1
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Yang Q, Zhuo Z, Qiu X, Luo R, Guo K, Wu H, Jiang R, Li J, Lian Q, Chen P, Sha W, Chen H. Adverse clinical outcomes and immunosuppressive microenvironment of RHO-GTPase activation pattern in hepatocellular carcinoma. J Transl Med 2024; 22:122. [PMID: 38297333 PMCID: PMC10832138 DOI: 10.1186/s12967-024-04926-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 01/23/2024] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Emerging evidence suggests that Rho GTPases play a crucial role in tumorigenesis and metastasis, but their involvement in the tumor microenvironment (TME) and prognosis of hepatocellular carcinoma (HCC) is not well understood. METHODS We aim to develop a tumor prognosis prediction system called the Rho GTPases-related gene score (RGPRG score) using Rho GTPase signaling genes and further bioinformatic analyses. RESULTS Our work found that HCC patients with a high RGPRG score had significantly worse survival and increased immunosuppressive cell fractions compared to those with a low RGPRG score. Single-cell cohort analysis revealed an immune-active TME in patients with a low RGPRG score, with strengthened communication from T/NK cells to other cells through MIF signaling networks. Targeting these alterations in TME, the patients with high RGPRG score have worse immunotherapeutic outcomes and decreased survival time in the immunotherapy cohort. Moreover, the RGPRG score was found to be correlated with survival in 27 other cancers. In vitro experiments confirmed that knockdown of the key Rho GTPase-signaling biomarker SFN significantly inhibited HCC cell proliferation, invasion, and migration. CONCLUSIONS This study provides new insight into the TME features and clinical use of Rho GTPase gene pattern at the bulk-seq and single-cell level, which may contribute to guiding personalized treatment and improving clinical outcome in HCC.
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Affiliation(s)
- Qi Yang
- Department of Gastroenterology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, Guangdong, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Zewei Zhuo
- Department of Gastroenterology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, Guangdong, China
- School of Medicine, South China University of Technology, Guangzhou, 510006, Guangdong, China
| | - Xinqi Qiu
- Cancer Prevention Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, People's Republic of China
| | - Ruibang Luo
- Department of Computer Science, The University of Hong Kong, Hong Kong, 999077, SAR, China
| | - Kehang Guo
- Department of Gastroenterology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, Guangdong, China
- Department of Critical Care Medicine, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Huihuan Wu
- Department of Gastroenterology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, Guangdong, China
- School of Medicine, South China University of Technology, Guangzhou, 510006, Guangdong, China
| | - Rui Jiang
- Department of Gastroenterology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, Guangdong, China
- School of Medicine, South China University of Technology, Guangzhou, 510006, Guangdong, China
| | - Jingwei Li
- Department of Gastroenterology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, Guangdong, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Qizhou Lian
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518118, Guangdong, China.
- Cord Blood Bank, Guangzhou Institute of Eugenics and Perinatology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 511436, Guangdong, China.
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong, 999077, SAR, China.
| | - Pengfei Chen
- Department of Laboratory Medicine, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, People's Republic of China.
| | - Weihong Sha
- Department of Gastroenterology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, Guangdong, China.
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China.
- School of Medicine, South China University of Technology, Guangzhou, 510006, Guangdong, China.
| | - Hao Chen
- Department of Gastroenterology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, Guangdong, China.
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China.
- School of Medicine, South China University of Technology, Guangzhou, 510006, Guangdong, China.
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2
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Rahman SJ, Chen SC, Wang YT, Gao Y, Schepmoes AA, Fillmore TL, Shi T, Chen H, Rodland KD, Massion PP, Grogan EL, Liu T. Validation of a Proteomic Signature of Lung Cancer Risk from Bronchial Specimens of Risk-Stratified Individuals. Cancers (Basel) 2023; 15:4504. [PMID: 37760474 PMCID: PMC10526486 DOI: 10.3390/cancers15184504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/07/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
A major challenge in lung cancer prevention and cure hinges on identifying the at-risk population that ultimately develops lung cancer. Previously, we reported proteomic alterations in the cytologically normal bronchial epithelial cells collected from the bronchial brushings of individuals at risk for lung cancer. The purpose of this study is to validate, in an independent cohort, a selected list of 55 candidate proteins associated with risk for lung cancer with sensitive targeted proteomics using selected reaction monitoring (SRM). Bronchial brushings collected from individuals at low and high risk for developing lung cancer as well as patients with lung cancer, from both a subset of the original cohort (batch 1: n = 10 per group) and an independent cohort of 149 individuals (batch 2: low risk (n = 32), high risk (n = 34), and lung cancer (n = 83)), were analyzed using multiplexed SRM assays. ALDH3A1 and AKR1B10 were found to be consistently overexpressed in the high-risk group in both batch 1 and batch 2 brushing specimens as well as in the biopsies of batch 1. Validation of highly discriminatory proteins and metabolic enzymes by SRM in a larger independent cohort supported their use to identify patients at high risk for developing lung cancer.
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Affiliation(s)
- S.M. Jamshedur Rahman
- Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; (S.M.J.R.); (P.P.M.)
| | - Sheau-Chiann Chen
- Department of Biostatistics, Vanderbilt University, Nashville, TN 37203, USA; (S.-C.C.); (H.C.)
| | - Yi-Ting Wang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.-T.W.); (Y.G.); (A.A.S.); (T.S.)
| | - Yuqian Gao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.-T.W.); (Y.G.); (A.A.S.); (T.S.)
| | - Athena A. Schepmoes
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.-T.W.); (Y.G.); (A.A.S.); (T.S.)
| | - Thomas L. Fillmore
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA;
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.-T.W.); (Y.G.); (A.A.S.); (T.S.)
| | - Heidi Chen
- Department of Biostatistics, Vanderbilt University, Nashville, TN 37203, USA; (S.-C.C.); (H.C.)
| | - Karin D. Rodland
- Department of Cell, Developmental, and Cancer Biology, Oregon Health and Science University, Portland, OR 97201, USA;
| | - Pierre P. Massion
- Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; (S.M.J.R.); (P.P.M.)
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN 37232, USA
| | - Eric L. Grogan
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN 37232, USA
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.-T.W.); (Y.G.); (A.A.S.); (T.S.)
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3
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Janßen C, Boskamp T, Le’Clerc Arrastia J, Otero Baguer D, Hauberg-Lotte L, Kriegsmann M, Kriegsmann K, Steinbuß G, Casadonte R, Kriegsmann J, Maaß P. Multimodal Lung Cancer Subtyping Using Deep Learning Neural Networks on Whole Slide Tissue Images and MALDI MSI. Cancers (Basel) 2022; 14:cancers14246181. [PMID: 36551667 PMCID: PMC9776684 DOI: 10.3390/cancers14246181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/12/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Artificial intelligence (AI) has shown potential for facilitating the detection and classification of tumors. In patients with non-small cell lung cancer, distinguishing between the most common subtypes, adenocarcinoma (ADC) and squamous cell carcinoma (SqCC), is crucial for the development of an effective treatment plan. This task, however, may still present challenges in clinical routine. We propose a two-modality, AI-based classification algorithm to detect and subtype tumor areas, which combines information from matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) data and digital microscopy whole slide images (WSIs) of lung tissue sections. The method consists of first detecting areas with high tumor cell content by performing a segmentation of the hematoxylin and eosin-stained (H&E-stained) WSIs, and subsequently classifying the tumor areas based on the corresponding MALDI MSI data. We trained the algorithm on six tissue microarrays (TMAs) with tumor samples from N = 232 patients and used 14 additional whole sections for validation and model selection. Classification accuracy was evaluated on a test dataset with another 16 whole sections. The algorithm accurately detected and classified tumor areas, yielding a test accuracy of 94.7% on spectrum level, and correctly classified 15 of 16 test sections. When an additional quality control criterion was introduced, a 100% test accuracy was achieved on sections that passed the quality control (14 of 16). The presented method provides a step further towards the inclusion of AI and MALDI MSI data into clinical routine and has the potential to reduce the pathologist's work load. A careful analysis of the results revealed specific challenges to be considered when training neural networks on data from lung cancer tissue.
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Affiliation(s)
- Charlotte Janßen
- Center for Industrial Mathematics (ZeTeM), University of Bremen, 28359 Bremen, Germany
- Correspondence:
| | - Tobias Boskamp
- Center for Industrial Mathematics (ZeTeM), University of Bremen, 28359 Bremen, Germany
- Bruker Daltonics, 28359 Bremen, Germany
| | | | - Daniel Otero Baguer
- Center for Industrial Mathematics (ZeTeM), University of Bremen, 28359 Bremen, Germany
| | - Lena Hauberg-Lotte
- Center for Industrial Mathematics (ZeTeM), University of Bremen, 28359 Bremen, Germany
| | - Mark Kriegsmann
- Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
- Institute of Pathology Wiesbaden, 65199 Wiesbaden, Germany
| | - Katharina Kriegsmann
- Department of Hematology, Oncology and Rheumatology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Georg Steinbuß
- Department of Hematology, Oncology and Rheumatology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | | | - Jörg Kriegsmann
- Proteopath, 54926 Trier, Germany
- Center for Histology, Cytology and Molecular Diagnostic, 54296 Trier, Germany
- Faculty of Medicine and Dentistry, Danube Private University, 3500 Krems, Austria
| | - Peter Maaß
- Center for Industrial Mathematics (ZeTeM), University of Bremen, 28359 Bremen, Germany
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4
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Kussrow A, Kammer MN, Massion PP, Webster R, Bornhop DJ. Assay Performance of a Label-Free, Solution-Phase CYFRA 21-1 Determination. ACS OMEGA 2022; 7:31916-31923. [PMID: 36120008 PMCID: PMC9476196 DOI: 10.1021/acsomega.2c02763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
CYFRA 21.1, a cytokeratin fragment of epithelial origin, has long been a valuable blood-based biomarker. As with most biomarkers, the clinical diagnostic value of CYFRA 21.1 is dependent on the quantitative performance of the assay. Looking toward translation, it is shown here that a free-solution assay (FSA) coupled with a compensated interferometric reader (CIR) can be used to provide excellent analytical performance in quantifying CYFRA 21.1 in patient serum samples. This report focuses on the analytical performance of the high-sensitivity (hs)-CYFRA 21.1 assay in the context of quantifying the biomarker in two indeterminate pulmonary nodule (IPN) patient cohorts totaling 179 patients. Each of the ten assay calibrations consisted of 6 concentrations, each run as 7 replicates (e.g., 10 × 6 × 7 data points) and were performed on two different instruments by two different operators. Coefficients of variation (CVs) for the hs-CYFRA 21.1 analytical figures of merit, limit of quantification (LOQ) of ca. 60 pg/mL, B max, initial slope, probe-target binding affinity, and reproducibility of quantifying an unknown were found to range from 2.5 to 8.3%. Our results demonstrate the excellent performance of our FSA-CIR hs-CYFRA 21-1 assay and a proof of concept for potentially redefining the performance characteristics of this existing important candidate biomarker.
