMCID: PMC3237079 DOI: 10.1074/mcp.m111.010298] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
A challenge in the treatment of lung cancer is the lack of early diagnostics. Here, we describe the application of monoclonal antibody proteomics for discovery of a panel of biomarkers for early detection (stage I) of non-small cell lung cancer (NSCLC). We produced large monoclonal antibody libraries directed against the natural form of protein antigens present in the plasma of NSCLC patients. Plasma biomarkers associated with the presence of lung cancer were detected via high throughput ELISA. Differential profiling of plasma proteomes of four clinical cohorts, totaling 301 patients with lung cancer and 235 healthy controls, identified 13 lung cancer-associated (p < 0.05) monoclonal antibodies. The monoclonal antibodies recognize five different cognate proteins identified using immunoprecipitation followed by mass spectrometry. Four of the five antigens were present in non-small cell lung cancer cells in situ. The approach is capable of generating independent antibodies against different epitopes of the same proteins, allowing fast translation to multiplexed sandwich assays. Based on these results, we have verified in two independent clinical collections a panel of five biomarkers for classifying patient disease status with a diagnostics performance of 77% sensitivity and 87% specificity. Combining CYFRA, an established cancer marker, with the panel resulted in a performance of 83% sensitivity at 95% specificity for stage I NSCLC.
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35
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Abstract
Since the advent of the new proteomics era more than a decade ago, large-scale studies of protein profiling have been exploited to identify the distinctive molecular signatures in a wide array of biological systems spanning areas of basic biological research, various disease states, and biomarker discovery directed toward therapeutic applications. Recent advances in protein separation and identification techniques have significantly improved proteomics approaches, leading to enhancement of the depth and breadth of proteome coverage. Proteomic signatures specific for invasive lung cancer and preinvasive lesions have begun to emerge. In this review we provide a critical assessment of the state of recent advances in proteomic approaches and the biological lessons they have yielded, with specific emphasis on the discovery of biomarker signatures for the early detection of lung cancer.
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36
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Arya SK, Bhansali S. Lung Cancer and Its Early Detection Using Biomarker-Based Biosensors. Chem Rev 2011; 111:6783-809. [DOI: 10.1021/cr100420s] [Citation(s) in RCA: 196] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Sunil K. Arya
- Bio-MEMS and Microsystem Lab, Department of Electrical Engineering, University of South Florida, 4202 East Fowler Avenue, ENB 118, Tampa, Florida 33620, United States
| | - Shekhar Bhansali
- Bio-MEMS and Microsystem Lab, Department of Electrical Engineering, University of South Florida, 4202 East Fowler Avenue, ENB 118, Tampa, Florida 33620, United States
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37
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Demkow U. Laboratory Medicine in the Scope of Proteomics and Genomics. EJIFCC 2010; 21:56-63. [PMID: 27683374 PMCID: PMC4975249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Advances in technology, especially in molecular biology, allow for a fast expansion of diagnostic methods in routine clinical practice. New proteomics and genomics technologies could be used for disease specific biomarker discovery and to monitor patient response to the therapy. Genomics and proteomics may also help to establish new, molecular classification of the disease. Applying genomic and proteomic methods to body fluids (serum, cerebrospinal fluid, urine, etc) and tissue extracts would place valuable objective analytical power in the hands of the clinician however validation of those methods is an important issue. The rapid expansion of the diagnostic tools based on developments in proteomic and genomic technologies can be fundamental for the development of personalized medicine.
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38
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Pang LY, Argyle D. Cancer stem cells and telomerase as potential biomarkers in veterinary oncology. Vet J 2010; 185:15-22. [PMID: 20580998 DOI: 10.1016/j.tvjl.2010.04.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Despite advances in chemotherapy and radiotherapy, cancer remains a disease of high morbidity and mortality in domestic animals. In parallel to the development of novel therapeutic interventions, appropriate biomarkers are required to detect early-stage disease and disease remission and relapse at both gross and molecular levels, and the effectiveness of therapy. The field of cancer pathogenesis has grown exponentially over the last decade, both in terms of our understanding of the underlying molecular events, and the technologies available to interrogate the cancer cell. This paper reviews the role of the telomerase enzyme and of telomere length as potential biomarkers in cancer. Furthermore, the potential role of cancer stem cells as biomarkers of malignancy and disease progression is assessed.
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Affiliation(s)
- Lisa Y Pang
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh Hospital for Small Animals, Easter Bush, Midlothian EH25 9RG, UK
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Imaging: Mass spectrometry in HNSCC--a peek at response prediction? Nat Rev Clin Oncol 2010; 7:193-5. [PMID: 20354544 DOI: 10.1038/nrclinonc.2010.35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
EGFR inhibitors provide benefit in patients with advanced and metastatic head and neck squamous cell carcinoma (HNSCC). Mass spectrometry profiling has been used to predict outcome in patients with HNSCC after EGFR inhibitor treatment, and may enable prior identification of patients most likely to benefit from these therapies. however, further validation in prospective studies is needed.
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