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Affiliation(s)
- Amanda
K. Kussrow
- Department
of Chemistry and The Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Michael N. Kammer
- Division
of Allergy, Pulmonary and Critical Care Medicine and Vanderbilt-Ingram
Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Pierre P. Massion
- Division
of Allergy, Pulmonary and Critical Care Medicine and Vanderbilt-Ingram
Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Rebekah Webster
- Department
of Chemistry and The Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Darryl J. Bornhop
- Department
of Chemistry and The Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
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5
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Kammer MN, Deppen SA, Antic S, Jamshedur Rahman S, Eisenberg R, Maldonado F, Aldrich MC, Sandler KL, Landman B, Massion PP, Grogan EL. The impact of the lung EDRN-CVC on Phase 1, 2, & 3 biomarker validation studies. Cancer Biomark 2022; 33:449-465. [DOI: 10.3233/cbm-210382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The Early Detection Research Network’s (EDRN) purpose is to discover, develop and validate biomarkers and imaging methods to detect early-stage cancers or at-risk individuals. The EDRN is composed of sites that fall into four categories: Biomarker Developmental Laboratories (BDL), Biomarker Reference Laboratories (BRL), Clinical Validation Centers (CVC) and Data Management and Coordinating Centers. Each component has a crucial role to play within the mission of the EDRN. The primary role of the CVCs is to support biomarker developers through validation trials on promising biomarkers discovered by both EDRN and non-EDRN investigators. The second round of funding for the EDRN Lung CVC at Vanderbilt University Medical Center (VUMC) was funded in October 2016 and we intended to accomplish the three missions of the CVCs: To conduct innovative research on the validation of candidate biomarkers for early cancer detection and risk assessment of lung cancer in an observational study; to compare biomarker performance; and to serve as a resource center for collaborative research within the Network and partner with established EDRN BDLs and BRLs, new laboratories and industry partners. This report outlines the impact of the VUMC EDRN Lung CVC and describes the role in promoting and validating biological and imaging biomarkers.
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Affiliation(s)
- Michael N. Kammer
- Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Stephen A. Deppen
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
- Tennessee Valley Healthcare System, Veterans Affairs, Nashville, TN, USA
| | - Sanja Antic
- Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - S.M. Jamshedur Rahman
- Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rosana Eisenberg
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Fabien Maldonado
- Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Melinda C. Aldrich
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kim L. Sandler
- Department of Radiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bennett Landman
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Pierre P. Massion
- Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Tennessee Valley Healthcare System, Veterans Affairs, Nashville, TN, USA
- Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eric L. Grogan
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
- Tennessee Valley Healthcare System, Veterans Affairs, Nashville, TN, USA
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6
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Lin M, Eberlin LS, Seeley EH. Reduced Hemoglobin Signal and Improved Detection of Endogenous Proteins in Blood-Rich Tissues for MALDI Mass Spectrometry Imaging. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:296-303. [PMID: 35061381 PMCID: PMC9041275 DOI: 10.1021/jasms.1c00300] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Mass spectrometry imaging provides a powerful approach for the direct analysis and spatial visualization of molecules in tissue sections. Using matrix-assisted laser desorption/ionization mass spectrometry, intact protein imaging has been widely investigated for biomarker analysis and diagnosis in a variety of tissue types and diseases. However, blood-rich or highly vascular tissues present a challenge in molecular imaging due to the high ionization efficiency of hemoglobin, which leads to ion suppression of endogenous proteins. Here, we describe a protocol to selectively reduce hemoglobin signal in blood-rich tissues that can easily be integrated into mass spectrometry imaging workflows.
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Affiliation(s)
- Monica Lin
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712
| | - Livia S. Eberlin
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712
- Department of Surgery, Baylor College of Medicine, Houston, TX 77030
- to whom correspondence may be addressed: ,
| | - Erin H. Seeley
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712
- to whom correspondence may be addressed: ,
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7
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Park H, Yamaguchi R, Imoto S, Miyano S. Uncovering Molecular Mechanisms of Drug Resistance via Network-Constrained Common Structure Identification. J Comput Biol 2022; 29:257-275. [DOI: 10.1089/cmb.2021.0314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Heewon Park
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Rui Yamaguchi
- Division of Cancer Systems Biology, Aichi Cancer Center Research Institute, Nagoya, Japan
- Division of Cancer Informatics, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Seiya Imoto
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Satoru Miyano
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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8
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Zakharova N, Kozyr A, Ryabokon AM, Indeykina M, Strelnikova P, Bugrova A, Nikolaev EN, Kononikhin AS. Mass spectrometry based proteome profiling of the exhaled breath condensate for lung cancer biomarkers search. Expert Rev Proteomics 2021; 18:637-642. [PMID: 34477466 DOI: 10.1080/14789450.2021.1976150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Lung cancer remains the most prevalent cause of cancer mortality worldwide mainly due to insufficient availability of early screening methods for wide-scale application. Exhaled breath condensate (EBC) is currently considered as one of the promising targets for early screening and is particularly attractive due to its absolutely noninvasive collection and possibility for long-term frozen storage. EBC proteome analysis can provide valuable information about the (patho)physiological changes in the respiratory system and may help to identify in time a high risk of lung cancer. Mass spectrometry (MS) profiling of EBC proteome seems to have no alternative in obtaining the most extensive data and characteristic marker panels for screening. AREAS COVERED This special report summarizes the data of several proteomic studies of EBC in normal and lung cancer (from 2012 to 2021, PubMed), focuses on the possible reasons for the significant discrepancy in the results, and discusses some aspects for special attention in further studies. EXPERT OPINION The significant discrepancy in the results of various studies primarily highlights the need to create standardized protocols for the collection and preparation of EBC for proteomic analysis. The application of quantitative and targeted LC-MS/MS based approaches seems to be the most promising in further EBC proteomic studies.
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Affiliation(s)
- Natalia Zakharova
- Laboratory of mass spectrometry of biomacromolecules Emanuel Institute for Biochemical Physics, Russian Academy of Science Moscow
| | - Anna Kozyr
- Laboratory of mass spectrometry of biomacromolecules Emanuel Institute for Biochemical Physics, Russian Academy of Science Moscow
| | - Anna M Ryabokon
- Laboratory of mass spectrometry of biomacromolecules Emanuel Institute for Biochemical Physics, Russian Academy of Science Moscow.,Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Maria Indeykina
- Laboratory of mass spectrometry of biomacromolecules Emanuel Institute for Biochemical Physics, Russian Academy of Science Moscow.,Laboratory of ion and molecular physics, V.l. Talrose Institute for Energy Problems of Chemical Physics, N.n. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Polina Strelnikova
- Laboratory of mass spectrometry of biomacromolecules Emanuel Institute for Biochemical Physics, Russian Academy of Science Moscow
| | - Anna Bugrova
- Laboratory of mass spectrometry of biomacromolecules Emanuel Institute for Biochemical Physics, Russian Academy of Science Moscow
| | - Eugene N Nikolaev
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Alexey S Kononikhin
- Laboratory of mass spectrometry of biomacromolecules Emanuel Institute for Biochemical Physics, Russian Academy of Science Moscow.,Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Skolkovo, Russia
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9
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Abbassi-Ghadi N, Antonowicz SS, McKenzie JS, Kumar S, Huang J, Jones EA, Strittmatter N, Petts G, Kudo H, Court S, Hoare JM, Veselkov K, Goldin R, Takáts Z, Hanna GB. De Novo Lipogenesis Alters the Phospholipidome of Esophageal Adenocarcinoma. Cancer Res 2020; 80:2764-2774. [PMID: 32345674 DOI: 10.1158/0008-5472.can-19-4035] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 03/19/2020] [Accepted: 04/23/2020] [Indexed: 11/16/2022]
Abstract
The incidence of esophageal adenocarcinoma is rising, survival remains poor, and new tools to improve early diagnosis and precise treatment are needed. Cancer phospholipidomes quantified with mass spectrometry imaging (MSI) can support objective diagnosis in minutes using a routine frozen tissue section. However, whether MSI can objectively identify primary esophageal adenocarcinoma is currently unknown and represents a significant challenge, as this microenvironment is complex with phenotypically similar tissue-types. Here, we used desorption electrospray ionization-MSI (DESI-MSI) and bespoke chemometrics to assess the phospholipidomes of esophageal adenocarcinoma and relevant control tissues. Multivariate models derived from phospholipid profiles of 117 patients were highly discriminant for esophageal adenocarcinoma both in discovery (AUC = 0.97) and validation cohorts (AUC = 1). Among many other changes, esophageal adenocarcinoma samples were markedly enriched for polyunsaturated phosphatidylglycerols with longer acyl chains, with stepwise enrichment in premalignant tissues. Expression of fatty acid and glycerophospholipid synthesis genes was significantly upregulated, and characteristics of fatty acid acyls matched glycerophospholipid acyls. Mechanistically, silencing the carbon switch ACLY in esophageal adenocarcinoma cells shortened glycerophospholipid chains, linking de novo lipogenesis to the phospholipidome. Thus, DESI-MSI can objectively identify invasive esophageal adenocarcinoma from a number of premalignant tissues and unveils mechanisms of phospholipidomic reprogramming. SIGNIFICANCE: These results call for accelerated diagnosis studies using DESI-MSI in the upper gastrointestinal endoscopy suite, as well as functional studies to determine how polyunsaturated phosphatidylglycerols contribute to esophageal carcinogenesis.
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Affiliation(s)
- Nima Abbassi-Ghadi
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Royal Surrey County Hospital, Guildford, Surrey, United Kingdom
| | - Stefan S Antonowicz
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - James S McKenzie
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Sacheen Kumar
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Department of Upper GI Surgery, Royal Marsden Hospital NHS Foundation Trust, London, United Kingdom
- Division of Radiotherapy & Imaging, Institute of Cancer Research, London, United Kingdom
| | - Juzheng Huang
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Emrys A Jones
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Nicole Strittmatter
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Gemma Petts
- Centre for Pathology, Imperial College London, London, United Kingdom
| | - Hiromi Kudo
- Centre for Pathology, Imperial College London, London, United Kingdom
| | - Stephen Court
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Jonathan M Hoare
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Kirill Veselkov
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Robert Goldin
- Centre for Pathology, Imperial College London, London, United Kingdom
| | - Zoltán Takáts
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom.
| | - George B Hanna
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom.
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10
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Gasparri R, Sedda G, Noberini R, Bonaldi T, Spaggiari L. Clinical Application of Mass Spectrometry-Based Proteomics in Lung Cancer Early Diagnosis. Proteomics Clin Appl 2020; 14:e1900138. [PMID: 32418314 DOI: 10.1002/prca.201900138] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 04/06/2020] [Indexed: 12/18/2022]
Abstract
The current knowledge on proteomic biomarker analysis for the early diagnosis of lung cancer is summarized, underlining the diversity among the results and the current interest in translating research results into clinical practice. A MEDLINE/PubMed literature search to retrieve all the papers published in the last 10 years is performed. Proteomics studies on lung cancer have gathered evidence on the potential role of biomarkers in early diagnosis. Although promising, none of them have proved to be sufficiently reliable to achieve validation. Future research should evolve toward a multipanel analysis of proteins, considering the possibility that individual biomarkers might not be specific enough to diagnose lung cancer, but could be related to oncological conditions.
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Affiliation(s)
- Roberto Gasparri
- Department of Thoracic Surgery, IEO, European Institute of Oncology IRCCS, Via Giuseppe Ripamonti 435, Milan, 20141, Italy
| | - Giulia Sedda
- Department of Thoracic Surgery, IEO, European Institute of Oncology IRCCS, Via Giuseppe Ripamonti 435, Milan, 20141, Italy
| | - Roberta Noberini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, Milan, 20139, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, Milan, 20139, Italy
| | - Lorenzo Spaggiari
- Department of Thoracic Surgery, IEO, European Institute of Oncology IRCCS, Via Giuseppe Ripamonti 435, Milan, 20141, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Via Festa del Perdono, Milan, 7 - 20122, Italy
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11
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Mo L, Wei B, Liang R, Yang Z, Xie S, Wu S, You Y. Exploring potential biomarkers for lung adenocarcinoma using LC-MS/MS metabolomics. J Int Med Res 2020; 48:300060519897215. [PMID: 32316791 PMCID: PMC7177994 DOI: 10.1177/0300060519897215] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 12/04/2019] [Indexed: 12/14/2022] Open
Abstract
Background The average 5-year survival rate of lung adenocarcinoma patients is only 15% to 17%, which is primarily due to late-stage diagnosis and a lack of specific prognostic evaluations that can recommend effective therapies. Additionally, there is no clinically recognized biomarker that is effective for early-stage diagnosis. Methods Tissue samples from 10 lung adenocarcinoma patients (both tumor and non-tumor tissues) and 10 benign lung tumor samples were collected. The significantly differentially represented metabolites from the three groups were analyzed by liquid chromatography and tandem mass spectrometry. Results Pathway analysis indicated that central carbon metabolism was the top altered pathway in lung adenocarcinoma, while protein digestion and absorption, and central carbon metabolism were the top altered pathways in benign lung tumors. Receiver operating characteristic curve analysis revealed that adenosine 3′-monophosphate, creatine, glycerol, and 14 other differential metabolites were potential sensitive and specific biomarkers for the diagnosis and prognosis of lung adenocarcinoma. Conclusion Our findings suggest that the metabolomics approach may be a useful method to detect potential biomarkers in lung adenocarcinoma patients.
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Affiliation(s)
- Liang Mo
- Department of Thoracic Surgery, the First Affiliated Hospital of
University of South China, Hengyang, Hunan Province, China
| | - Bing Wei
- Department of Thoracic Surgery, the First Affiliated Hospital of
University of South China, Hengyang, Hunan Province, China
| | - Renji Liang
- Department of Thoracic Surgery, the First Affiliated Hospital of
University of South China, Hengyang, Hunan Province, China
| | - Zhi Yang
- Department of Thoracic Surgery, the First Affiliated Hospital of
University of South China, Hengyang, Hunan Province, China
| | - Shouzhi Xie
- Department of Thoracic Surgery, the First Affiliated Hospital of
University of South China, Hengyang, Hunan Province, China
| | - Shengrong Wu
- Department of Thoracic Surgery, the First Affiliated Hospital of
University of South China, Hengyang, Hunan Province, China
| | - Yong You
- Medical College, University of South China, Hengyang, Hunan
Province, China
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12
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Patterson NH, Tuck M, Lewis A, Kaushansky A, Norris JL, Van de Plas R, Caprioli RM. Next Generation Histology-Directed Imaging Mass Spectrometry Driven by Autofluorescence Microscopy. Anal Chem 2018; 90:12404-12413. [PMID: 30274514 DOI: 10.1021/acs.analchem.8b02885] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Histology-directed imaging mass spectrometry (IMS) is a spatially targeted IMS acquisition method informed by expert annotation that provides rapid molecular characterization of select tissue structures. The expert annotations are usually determined on digital whole slide images of histological stains where the staining preparation is incompatible with optimal IMS preparation, necessitating serial sections: one for annotation, one for IMS. Registration is then used to align staining annotations onto the IMS tissue section. Herein, we report a next-generation histology-directed platform implementing IMS-compatible autofluorescence (AF) microscopy taken prior to any staining or IMS. The platform enables two histology-directed workflows, one that improves the registration process between two separate tissue sections using automated, computational monomodal AF-to-AF microscopy image registration, and a registration-free approach that utilizes AF directly to identify ROIs and acquire IMS on the same section. The registration approach is fully automated and delivers state of the art accuracy in histology-directed workflows for transfer of annotations (∼3-10 μm based on 4 organs from 2 species) while the direct AF approach is registration-free, allowing targeting of the finest structures visible by AF microscopy. We demonstrate the platform in biologically relevant case studies of liver stage malaria and human kidney disease with spatially targeted acquisition of sparsely distributed (composing less than one tenth of 1% of the tissue section area) malaria infected mouse hepatocytes and glomeruli in the human kidney case study.
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Affiliation(s)
| | | | - Adam Lewis
- Center for Infectious Disease Research , formerly Seattle Biomedical Research Institute, Seattle , Washington 98109 , United States.,Department of Global Health , University of Washington , Seattle , Washington 98195 , United States
| | - Alexis Kaushansky
- Center for Infectious Disease Research , formerly Seattle Biomedical Research Institute, Seattle , Washington 98109 , United States.,Department of Global Health , University of Washington , Seattle , Washington 98195 , United States
| | | | - Raf Van de Plas
- Delft Center for Systems and Control (DCSC) , Delft University of Technology , 2628 CD , Delft , The Netherlands
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13
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Greco V, Piras C, Pieroni L, Ronci M, Putignani L, Roncada P, Urbani A. Applications of MALDI-TOF mass spectrometry in clinical proteomics. Expert Rev Proteomics 2018; 15:683-696. [PMID: 30058389 DOI: 10.1080/14789450.2018.1505510] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
INTRODUCTION The development of precision medicine requires advanced technologies to address the multifactorial disease stratification and to support personalized treatments. Among omics techniques, proteomics based on Mass Spectrometry (MS) is becoming increasingly relevant in clinical practice allowing a phenotypic characterization of the dynamic functional status of the organism. From this perspective, Matrix Assisted Laser Desorption Ionization Time of Flight (MALDI-TOF) MS is a suitable platform for providing a high-throughput support to clinics. Areas covered: This review aims to provide an updated overview of MALDI-TOF MS applications in clinical proteomics. The most relevant features of this analysis have been discussed, highlighting both pre-analytical and analytical factors that are crucial in proteomics studies. Particular emphasis is placed on biofluids proteomics for biomarkers discovery and on recent progresses in clinical microbiology, drug monitoring, and minimal residual disease (MRD). Expert commentary: Despite some analytical limitations, the latest technological advances together with the easiness of use, the low time and low cost consuming and the high throughput are making MALDI-TOF MS instruments very attractive for the clinical practice. These features offer a significant potential for the routine of the clinical laboratory and ultimately for personalized medicine.
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Affiliation(s)
- Viviana Greco
- a Institute of Biochemistry and Clinical Biochemistry , Università Cattolica del Sacro Cuore , Rome , Italy.,b Department of Laboratory Diagnostic and Infectious Diseases , Fondazione Policlinico Universitario Agostino Gemelli-IRCCS , Rome , Italy
| | - Cristian Piras
- c Dipartimento di Medicina Veterinaria , Università degli studi di Milano , Milano , Italy
| | - Luisa Pieroni
- d Proteomics and Metabonomics Unit , IRCCS-Fondazione Santa Lucia , Rome , Italy
| | - Maurizio Ronci
- d Proteomics and Metabonomics Unit , IRCCS-Fondazione Santa Lucia , Rome , Italy.,e Department of Medical, Oral and Biotechnological Sciences , University "G. D'Annunzio" of Chieti-Pescara , Chieti , Italy
| | - Lorenza Putignani
- f Unit of Parasitology Bambino Gesù Children's Hospital , IRCCS , Rome , Italy.,g Unit of Human Microbiome , Bambino Gesù Children's Hospital, IRCCS , Rome , Italy
| | - Paola Roncada
- h Dipartimento di Scienze della Salute , Università degli studi "Magna Græcia" di Catanzaro , Catanzaro , Italy
| | - Andrea Urbani
- a Institute of Biochemistry and Clinical Biochemistry , Università Cattolica del Sacro Cuore , Rome , Italy.,b Department of Laboratory Diagnostic and Infectious Diseases , Fondazione Policlinico Universitario Agostino Gemelli-IRCCS , Rome , Italy
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14
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Jaegger CF, Negrão F, Assis DM, Belaz KRA, Angolini CFF, Fernandes AMAP, Santos VG, Pimentel A, Abánades DR, Giorgio S, Eberlin MN, Rocha DFO. MALDI MS imaging investigation of the host response to visceral leishmaniasis. MOLECULAR BIOSYSTEMS 2018; 13:1946-1953. [PMID: 28758666 DOI: 10.1039/c7mb00306d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Mass spectrometry imaging (MSI) of animal tissues has become an important tool for in situ molecular analyses and biomarker studies in several clinical areas, but there are few applications in parasitological studies. Leishmaniasis is a neglected tropical disease, and experimental mouse models have been essential to evaluate pathological and immunological processes and to develop diagnostic methods. Herein we have employed MALDI MSI to examine peptides and low molecular weight proteins (2 to 20 kDa) differentially expressed in the liver during visceral leishmaniasis in mice models. We analyzed liver sections of Balb/c mice infected with Leishmania infantum using the SCiLS Lab software for statistical analysis, which facilitated data interpretation and thus highlighted several key proteins and/or peptides. We proposed a decision tree classification for visceral leishmaniasis with distinct phases of the disease, which are named here as healthy, acute infection and chronic infection. Among others, the ion of m/z 4963 was the most important to identify acute infection and was tentatively identified as Thymosin β4. This peptide was previously established as a recovery factor in the human liver and might participate in the response of mice to Leishmania infection. This preliminary investigation shows the potential of MALDI MSI to complement classical compound selective imaging techniques and to explore new features not yet recognized by these approaches.
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Affiliation(s)
- C F Jaegger
- ThoMSon Mass Spectrometry Laboratory, University of Campinas - UNICAMP, Campinas, SP, Brazil.
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15
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Su DW, Nieva J. Biophysical technologies for understanding circulating tumor cell biology and metastasis. Transl Lung Cancer Res 2017; 6:473-485. [PMID: 28904890 DOI: 10.21037/tlcr.2017.05.08] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
An understanding of cancer evolution in lung cancer with its associated resistance to therapy can only be achieved with repeated sampling and analysis of the cancer. Given the high risks and costs associated with repeat physical biopsy, alternative technologies must be applied. Several modalities exist for analysis and re-analysis of cancer biology. Among them are the CellSearch platform, the CTC chip, and the high-definition CTC platform. While the former is primarily able to provide prognosticating information in the form of CTC enumeration, the latter two have the advantage of serving as a platform to study tumor biology. Techniques for analysis of single cell genomics, as well as protein expression on a single cell basis provide scientists with the capacity to understand cancer cell populations as a collection of individual cells, rather than as an average of all cells. A multimodal combination of circulating tumor DNAs (ctDNAs), CTCs, proteomics, and CTC-derived xenografts (CDXs) to create computational models useful in diagnosis, prognostication, and predictiveness to treatment is likely the future of tailoring individualized cancer care.
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Affiliation(s)
- Derrick W Su
- Norris Cancer Center, University of Southern California, Los Angeles, USA
| | - Jorge Nieva
- Norris Cancer Center, University of Southern California, Los Angeles, USA
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16
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Preinvasive disease of the airway. Cancer Treat Rev 2017; 58:77-90. [DOI: 10.1016/j.ctrv.2017.05.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/23/2017] [Accepted: 05/27/2017] [Indexed: 01/20/2023]
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17
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Beane J, Mazzilli SA, Tassinari AM, Liu G, Zhang X, Liu H, Buncio AD, Dhillon SS, Platero SJ, Lenburg ME, Reid ME, Lam S, Spira AE. Detecting the Presence and Progression of Premalignant Lung Lesions via Airway Gene Expression. Clin Cancer Res 2017; 23:5091-5100. [PMID: 28533227 DOI: 10.1158/1078-0432.ccr-16-2540] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 03/23/2017] [Accepted: 05/17/2017] [Indexed: 11/16/2022]
Abstract
Purpose: Lung cancer is the leading cause of cancer-related death in the United States. The molecular events preceding the onset of disease are poorly understood, and no effective tools exist to identify smokers with premalignant lesions (PMLs) that will progress to invasive cancer. Prior work identified molecular alterations in the smoke-exposed airway field of injury associated with lung cancer. Here, we focus on an earlier stage in the disease process leveraging the airway field of injury to study PMLs and its utility in lung cancer chemoprevention.Experimental Design: Bronchial epithelial cells from normal appearing bronchial mucosa were profiled by mRNA-Seq from subjects with (n = 50) and without (n = 25) PMLs. Using surrogate variable and gene set enrichment analysis, we identified genes, pathways, and lung cancer-related gene sets differentially expressed between subjects with and without PMLs. A computational pipeline was developed to build and test a chemoprevention-relevant biomarker.Results: We identified 280 genes in the airway field associated with the presence of PMLs. Among the upregulated genes, oxidative phosphorylation was strongly enriched, and IHC and bioenergetics studies confirmed pathway findings in PMLs. The relationship between PMLs and squamous cell carcinomas (SCC) was also confirmed using published lung cancer datasets. The biomarker performed well predicting the presence of PMLs (AUC = 0.92, n = 17), and changes in the biomarker score associated with progression/stability versus regression of PMLs (AUC = 0.75, n = 51).Conclusions: Transcriptomic alterations in the airway field of smokers with PMLs reflect metabolic and early lung SCC alterations and may be leveraged to stratify smokers at high risk for PML progression and monitor outcome in chemoprevention trials. Clin Cancer Res; 23(17); 5091-100. ©2017 AACR.
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Affiliation(s)
- Jennifer Beane
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts.
| | - Sarah A Mazzilli
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Anna M Tassinari
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Gang Liu
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Xiaohui Zhang
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Hanqiao Liu
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Anne Dy Buncio
- Department of Medicine, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Samjot S Dhillon
- Department of Medicine, Roswell Park Cancer Institute, Buffalo, New York
| | - Suso J Platero
- Janssen Research and Development, Spring House, Pennsylvania
| | - Marc E Lenburg
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Mary E Reid
- Department of Medicine, Roswell Park Cancer Institute, Buffalo, New York
| | - Stephen Lam
- Department of Medicine, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Avrum E Spira
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
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18
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Ucal Y, Durer ZA, Atak H, Kadioglu E, Sahin B, Coskun A, Baykal AT, Ozpinar A. Clinical applications of MALDI imaging technologies in cancer and neurodegenerative diseases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:795-816. [PMID: 28087424 DOI: 10.1016/j.bbapap.2017.01.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 12/08/2016] [Accepted: 01/06/2017] [Indexed: 12/25/2022]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) imaging mass spectrometry (IMS) enables localization of analytes of interest along with histology. More specifically, MALDI-IMS identifies the distributions of proteins, peptides, small molecules, lipids, and drugs and their metabolites in tissues, with high spatial resolution. This unique capacity to directly analyze tissue samples without the need for lengthy sample preparation reduces technical variability and renders MALDI-IMS ideal for the identification of potential diagnostic and prognostic biomarkers and disease gradation. MALDI-IMS has evolved rapidly over the last decade and has been successfully used in both medical and basic research by scientists worldwide. In this review, we explore the clinical applications of MALDI-IMS, focusing on the major cancer types and neurodegenerative diseases. In particular, we re-emphasize the diagnostic potential of IMS and the challenges that must be confronted when conducting MALDI-IMS in clinical settings. 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)
- Yasemin Ucal
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Zeynep Aslıhan Durer
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Hakan Atak
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Elif Kadioglu
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Betul Sahin
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Abdurrahman Coskun
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Ahmet Tarık Baykal
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey
| | - Aysel Ozpinar
- Acibadem University, Department of Medical Biochemistry, School of Medicine, Istanbul, Turkey.
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19
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Arentz G, Mittal P, Zhang C, Ho YY, Briggs M, Winderbaum L, Hoffmann MK, Hoffmann P. Applications of Mass Spectrometry Imaging to Cancer. Adv Cancer Res 2017; 134:27-66. [PMID: 28110654 DOI: 10.1016/bs.acr.2016.11.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Pathologists play an essential role in the diagnosis and prognosis of benign and cancerous tumors. Clinicians provide tissue samples, for example, from a biopsy, which are then processed and thin sections are placed onto glass slides, followed by staining of the tissue with visible dyes. Upon processing and microscopic examination, a pathology report is provided, which relies on the pathologist's interpretation of the phenotypical presentation of the tissue. Targeted analysis of single proteins provide further insight and together with clinical data these results influence clinical decision making. Recent developments in mass spectrometry facilitate the collection of molecular information about such tissue specimens. These relatively new techniques generate label-free mass spectra across tissue sections providing nonbiased, nontargeted molecular information. At each pixel with spatial coordinates (x/y) a mass spectrum is acquired. The acquired mass spectrums can be visualized as intensity maps displaying the distribution of single m/z values of interest. Based on the sample preparation, proteins, peptides, lipids, small molecules, or glycans can be analyzed. The generated intensity maps/images allow new insights into tumor tissues. The technique has the ability to detect and characterize tumor cells and their environment in a spatial context and combined with histological staining, can be used to aid pathologists and clinicians in the diagnosis and management of cancer. Moreover, such data may help classify patients to aid therapy decisions and predict outcomes. The novel complementary mass spectrometry-based methods described in this chapter will contribute to the transformation of pathology services around the world.
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Affiliation(s)
- G Arentz
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA, Australia
| | - P Mittal
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA, Australia
| | - C Zhang
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA, Australia
| | - Y-Y Ho
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - M Briggs
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA, Australia; ARC Centre for Nanoscale BioPhotonics (CNBP), University of Adelaide, Adelaide, SA, Australia
| | - L Winderbaum
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - M K Hoffmann
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA, Australia
| | - P Hoffmann
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA, Australia.
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20
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Rahman SMJ, Ji X, Zimmerman LJ, Li M, Harris BK, Hoeksema MD, Trenary IA, Zou Y, Qian J, Slebos RJ, Beane J, Spira A, Shyr Y, Eisenberg R, Liebler DC, Young JD, Massion PP. The airway epithelium undergoes metabolic reprogramming in individuals at high risk for lung cancer. JCI Insight 2016; 1:e88814. [PMID: 27882349 DOI: 10.1172/jci.insight.88814] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The molecular determinants of lung cancer risk remain largely unknown. Airway epithelial cells are prone to assault by risk factors and are considered to be the primary cell type involved in the field of cancerization. To investigate risk-associated changes in the bronchial epithelium proteome that may offer new insights into the molecular pathogenesis of lung cancer, proteins were identified in the airway epithelial cells of bronchial brushing specimens from risk-stratified individuals by shotgun proteomics. Differential expression of selected proteins was validated by parallel reaction monitoring mass spectrometry in an independent set of individual bronchial brushings. We identified 2,869 proteins, of which 312 proteins demonstrated a trend in expression. Pathway analysis revealed enrichment of carbohydrate metabolic enzymes in high-risk individuals. Glucose consumption and lactate production were increased in human bronchial epithelial BEAS2B cells treated with cigarette smoke condensate for 7 months. Increased lipid biosynthetic capacity and net reductive carboxylation were revealed by metabolic flux analyses of [U-13C5] glutamine in this in vitro model, suggesting profound metabolic reprogramming in the airway epithelium of high-risk individuals. These results provide a rationale for the development of potentially new chemopreventive strategies and selection of patients for surveillance programs.
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Affiliation(s)
- S M Jamshedur Rahman
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Cancer Early Detection and Prevention Initiative, Vanderbilt Ingram Cancer Center
| | - Xiangming Ji
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Cancer Early Detection and Prevention Initiative, Vanderbilt Ingram Cancer Center
| | | | - Ming Li
- Department of Biostatistics, and
| | - Bradford K Harris
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Cancer Early Detection and Prevention Initiative, Vanderbilt Ingram Cancer Center
| | - Megan D Hoeksema
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Cancer Early Detection and Prevention Initiative, Vanderbilt Ingram Cancer Center
| | - Irina A Trenary
- Department of Chemical and Biomolecular Engineering, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Yong Zou
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Cancer Early Detection and Prevention Initiative, Vanderbilt Ingram Cancer Center
| | - Jun Qian
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Cancer Early Detection and Prevention Initiative, Vanderbilt Ingram Cancer Center
| | | | - Jennifer Beane
- Pulmonary Center and Section of Computational Biomedicine, Department of Medicine, Boston University Medical Center, Boston, Massachusetts, USA
| | - Avrum Spira
- Pulmonary Center and Section of Computational Biomedicine, Department of Medicine, Boston University Medical Center, Boston, Massachusetts, USA
| | - Yu Shyr
- Department of Biostatistics, and
| | | | | | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Department of Molecular Physiology and Biophysics, and
| | - Pierre P Massion
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Cancer Early Detection and Prevention Initiative, Vanderbilt Ingram Cancer Center.,Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Veterans Affairs, Tennessee Valley Healthcare System, Nashville, Tennessee, USA
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21
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Apparicio M, Santos VG, Rocha D, Ferreira CR, Macente BI, Magalhães GM, Alves AE, Motheo TF, Padilha-Nakaghi LC, Pires-Buttler EA, Luvoni GC, Eberlin MN, Vicente W. Matrix-assisted laser desorption/ionization imaging mass spectrometry for the spatial location of feline oviductal proteins. Reprod Domest Anim 2016; 52 Suppl 2:88-92. [PMID: 27807892 DOI: 10.1111/rda.12842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
With the purpose of identifying factors involved in early stages of embryo development in the domestic cat, matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) was used for the first time to describe the spatial localization of proteins in the oviducts of queens. Oviducts were obtained from two 2 and 4 years old cross-bred queens, divided into three segments, snap-frozen in liquid nitrogen and then stored at -80°C until use. Next, they were sectioned in a cryostat, fixed on ITO (indium tin oxide) conductive glass slides for MALDI-IMS and serial sections were collected on microscope slides for histology. As confirmed by histology, MALDI-IMS was able to show contrasting protein distributions in the oviductal infundibulum, ampulla and isthmus. Mass spectra were characterized by abundant ions of m/z 1,259, 4,939, 4,960 and 10,626, which have been tentatively attributed to keratin, thymosin β10, thymosin β4 and S100, respectively. Keratin and thymosins are involved in the biological response to tissue damage. S100 proteins are calcium-modulated proteins implicated in a variety of cellular activities, including cell differentiation and regulation of cell motility. These results suggest that protein composition differs between segments of the cat oviduct, which corresponds to morphological changes within these sections. Further functional studies could elucidate the effects of these proteins on feline reproductive physiology.
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Affiliation(s)
- M Apparicio
- Programa de Mestrado em Ciência Animal, Universidade de Franca, UNIFRAN, Franca/SP, Brazil
| | - V G Santos
- Thomson Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas, UNICAMP, Campinas/SP, Brazil
| | - Dfo Rocha
- Thomson Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas, UNICAMP, Campinas/SP, Brazil
| | - C R Ferreira
- Thomson Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas, UNICAMP, Campinas/SP, Brazil
| | - B I Macente
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, UNESP, Jaboticabal/SP, Brazil
| | - G M Magalhães
- Programa de Mestrado em Ciência Animal, Universidade de Franca, UNIFRAN, Franca/SP, Brazil
| | - A E Alves
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, UNESP, Jaboticabal/SP, Brazil
| | - T F Motheo
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, UNESP, Jaboticabal/SP, Brazil
| | - L C Padilha-Nakaghi
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, UNESP, Jaboticabal/SP, Brazil
| | - E A Pires-Buttler
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, UNESP, Jaboticabal/SP, Brazil
| | - G C Luvoni
- Dipartimento di Scienze Veterinarie per la Salute, la Produzione Animale e la Sicurezza Alimentare, Università degli Studi di Milano, Milan, Italy
| | - M N Eberlin
- Thomson Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas, UNICAMP, Campinas/SP, Brazil
| | - Wrr Vicente
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, UNESP, Jaboticabal/SP, Brazil
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Schwamborn K, Kriegsmann M, Weichert W. MALDI imaging mass spectrometry - From bench to bedside. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:776-783. [PMID: 27810414 DOI: 10.1016/j.bbapap.2016.10.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 10/24/2016] [Accepted: 10/28/2016] [Indexed: 10/20/2022]
Abstract
Today, pathologists face many challenges in defining the precise morphomolecular diagnosis and in guiding clinicians to the optimal patients' treatment. To achieve this goal, increasingly, classical histomorphological methods have to be supplemented by high throughput molecular assays. Since MALDI imaging mass spectrometry (IMS) enables the assessment of spatial molecular arrangements in tissue sections, it goes far beyond microscopy in providing hundreds of different molecular images from a single scan without the need of target-specific reagents. Thus, this technology has the potential to uncover new markers for diagnostic purposes or markers that correlate with disease severity as well as prognosis and therapeutic response. Additionally, in the future MALDI IMS based classifiers measured with this technology in real time in the diagnostic setting might be applicable in the routine diagnostic setting. In this review, recently published studies that show the usefulness, advantages, and applicability of MALDI IMS in different fields of pathology (diagnosis, prognosis and treatment response) are highlighted. 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)
- Kristina Schwamborn
- Institute of Pathology, Technische Universität München (TUM), Munich, Germany.
| | - Mark Kriegsmann
- University of Heidelberg, Department of Pathology, Heidelberg, Germany
| | - Wilko Weichert
- Institute of Pathology, Technische Universität München (TUM), Munich, Germany
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Brioude G, Brégeon F, Trousse D, Flaudrops C, Secq V, De Dominicis F, Chabrières E, D'journo XB, Raoult D, Thomas PA. Rapid Diagnosis of Lung Tumors, a Feasability Study Using Maldi-Tof Mass Spectrometry. PLoS One 2016; 11:e0155449. [PMID: 27228175 PMCID: PMC4881980 DOI: 10.1371/journal.pone.0155449] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 04/28/2016] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVE Despite recent advances in imaging and core or endoscopic biopsies, a percentage of patients have a major lung resection without diagnosis. We aimed to assess the feasibility of a rapid tissue preparation/analysis to discriminate cancerous from non-cancerous lung tissue. METHODS Fresh sample preparations were analyzed with the Microflex LTTM MALDI-TOF analyzer. Each main reference spectra (MSP) was consecutively included in a database. After definitive pathological diagnosis, each MSP was labeled as either cancerous or non-cancerous (normal, inflammatory, infectious nodules). A strategy was constructed based on the number of concordant responses of a mass spectrometry scoring algorithm. A 3-step evaluation included an internal and blind validation of a preliminary database (n = 182 reference spectra from the 100 first patients), followed by validation on a whole cohort database (n = 300 reference spectra from 159 patients). Diagnostic performance indicators were calculated. RESULTS 127 cancerous and 173 non-cancerous samples (144 peripheral biopsies and 29 inflammatory or infectious lesions) were processed within 30 minutes after biopsy sampling. At the most discriminatory level, the samples were correctly classified with a sensitivity, specificity and global accuracy of 92.1%, 97.1% and 95%, respectively. CONCLUSIONS The feasibility of rapid MALDI-TOF analysis, coupled with a very simple lung preparation procedure, appears promising and should be tested in several surgical settings where rapid on-site evaluation of abnormal tissue is required. In the operating room, it appears promising in case of tumors with an uncertain preoperative diagnosis and should be tested as a complementary approach to frozen-biopsy analysis.
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Affiliation(s)
- Geoffrey Brioude
- Service de chirurgie thoracique et des maladies de l'œsophage, Pôle cardio-vasculaire et thoracique, Centre Hospitalo-Universitaire Nord, Assistance publique-Hôpitaux de Marseille, Aix-Marseille université, Marseille, France
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, URMITE CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - Fabienne Brégeon
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, URMITE CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
- Service desExplorations Fonctionnelles Respiratoires Centre Hospitalo-Universitaire Nord, Pôle cardio-vasculaire et thoracique, Assistance Publique Hôpitaux de Marseille, Marseille, France
| | - Delphine Trousse
- Service de chirurgie thoracique et des maladies de l'œsophage, Pôle cardio-vasculaire et thoracique, Centre Hospitalo-Universitaire Nord, Assistance publique-Hôpitaux de Marseille, Aix-Marseille université, Marseille, France
| | - Christophe Flaudrops
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, URMITE CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - Véronique Secq
- Service d'anatomie pathologique, hôpital Nord, Aix Marseille université, Marseille, France
| | - Florence De Dominicis
- Service de chirurgie thoracique et des maladies de l'œsophage, Pôle cardio-vasculaire et thoracique, Centre Hospitalo-Universitaire Nord, Assistance publique-Hôpitaux de Marseille, Aix-Marseille université, Marseille, France
| | - Eric Chabrières
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, URMITE CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
- Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie,Centre Hospitalo-Universitaire Timone, Assistance publique des hôpitaux de Marseille, Marseille, France
| | - Xavier-Benoit D'journo
- Service de chirurgie thoracique et des maladies de l'œsophage, Pôle cardio-vasculaire et thoracique, Centre Hospitalo-Universitaire Nord, Assistance publique-Hôpitaux de Marseille, Aix-Marseille université, Marseille, France
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, URMITE CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, URMITE CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
- Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie,Centre Hospitalo-Universitaire Timone, Assistance publique des hôpitaux de Marseille, Marseille, France
| | - Pascal-Alexandre Thomas
- Service de chirurgie thoracique et des maladies de l'œsophage, Pôle cardio-vasculaire et thoracique, Centre Hospitalo-Universitaire Nord, Assistance publique-Hôpitaux de Marseille, Aix-Marseille université, Marseille, France
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, URMITE CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
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Carlred L, Michno W, Kaya I, Sjövall P, Syvänen S, Hanrieder J. Probing amyloid-β pathology in transgenic Alzheimer's disease (tgArcSwe) mice using MALDI imaging mass spectrometry. J Neurochem 2016; 138:469-78. [PMID: 27115712 DOI: 10.1111/jnc.13645] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Revised: 04/01/2016] [Accepted: 04/22/2016] [Indexed: 11/30/2022]
Abstract
The pathological mechanisms underlying Alzheimer's disease (AD) are still not understood. The disease pathology is characterized by the accumulation and aggregation of amyloid-β (Aβ) peptides into extracellular plaques, however the factors that promote neurotoxic Aβ aggregation remain elusive. Imaging mass spectrometry (IMS) is a powerful technique to comprehensively elucidate the spatial distribution patterns of lipids, peptides and proteins in biological tissues. In the present study, matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS)-based imaging was used to study Aβ deposition in transgenic mouse brain tissue and to elucidate the plaque-associated chemical microenvironment. The imaging experiments were performed in brain sections of transgenic Alzheimer's disease mice carrying the Arctic and Swedish mutation of amyloid-beta precursor protein (tgArcSwe). Multivariate image analysis was used to interrogate the IMS data for identifying pathologically relevant, anatomical features based on their chemical identity. This include cortical and hippocampal Aβ deposits, whose amyloid peptide content was further verified using immunohistochemistry and laser microdissection followed by MALDI MS analysis. Subsequent statistical analysis on spectral data of regions of interest revealed brain region-specific differences in Aβ peptide aggregation. Moreover, other plaque-associated protein species were identified including macrophage migration inhibitory factor suggesting neuroinflammatory processes and glial cell reactivity to be involved in AD pathology. The presented data further highlight the potential of IMS as a powerful approach in neuropathology. Hanrieder et al. described an imaging mass spectrometry based study on comprehensive spatial profiling of C-terminally truncated Aβ species within individual plaques in tgArcSwe mice. Here, brain region-dependent differences in Aβ truncation and other plaque-associated proteins, such as macrophage migration inhibitory factor, were observed. The data shed further light on plaque-associated molecular mechanisms implicated in Alzheimer's pathogenesis. Cover image for this issue: doi: 10.1111/jnc.13328.
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Affiliation(s)
- Louise Carlred
- SP Technical Research Institute of Sweden, Borås, Sweden.,Department of Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Wojciech Michno
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Ibrahim Kaya
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Peter Sjövall
- SP Technical Research Institute of Sweden, Borås, Sweden.,Department of Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Stina Syvänen
- Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
| | - Jörg Hanrieder
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden.,Department of Molecular Neuroscience, Institute of Neurology, University College London, London, UK
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25
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Ren G, Krawetz R. Applying computation biology and "big data" to develop multiplex diagnostics for complex chronic diseases such as osteoarthritis. Biomarkers 2016; 20:533-9. [PMID: 26809774 PMCID: PMC4819822 DOI: 10.3109/1354750x.2015.1105499] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The data explosion in the last decade is revolutionizing diagnostics research and the healthcare industry, offering both opportunities and challenges. These high-throughput “omics” techniques have generated more scientific data in the last few years than in the entire history of mankind. Here we present a brief summary of how “big data” have influenced early diagnosis of complex diseases. We will also review some of the most commonly used “omics” techniques and their applications in diagnostics. Finally, we will discuss the issues brought by these new techniques when translating laboratory discoveries to clinical practice.
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Affiliation(s)
- Guomin Ren
- a McCaig Institute for Bone & Joint Health, University of Calgary , Calgary , AB , Canada
| | - Roman Krawetz
- a McCaig Institute for Bone & Joint Health, University of Calgary , Calgary , AB , Canada .,b Department of Surgery , University of Calgary , Calgary , AB , Canada , and.,c Department of Anatomy and Cell Biology , University of Calgary , Calgary , AB , Canada
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26
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Xie H, Chen Z, Wang G. [Research Progress of Biomakers Proteomics-based in Lung Cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2015; 18:391-6. [PMID: 26104898 PMCID: PMC5999909 DOI: 10.3779/j.issn.1009-3419.2015.06.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
蛋白组学技术可以应用于癌症研究来检测差异蛋白质表达以发现癌症生物标志物。肺癌的生物标志物在肺癌早期诊断、指导治疗和预后监测方面起着关键作用。因此,迫切需要确定新的早期诊断和预后指标以开辟新的治疗途径。本文简要介绍了基于蛋白质组学的肺癌生物标志物的最新研究报告。他包括作为诊断、预后和预测性的生物标志物,以及基于最近发表文献的基础上和我们所做的相关工作的总结。
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Affiliation(s)
- Hui Xie
- Baodi Clinical Hospital, Tianjin Medical University, Tianjin 301800, China
| | - Zhengang Chen
- Baodi Clinical Hospital, Tianjin Medical University, Tianjin 301800, China
| | - Guangshun Wang
- Baodi Clinical Hospital, Tianjin Medical University, Tianjin 301800, China
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27
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Karimi P, Shahrokni A, Ranjbar MRN. Implementation of proteomics for cancer research: past, present, and future. Asian Pac J Cancer Prev 2015; 15:2433-8. [PMID: 24761843 DOI: 10.7314/apjcp.2014.15.6.2433] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Cancer is the leading cause of the death, accounts for about 13% of all annual deaths worldwide. Many different fields of science are collaborating together studying cancer to improve our knowledge of this lethal disease, and find better solutions for diagnosis and treatment. Proteomics is one of the most recent and rapidly growing areas in molecular biology that helps understanding cancer from an omics data analysis point of view. The human proteome project was officially initiated in 2008. Proteomics enables the scientists to interrogate a variety of biospecimens for their protein contents and measure the concentrations of these proteins. Current necessary equipment and technologies for cancer proteomics are mass spectrometry, protein microarrays, nanotechnology and bioinformatics. In this paper, we provide a brief review on proteomics and its application in cancer research. After a brief introduction including its definition, we summarize the history of major previous work conducted by researchers, followed by an overview on the role of proteomics in cancer studies. We also provide a list of different utilities in cancer proteomics and investigate their advantages and shortcomings from theoretical and practical angles. Finally, we explore some of the main challenges and conclude the paper with future directions in this field.
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Affiliation(s)
- Parisa Karimi
- Johns Hopkins Bloomberg School of Public Health, Baltimore, USA E-mail :
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28
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Kriegsmann J, Kriegsmann M, Casadonte R. MALDI TOF imaging mass spectrometry in clinical pathology: a valuable tool for cancer diagnostics (review). Int J Oncol 2014; 46:893-906. [PMID: 25482502 DOI: 10.3892/ijo.2014.2788] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 11/04/2014] [Indexed: 11/06/2022] Open
Abstract
Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) imaging mass spectrometry (IMS) is an evolving technique in cancer diagnostics and combines the advantages of mass spectrometry (proteomics), detection of numerous molecules, and spatial resolution in histological tissue sections and cytological preparations. This method allows the detection of proteins, peptides, lipids, carbohydrates or glycoconjugates and small molecules.Formalin-fixed paraffin-embedded tissue can also be investigated by IMS, thus, this method seems to be an ideal tool for cancer diagnostics and biomarker discovery. It may add information to the identification of tumor margins and tumor heterogeneity. The technique allows tumor typing, especially identification of the tumor of origin in metastatic tissue, as well as grading and may provide prognostic information. IMS is a valuable method for the identification of biomarkers and can complement histology, immunohistology and molecular pathology in various fields of histopathological diagnostics, especially with regard to identification and grading of tumors.
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Affiliation(s)
- Jörg Kriegsmann
- MVZ for Histology, Cytology and Molecular Diagnostics, Trier, Germany
| | - Mark Kriegsmann
- Institute for Pathology, University of Heidelberg, Heidelberg, Germany
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29
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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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30
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Tanvetyanon T, Creelan BC, Chiappori AA. Current clinical application of genomic and proteomic profiling in non-small-cell lung cancer. Cancer Control 2014; 21:32-9. [PMID: 24357739 DOI: 10.1177/107327481402100105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Genomic or proteomic profiling of cancer can be broadly defined as a systematic grouping of cancer based on its genetic or protein makeup. In the management of non-small-cell lung cancer (NSCLC), genomic and proteomic profiling applications have become useful in early disease detection, diagnosis, treatment, and prognostication. METHODS We reviewed the recent literature on the applications of genomic and proteomic profiling in NSCLC. Important applications were summarized into those already adopted as standard care and those still under investigation. RESULTS For genomic profiling, testing for EGFR mutation and ALK rearrangement has become routine for adenocarcinoma. Multiplex assay and malignancy-risk gene signature are both important applications in development. A test to predict outcome after treatment with an epidermal growth factor rector/tyrosine kinase inhibitor and a screening blood test for lung cancer are being investigated for use in proteomic profiling. CONCLUSIONS Genomic profiling is routine in patients with NSCLC, and proteomic profiling shows promise. Additional genomic and proteomic profiling applications may also prove to be useful contributions in the care of these patients.
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Affiliation(s)
- Tawee Tanvetyanon
- Thoracic Oncology Program, Moffitt Cancer Center, Tampa FL 33612, USA.
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31
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Bühnemann C, Li S, Yu H, Branford White H, Schäfer KL, Llombart-Bosch A, Machado I, Picci P, Hogendoorn PCW, Athanasou NA, Noble JA, Hassan AB. Quantification of the heterogeneity of prognostic cellular biomarkers in ewing sarcoma using automated image and random survival forest analysis. PLoS One 2014; 9:e107105. [PMID: 25243408 PMCID: PMC4171480 DOI: 10.1371/journal.pone.0107105] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 08/12/2014] [Indexed: 02/05/2023] Open
Abstract
Driven by genomic somatic variation, tumour tissues are typically heterogeneous, yet unbiased quantitative methods are rarely used to analyse heterogeneity at the protein level. Motivated by this problem, we developed automated image segmentation of images of multiple biomarkers in Ewing sarcoma to generate distributions of biomarkers between and within tumour cells. We further integrate high dimensional data with patient clinical outcomes utilising random survival forest (RSF) machine learning. Using material from cohorts of genetically diagnosed Ewing sarcoma with EWSR1 chromosomal translocations, confocal images of tissue microarrays were segmented with level sets and watershed algorithms. Each cell nucleus and cytoplasm were identified in relation to DAPI and CD99, respectively, and protein biomarkers (e.g. Ki67, pS6, Foxo3a, EGR1, MAPK) localised relative to nuclear and cytoplasmic regions of each cell in order to generate image feature distributions. The image distribution features were analysed with RSF in relation to known overall patient survival from three separate cohorts (185 informative cases). Variation in pre-analytical processing resulted in elimination of a high number of non-informative images that had poor DAPI localisation or biomarker preservation (67 cases, 36%). The distribution of image features for biomarkers in the remaining high quality material (118 cases, 104 features per case) were analysed by RSF with feature selection, and performance assessed using internal cross-validation, rather than a separate validation cohort. A prognostic classifier for Ewing sarcoma with low cross-validation error rates (0.36) was comprised of multiple features, including the Ki67 proliferative marker and a sub-population of cells with low cytoplasmic/nuclear ratio of CD99. Through elimination of bias, the evaluation of high-dimensionality biomarker distribution within cell populations of a tumour using random forest analysis in quality controlled tumour material could be achieved. Such an automated and integrated methodology has potential application in the identification of prognostic classifiers based on tumour cell heterogeneity.
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Affiliation(s)
- Claudia Bühnemann
- CR-UK, Tumour Growth Group, Oxford Molecular Pathology Institute, Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Simon Li
- Institute of Biomedical Engineering, Department of Engineering Science, Old Road Campus Research Building, University of Oxford, Headington, Oxford, United Kingdom
| | - Haiyue Yu
- CR-UK, Tumour Growth Group, Oxford Molecular Pathology Institute, Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom; Institute of Biomedical Engineering, Department of Engineering Science, Old Road Campus Research Building, University of Oxford, Headington, Oxford, United Kingdom
| | - Harriet Branford White
- CR-UK, Tumour Growth Group, Oxford Molecular Pathology Institute, Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Karl L Schäfer
- Institute of Pathology, Heinrich-Heine University, Medical Faculty, Düsseldorf, Germany
| | | | - Isidro Machado
- Pathology Department, University of Valencia, Valencia, Spain
| | - Piero Picci
- Research, The Rizzoli Institute, Bologna, Italy
| | | | - Nicholas A Athanasou
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Nuffield Orthopaedic Centre, University of Oxford, Oxford, United Kingdom
| | - J Alison Noble
- Institute of Biomedical Engineering, Department of Engineering Science, Old Road Campus Research Building, University of Oxford, Headington, Oxford, United Kingdom
| | - A Bassim Hassan
- CR-UK, Tumour Growth Group, Oxford Molecular Pathology Institute, Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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32
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Lung Cancer Screening Beyond Low-Dose Computed Tomography: The Role of Novel Biomarkers. Lung 2014; 192:639-48. [DOI: 10.1007/s00408-014-9636-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 07/28/2014] [Indexed: 02/07/2023]
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33
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MALDI-ToF mass spectrometry for the rapid diagnosis of cancerous lung nodules. PLoS One 2014; 9:e97511. [PMID: 24830707 PMCID: PMC4022527 DOI: 10.1371/journal.pone.0097511] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 04/16/2014] [Indexed: 01/03/2023] Open
Abstract
Recently, tissue-based methods for proteomic analysis have been used in clinical research and appear reliable for digestive, brain, lymphomatous, and lung cancers classification. However simple, tissue-based methods that couple signal analysis to tissue imaging are time consuming. To assess the reliability of a method involving rapid tissue preparation and analysis to discriminate cancerous from non-cancerous tissues, we tested 141 lung cancer/non-tumor pairs and 8 unique lung cancer samples among the stored frozen samples of 138 patients operated on during 2012. Samples were crushed in water, and 1.5 µl was spotted onto a steel target for analysis with the Microflex LT analyzer (Bruker Daltonics). Spectra were analyzed using ClinProTools software. A set of samples was used to generate a random classification model on the basis of a list of discriminant peaks sorted with the k-nearest neighbor genetic algorithm. The rest of the samples (n = 43 cancerous and n = 41 non-tumoral) was used to verify the classification capability and calculate the diagnostic performance indices relative to the histological diagnosis. The analysis found 53 m/z valid peaks, 40 of which were significantly different between cancerous and non-tumoral samples. The selected genetic algorithm model identified 20 potential peaks from the training set and had 98.81% recognition capability and 89.17% positive predictive value. In the blinded set, this method accurately discriminated the two classes with a sensitivity of 86.7% and a specificity of 95.1% for the cancer tissues and a sensitivity of 87.8% and a specificity of 95.3% for the non-tumor tissues. The second model generated to discriminate primary lung cancer from metastases was of lower quality. The reliability of MALDI-ToF analysis coupled with a very simple lung preparation procedure appears promising and should be tested in the operating room on fresh samples coupled with the pathological examination.
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Harris FT, Rahman SMJ, Hassanein M, Qian J, Hoeksema MD, Chen H, Eisenberg R, Chaurand P, Caprioli RM, Shiota M, Massion PP. Acyl-coenzyme A-binding protein regulates Beta-oxidation required for growth and survival of non-small cell lung cancer. Cancer Prev Res (Phila) 2014; 7:748-57. [PMID: 24819876 DOI: 10.1158/1940-6207.capr-14-0057] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We identified acyl-coenzyme A-binding protein (ACBP) as part of a proteomic signature predicting the risk of having lung cancer. Because ACBP is known to regulate β-oxidation, which in turn controls cellular proliferation, we hypothesized that ACBP contributes to regulation of cellular proliferation and survival of non-small cell lung cancer (NSCLC) by modulating β-oxidation. We used matrix-assisted laser desorption/ionization-imaging mass spectrometry (MALDI-IMS) and immunohistochemistry (IHC) to confirm the tissue localization of ABCP in pre-invasive and invasive NSCLCs. We correlated ACBP gene expression levels in NSCLCs with clinical outcomes. In loss-of-function studies, we tested the effect of the downregulation of ACBP on cellular proliferation and apoptosis in normal bronchial and NSCLC cell lines. Using tritiated-palmitate ((3)H-palmitate), we measured β-oxidation levels and tested the effect of etomoxir, a β-oxidation inhibitor, on proliferation and apoptosis. MALDI-IMS and IHC analysis confirmed that ACBP is overexpressed in pre-invasive and invasive lung cancers. High ACBP gene expression levels in NSCLCs correlated with worse survival (HR = 1.73). We observed a 40% decrease in β-oxidation and concordant decreases in proliferation and increases in apoptosis in ACBP-depleted NSCLC cells as compared with bronchial airway epithelial cells. Inhibition of β-oxidation by etomoxir in ACBP-overexpressing cells produced dose-dependent decrease in proliferation and increase in apoptosis (P = 0.01 and P < 0.001, respectively). These data suggest a role for ACBP in controlling lung cancer progression by regulating β-oxidation.
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Affiliation(s)
- Fredrick T Harris
- Authors' Affiliations: Department of Biochemistry and Cancer Biology, Meharry Medical College; Division of Allergy, Pulmonary and Critical Care Medicine, Departments of
| | | | - Mohamed Hassanein
- Division of Allergy, Pulmonary and Critical Care Medicine, Departments of
| | - Jun Qian
- Division of Allergy, Pulmonary and Critical Care Medicine, Departments of
| | - Megan D Hoeksema
- Division of Allergy, Pulmonary and Critical Care Medicine, Departments of
| | | | | | - Pierre Chaurand
- Department of Chemistry, Université de Montréal, Montreal, Quebec, Canada
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine
| | | | - Pierre P Massion
- Division of Allergy, Pulmonary and Critical Care Medicine, Departments of Veterans Affairs Medical Center, Nashville, Tennessee; and
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35
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Casadonte R, Kriegsmann M, Zweynert F, Friedrich K, Baretton G, Bretton G, Otto M, Deininger SO, Paape R, Belau E, Suckau D, Aust D, Pilarsky C, Kriegsmann J. Imaging mass spectrometry to discriminate breast from pancreatic cancer metastasis in formalin-fixed paraffin-embedded tissues. Proteomics 2014; 14:956-64. [PMID: 24482424 DOI: 10.1002/pmic.201300430] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 12/17/2013] [Accepted: 12/29/2013] [Indexed: 11/07/2022]
Abstract
Diagnosis of the origin of metastasis is mandatory for adequate therapy. In the past, classification of tumors was based on histology (morphological expression of a complex protein pattern), while supportive immunohistochemical investigation relied only on few "tumor specific" proteins. At present, histopathological diagnosis is based on clinical information, morphology, immunohistochemistry, and may include molecular methods. This process is complex, expensive, requires an experienced pathologist and may be time consuming. Currently, proteomic methods have been introduced in various clinical disciplines. MALDI imaging MS combines detection of numerous proteins with morphological features, and seems to be the ideal tool for objective and fast histopathological tumor classification. To study a special tumor type and to identify predictive patterns that could discriminate metastatic breast from pancreatic carcinoma MALDI imaging MS was applied to multitissue paraffin blocks. A statistical classification model was created using a training set of primary carcinoma biopsies. This model was validated on two testing sets of different breast and pancreatic carcinoma specimens. We could discern breast from pancreatic primary tumors with an overall accuracy of 83.38%, a sensitivity of 85.95% and a specificity of 76.96%. Furthermore, breast and pancreatic liver metastases were tested and classified correctly.
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36
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Le Faouder J, Laouirem S, Alexandrov T, Ben-Harzallah S, Léger T, Albuquerque M, Bedossa P, Paradis V. Tumoral heterogeneity of hepatic cholangiocarcinomas revealed by MALDI imaging mass spectrometry. Proteomics 2014; 14:965-72. [DOI: 10.1002/pmic.201300463] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 01/24/2014] [Accepted: 01/27/2014] [Indexed: 01/29/2023]
Affiliation(s)
- Julie Le Faouder
- Claude Bernard Institute; Paris-Diderot University; Paris France
- INSERM U773; Biomedical Research Center; Paris-Diderot University; Paris France
| | - Samira Laouirem
- INSERM U773; Biomedical Research Center; Paris-Diderot University; Paris France
| | - Theodore Alexandrov
- Center for Industrial Mathematics; University of Bremen; Bremen Germany
- Steinbeis Innovation Center SCiLS Research; Bremen Germany
- SCiLS GmbH; Bremen Germany
- Skaggs School of Pharmacy and Pharmaceutical Sciences; University of California San Diego; La Jolla CA USA
| | | | - Thibaut Léger
- Mass Spectrometry Facility; Jacques Monod Institute; UMR7592-CNRS; University Paris-Diderot; Paris France
| | - Miguel Albuquerque
- Pathology Department; Beaujon Hospital; Assistance Publique-Hôpitaux de Paris; Clichy France
| | - Pierre Bedossa
- INSERM U773; Biomedical Research Center; Paris-Diderot University; Paris France
- Pathology Department; Beaujon Hospital; Assistance Publique-Hôpitaux de Paris; Clichy France
| | - Valérie Paradis
- INSERM U773; Biomedical Research Center; Paris-Diderot University; Paris France
- Pathology Department; Beaujon Hospital; Assistance Publique-Hôpitaux de Paris; Clichy France
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37
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Zhang D, Ren WH, Gao Y, Wang NY, Wu WJ. Clinical significance and prognostic value of pentraxin-3 as serologic biomarker for lung cancer. Asian Pac J Cancer Prev 2014; 14:4215-21. [PMID: 23991979 DOI: 10.7314/apjcp.2013.14.7.4215] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
PURPOSES Lung cancer is prevalent worldwide and improvements in timely and effective diagnosis are need. Pentraxin-3 as a novel serum marker for lung cancer (LC) has not been validated in large cohort studies. The aim of the study was to assess its clinical value in diagnosis and prognosis. METHODS We analyzed serum PTX-3 levels in a total of 1,605 patients with LC, benign lung diseases and healthy controls, as well as 493 non- lung cancer patients including 12 different types of cancers. Preoperative and postoperative data were further assessed in patients undergoing LC resection. The diagnostic performance of PTX-3 for LC and early-stage LC was assessed using receiver operating characteristics (ROC) by comparing with serum carcinoembryonic antigen (CEA), cytokeratin 19 fragments (CYFRA 21-1). RESULTS Levels of PTX-3 in serum were significantly higher in patients with LC than all controls. ROC curves showed the optimum diagnostic cutoff was 8.03ng/mL (AUC 0.823, [95%CI 0.789-0.856], sensitivity 72.8%, and specificity 77.3% in the test cohort; 0.802, [95%CI 0.762-0.843], sensitivity 69.7%, and specificity 76.4% in the validate cohort). Similar diagnostic performance of PTX-3 was observed for early-stage LC. PTX-3 decreased following surgical resection of LC and increased with tumor recurrence. Significantly elevated PTX-3 levels were also seen in patients with non-lung cancers. CONCLUSIONS The present data revealed that PTX-3 was significantly increased in both tissue and serum samples in LC patients. PTX-3 is a valuable biomarker for LC and improved identification of patients with LC and early-stage LC from those with non-malignant lung diseases.
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Affiliation(s)
- Dai Zhang
- Department of Clinical Laboratory, the First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China.
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38
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Li C, Hong W. Research status and funding trends of lung cancer biomarkers. J Thorac Dis 2013; 5:698-705. [PMID: 24255784 DOI: 10.3978/j.issn.2072-1439.2013.10.10] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 10/11/2013] [Indexed: 01/11/2023]
Abstract
Lung cancer is one of malignant tumors with the highest morbidity and mortality in the world. At present, research of early diagnosis, treatment, prognosis, and metastasis associated biomarkers is most active. This article reviewed the research status of lung cancer biomarkers and analyzed the funding situation in the field of lung cancer markers in recent 10 years in China and abroad, to provide a reference for the future basic and clinical translational research of lung cancer biomarkers.
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Affiliation(s)
- Cui Li
- Department of Health Science, National Natural Science Fundation of China, Beijing 100083, China
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39
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Bocklitz TW, Crecelius AC, Matthäus C, Tarcea N, von Eggeling F, Schmitt M, Schubert US, Popp J. Deeper understanding of biological tissue: quantitative correlation of MALDI-TOF and Raman imaging. Anal Chem 2013; 85:10829-34. [PMID: 24127731 DOI: 10.1021/ac402175c] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In order to achieve a comprehensive description of biological tissue, spectral information about proteins, lipids, nucleic acids, and other biochemical components need to be obtained concurrently. Different analytical techniques may be combined to record complementary information of the same sample. Established techniques, which can be utilized to elucidate the biochemistry of tissue samples are, for instance, MALDI-TOF-MS and Raman microscopic imaging. With this contribution, we combine these two techniques for the first time. The combination of both techniques allows the utilization and interpretation of complementary information (i.e., the information about the protein composition derived from the Raman spectra with data of the lipids analyzed by the MALDI-TOF measurements). Furthermore, we demonstrate how spectral information from MALDI-TOF experiments can be utilized to interpret Raman spectra.
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Affiliation(s)
- T W Bocklitz
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University Jena , Helmholtzweg 4, D-07743 Jena, Germany
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40
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Alberg AJ, Brock MV, Ford JG, Samet JM, Spivack SD. Epidemiology of lung cancer: Diagnosis and management of lung cancer, 3rd ed: American College of Chest Physicians evidence-based clinical practice guidelines. Chest 2013; 143:e1S-e29S. [PMID: 23649439 DOI: 10.1378/chest.12-2345] [Citation(s) in RCA: 458] [Impact Index Per Article: 41.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Ever since a lung cancer epidemic emerged in the mid-1900 s, the epidemiology of lung cancer has been intensively investigated to characterize its causes and patterns of occurrence. This report summarizes the key findings of this research. METHODS A detailed literature search provided the basis for a narrative review, identifying and summarizing key reports on population patterns and factors that affect lung cancer risk. RESULTS Established environmental risk factors for lung cancer include smoking cigarettes and other tobacco products and exposure to secondhand tobacco smoke, occupational lung carcinogens, radiation, and indoor and outdoor air pollution. Cigarette smoking is the predominant cause of lung cancer and the leading worldwide cause of cancer death. Smoking prevalence in developing nations has increased, starting new lung cancer epidemics in these nations. A positive family history and acquired lung disease are examples of host factors that are clinically useful risk indicators. Risk prediction models based on lung cancer risk factors have been developed, but further refinement is needed to provide clinically useful risk stratification. Promising biomarkers of lung cancer risk and early detection have been identified, but none are ready for broad clinical application. CONCLUSIONS Almost all lung cancer deaths are caused by cigarette smoking, underscoring the need for ongoing efforts at tobacco control throughout the world. Further research is needed into the reasons underlying lung cancer disparities, the causes of lung cancer in never smokers, the potential role of HIV in lung carcinogenesis, and the development of biomarkers.
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Affiliation(s)
- Anthony J Alberg
- Hollings Cancer Center and the Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC.
| | - Malcolm V Brock
- Department of Surgery, School of Medicine, Johns Hopkins University, Baltimore, MD
| | - Jean G Ford
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Jonathan M Samet
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Simon D Spivack
- Division of Pulmonary Medicine, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY
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41
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Hensing TA, Salgia R. Molecular biomarkers for future screening of lung cancer. J Surg Oncol 2013; 108:327-33. [PMID: 23893423 DOI: 10.1002/jso.23382] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 06/28/2013] [Indexed: 12/28/2022]
Abstract
The Landmark National Lung Screening Trial established the potential for low dose CT screening (LDCT) to reduce lung cancer-specific mortality in high-risk patients as defined by smoking history and age. However, the prevalence of lung cancer in asymptomatic smokers selected based on the NLST criteria is low. Recent advances have facilitated biomarker discovery for early diagnosis of lung cancer through the analysis of surrogate tissues, including airway epithelium, sputum, exhaled breath, and blood. Although a number of candidate diagnostic biomarkers have been described, none have been validated for use in the clinical setting. The NLST ACRIN biomarker repository is a valuable resource of annotated biological specimens that were collected during the NLST trial, which has the potential to facilitate validation of candidate biomarkers for early diagnosis identified in discovery trials. It will be important to perform retrospective and prospective analysis of biomarkers to screen for lung cancer. The review below summarizes some of our understanding of biomarkers in screening.
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Affiliation(s)
- Thomas A Hensing
- NorthShore University HealthSystem, Clinical Associate Professor of Medicine, University of Chicago Pritzker, Chicago, Illinois
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42
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Daniels JMA, Sutedja TG. Detection and minimally invasive treatment of early squamous lung cancer. Ther Adv Med Oncol 2013; 5:235-48. [PMID: 23858332 DOI: 10.1177/1758834013482345] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) is the most common cause of cancer deaths worldwide. The majority of patents presenting with NSCLC have advanced disease, which precludes curative treatment. Early detection and treatment might result in the identification of more patients with early central lung cancer and improve survival. In addition, the study of early lung cancer improves understanding of lung carcinogenesis and might also reveal new treatment targets for advanced lung cancer. Bronchoscopic investigation of the central airways can reveal both early central lung cancer in situ (stage 0) and other preinvasive lesions such as dysplasia. In the current review we discuss the detection of early squamous lung cancer, the natural history of preinvasive lesions and whether biomarkers can be used to predict progression to cancer. Finally we will review the staging and management of preinvasive lung cancer lesions and the different therapeutic modalities that are available.
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Affiliation(s)
- Johannes M A Daniels
- Department of Pulmonary Diseases, Z 4A48, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
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Abstract
Lung cancer is the leading cause of cancer death worldwide, making it an attractive disease for chemoprevention. Although avoidance of tobacco use and smoking cessation will have the greatest impact on lung cancer development, chemoprevention could prove to be very effective, particularly in former smokers. Chemoprevention is the use of agents to reverse or inhibit carcinogenesis and has been successfully applied to other common malignancies. Despite prior studies in lung cancer chemoprevention failing to identify effective agents, we now have the ability to identify high-risk populations, and our understanding of lung tumour and premalignant biology continues to advance. There are distinct histological lesions that can be reproducibly graded as precursors of non-small-cell lung cancer and similar precursor lesions exist for adenocarcinoma. These premalignant lesions are being targeted by chemopreventive agents in current trials and will continue to be studied in the future. In addition, biomarkers that predict risk and response to targeted agents are being investigated and validated. In this Review, we discuss the principles of chemoprevention, data from preclinical models, completed clinical trials and observational studies, and describe new treatments for novel targeted pathways and future chemopreventive efforts.
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Affiliation(s)
- Robert L Keith
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, VA Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, 1055 Clermont Street, Box 151, Denver, CO 80220, USA. robert.keith@ ucdenver.edu
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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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45
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Norris JL, Caprioli RM. Analysis of tissue specimens by matrix-assisted laser desorption/ionization imaging mass spectrometry in biological and clinical research. Chem Rev 2013; 113:2309-42. [PMID: 23394164 PMCID: PMC3624074 DOI: 10.1021/cr3004295] [Citation(s) in RCA: 509] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Jeremy L. Norris
- National Research Resource for Imaging Mass Spectrometry, Mass Spectrometry Research Center, and Department of Biochemistry, Vanderbilt University School of Medicine, 9160 Medical Research Building III, 465 21st Avenue South, Nashville, TN 37232-8575
| | - Richard M. Caprioli
- National Research Resource for Imaging Mass Spectrometry, Mass Spectrometry Research Center, and Department of Biochemistry, Vanderbilt University School of Medicine, 9160 Medical Research Building III, 465 21st Avenue South, Nashville, TN 37232-8575
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46
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Harris GA, Nicklay JJ, Caprioli RM. Localized in situ hydrogel-mediated protein digestion and extraction technique for on-tissue analysis. Anal Chem 2013; 85:2717-23. [PMID: 23402265 DOI: 10.1021/ac3031493] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A simultaneous on-tissue proteolytic digestion and extraction method is described for the in situ analysis of proteins from spatially distinct areas of a tissue section. The digestion occurs on-tissue within a hydrogel network, and peptides extracted from this gel are identified with liquid chromatography tandem MS (LC-MS/MS). The hydrogels are compatible with solubility agents (e.g., chaotropes and detergents) known to improve enzymatic digestion of proteins. Additionally, digestions and extractions are compatible with imaging mass spectrometry (IMS) experiments. As an example application, an initial IMS experiment was conducted to profile lipid species using a traveling wave ion mobility mass spectrometer. On-tissue MS/MS was also performed on the same tissue section to identify lipid ions that showed spatial differences. Subsequently, the section underwent an on-tissue hydrogel digestion to reveal 96 proteins that colocalized to the rat brain cerebellum. Hematoxylin and eosin (H & E) staining was then performed to provide additional histological information about the tissue structure. This technology provides a versatile workflow that can be used to correlate multiple complementary analytical approaches in the analysis of a single tissue section.
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Affiliation(s)
- Glenn A Harris
- Department of Biochemistry and the Mass Spectrometry Research Center, Vanderbilt University, 9160 MRB3, 465 21st Avenue South, Nashville, Tennessee 37235, United States
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47
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Radzikowska E, Roszkowski-Sliz K, Chabowski M, Glaz P. Influence of delays in diagnosis and treatment on survival in small cell lung cancer patients. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 788:355-62. [PMID: 23835998 DOI: 10.1007/978-94-007-6627-3_48] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The purpose of this study was to evaluate the influence on survival of delays in the diagnosis and treatment in an unselected population of small cell lung (SCLC) patients. Demographic and disease data of 3,479 SCLC patients were registered in the National Tuberculosis and Lung Diseases Research Institute in Warsaw, Poland during 1995-1998. In 50 % of patients, treatment started within 78 days from the appearance of first symptom(s). The median delay was 30 days (mean 47 days) and the median referral delay to a specialist was 19 days (mean 36 days). Half of SCLC patients were diagnosed during 34 days (mean 55 days). The mean time elapse from the diagnosis to the onset of therapy was 30 days (median 6 days). The multivariate analysis revealed that male gender-HR (hazard ratio = 1.2), ECOG Performance Status of 2 (HR = 1.5) and 3 + 4 (HR = 2.4), and clinical stage III (HR = 1.3) and IV (HR = 1.9) of the disease were independent negative predictors of survival. The patients treated with surgery and combined modality treatment had a better prognosis than those treated with chemoradiotherapy (HR = 1.6), chemotherapy (HR = 2.5), symptomatically (HR = 4.0), or those who refused therapy (HR = 3.9). The delay in the diagnosis and treatment had no effect on survival. Interestingly, patients who were diagnosed faster (below 42 days) actually had a worse prognosis than those diagnosed later. We conclude that a prolonged workup of SCLC patients and an extended time for treatment onset have a positive influence on survival, which may likely have to do with the determination of disease stage and more targeted treatment.
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Affiliation(s)
- E Radzikowska
- Third Department of Lung Diseases, National Institute of Tuberculosis and Lung Diseases, 26 Plocka St, 01-138, Warsaw, Poland,
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48
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Hood MI, Mortensen BL, Moore JL, Zhang Y, Kehl-Fie TE, Sugitani N, Chazin WJ, Caprioli RM, Skaar EP. Identification of an Acinetobacter baumannii zinc acquisition system that facilitates resistance to calprotectin-mediated zinc sequestration. PLoS Pathog 2012; 8:e1003068. [PMID: 23236280 PMCID: PMC3516566 DOI: 10.1371/journal.ppat.1003068] [Citation(s) in RCA: 201] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Accepted: 10/18/2012] [Indexed: 02/06/2023] Open
Abstract
Acinetobacter baumannii is an important nosocomial pathogen that accounts for up to 20 percent of infections in intensive care units worldwide. Furthermore, A. baumannii strains have emerged that are resistant to all available antimicrobials. These facts highlight the dire need for new therapeutic strategies to combat this growing public health threat. Given the critical role for transition metals at the pathogen-host interface, interrogating the role for these metals in A. baumannii physiology and pathogenesis could elucidate novel therapeutic strategies. Toward this end, the role for calprotectin- (CP)-mediated chelation of manganese (Mn) and zinc (Zn) in defense against A. baumannii was investigated. These experiments revealed that CP inhibits A. baumannii growth in vitro through chelation of Mn and Zn. Consistent with these in vitro data, Imaging Mass Spectrometry revealed that CP accompanies neutrophil recruitment to the lung and accumulates at foci of infection in a murine model of A. baumannii pneumonia. CP contributes to host survival and control of bacterial replication in the lung and limits dissemination to secondary sites. Using CP as a probe identified an A. baumannii Zn acquisition system that contributes to Zn uptake, enabling this organism to resist CP-mediated metal chelation, which enhances pathogenesis. Moreover, evidence is provided that Zn uptake across the outer membrane is an energy-dependent process in A. baumannii. Finally, it is shown that Zn limitation reverses carbapenem resistance in multidrug resistant A. baumannii underscoring the clinical relevance of these findings. Taken together, these data establish Zn acquisition systems as viable therapeutic targets to combat multidrug resistant A. baumannii infections. Acinetobacter baumannii is a bacterium responsible for an increasing number of infections in the hospital setting. These infections are particularly challenging because most strains of A. baumannii are resistant to commonly used antibiotics. Unfortunately, there is relatively little known about this organism and how it causes disease, making it difficult to identify new drug targets. In order to address this problem we examined the role for nutrient manganese (Mn) and zinc (Zn) in A. baumannii infections. We have determined that the host protein, calprotectin (CP), contributes to defense against A. baumannii pneumonia through chelation of nutrient Mn and Zn. Moreover, employing purified calprotectin as a probe allowed us to identify a Zn acquisition system in A. baumannii that is required for efficient Zn uptake in vitro and full pathogenesis in vivo. Finally, we demonstrate that inhibiting Zn acquisition can reverse antibiotic resistance mechanisms that rely on Zn-dependent enzymes. Taken together, these results demonstrate the importance of Zn acquisition to A. baumannii pathogenesis and antibiotic resistance, establishing Zn acquisition as a potential target for therapeutic development.
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MESH Headings
- Acinetobacter Infections/drug therapy
- Acinetobacter Infections/genetics
- Acinetobacter Infections/immunology
- Acinetobacter baumannii/genetics
- Acinetobacter baumannii/immunology
- Acinetobacter baumannii/pathogenicity
- Animals
- Biological Transport, Active
- Carbapenems/pharmacology
- Disease Models, Animal
- Drug Resistance, Multiple, Bacterial/drug effects
- Drug Resistance, Multiple, Bacterial/genetics
- Drug Resistance, Multiple, Bacterial/immunology
- Humans
- Leukocyte L1 Antigen Complex/immunology
- Lung/immunology
- Lung/pathology
- Manganese/immunology
- Mice
- Mice, Knockout
- Neutrophil Infiltration/genetics
- Neutrophil Infiltration/immunology
- Neutrophils/immunology
- Neutrophils/pathology
- Pneumonia, Bacterial/genetics
- Pneumonia, Bacterial/immunology
- Pneumonia, Bacterial/pathology
- Zinc/immunology
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Affiliation(s)
- M. Indriati Hood
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Brittany L. Mortensen
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Jessica L. Moore
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Yaofang Zhang
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Thomas E. Kehl-Fie
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Norie Sugitani
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Walter J. Chazin
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Richard M. Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Eric P. Skaar
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail:
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Oak CH, Wilson D, Lee HJ, Lim HJ, Park EK. Potential molecular approaches for the early diagnosis of lung cancer (review). Mol Med Rep 2012; 6:931-6. [PMID: 22923136 DOI: 10.3892/mmr.2012.1042] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Accepted: 08/13/2012] [Indexed: 11/06/2022] Open
Abstract
Lung cancer is the leading cause of mortality from cancer among men and women worldwide. More individuals die each year of lung cancer than of colon, breast and prostate cancer combined. Despite new diagnostic techniques, the overall 5-year survival rate remains at approximately 15% and the majority of patients still present with advanced disease. Therefore, lung cancer is the most lethal cancer at present. Diagnosing and treating cancer at its early stages, ideally during the precancerous stages, could increase the 5-year survival rate by 3-4‑fold, with the possibility of cure. To date, no screening method has been shown to decrease the disease-specific mortality rate. This review describes issues related to early lung cancer screening and their rationale, the management of primary cancers detected by screening and the different approaches that have been tested for cancer screening; these include imaging techniques, bronchoscopies and molecular screening, such as analysis of epigenomics using different noninvasive or invasive sources, such as blood, sputum, bronchoscopic samples and exhaled breath.
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Affiliation(s)
- Chul Ho Oak
- Department of Internal Medicine, College of Medicine, Kosin University, Busan, Republic of Korea
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50
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Imaging mass spectrometry in biomarker discovery and validation. J Proteomics 2012; 75:4990-4998. [PMID: 22749859 DOI: 10.1016/j.jprot.2012.06.015] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 06/13/2012] [Accepted: 06/18/2012] [Indexed: 12/27/2022]
Abstract
Biomarker discovery and validation involves the consideration of many issues and challenges in order to be effectively used for translation from bench to bedside. Imaging mass spectrometry (IMS) is a new technology to assess spatial molecular arrangements in tissue sections, going far beyond microscopy in providing hundreds of different molecular images from a single scan without the need of target-specific reagents. The possibility to correlate distribution maps of multiple analytes with histological and clinical features makes it an ideal tool to discover diagnostic and prognostic markers of diseases. Some recently published studies that show the usefulness and advantages of this technology in the field of cancer research are highlighted.
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