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1
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Bouchard G, Zhang W, Ilerten I, Li I, Bhattacharya A, Li Y, Trope W, Shrager JB, Kuo C, Ozawa MG, Giaccia AJ, Tian L, Plevritis SK. A quantitative spatial cell-cell colocalizations framework enabling comparisons between in vitro assembloids and pathological specimens. Nat Commun 2025; 16:1392. [PMID: 39915493 PMCID: PMC11802768 DOI: 10.1038/s41467-024-55129-6] [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: 11/30/2023] [Accepted: 11/29/2024] [Indexed: 02/09/2025] Open
Abstract
Spatial omics is enabling unprecedented tissue characterization, but the ability to adequately compare spatial features across samples under different conditions is lacking. We propose a quantitative framework that catalogs significant, normalized, colocalizations between pairs of cell subpopulations, enabling comparisons among a variety of biological samples. We perform cell-pair colocalization analysis on multiplexed immunofluorescence images of assembloids constructed with lung adenocarcinoma (LUAD) organoids and cancer-associated fibroblasts derived from human tumors. Our data show that assembloids recapitulate human LUAD tumor-stroma spatial organization, justifying their use as a tool for investigating the spatial biology of human disease. Intriguingly, drug-perturbation studies identify drug-induced spatial rearrangements that also appear in treatment-naïve human tumor samples, suggesting potential directions for characterizing spatial (re)-organization related to drug resistance. Moreover, our work provides an opportunity to quantify spatial data across different samples, with the common goal of building catalogs of spatial features associated with disease processes and drug response.
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Affiliation(s)
- Gina Bouchard
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Weiruo Zhang
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Ilayda Ilerten
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Irene Li
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Asmita Bhattacharya
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Yuanyuan Li
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Winston Trope
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Joseph B Shrager
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
- Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
| | - Calvin Kuo
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Michael G Ozawa
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Amato J Giaccia
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
- Department of Oncology, University of Oxford, Oxford, UK
| | - Lu Tian
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Sylvia K Plevritis
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
- Department of Radiology, Stanford University, Stanford, CA, USA.
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2
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Khartchenko AF, Lam T, Herr AE. Single-cell differential detergent fractionation for detection of cytokeratin 8 proteoforms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.21.634008. [PMID: 39896550 PMCID: PMC11785136 DOI: 10.1101/2025.01.21.634008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/04/2025]
Abstract
Simultaneous profiling of proteoforms and nucleic acids at the single-cell level, i.e., multi omics, directly links the central dogma. However, current single-cell approaches are limited in their ability to identify proteoforms while preserving the nucleus for further analysis. This limitation is especially pronounced in proteins where their proteoforms present diverse biological functions such as cytokeratin 8 (CK8), which, while commonly known for its structural role, is also involved in several diseases. Here, we present a single-cell western blot (scWB) integrated with differential detergent fractionation (DDF) to selectively solubilize and separate CK8 proteoforms while preserving nuclear integrity for subsequent nucleus-based assays. We report on assay development, including screening a panel of lysis buffers based on nonionic detergents and electrophoresis conditions to achieve a separation resolution between two proteoforms of up to 0.94 with an electric field of 30 V/cm, while preserving an intact nucleus. The cytoplasm-specific lysis approach (DDF buffer) demonstrated comparable solubilization efficiency to whole-cell solubilization (RIPA buffer), achieving proteoform solubilization in 14.3% and 10.3% of solubilized cells using DDF and RIPA buffers, respectively, while keeping the nucleus intact. To understand the broad applicability of the assay conditions, we scrutinized electrophoresis performance for resolving CK8 proteoforms across a panel of widely used breast cancer cell lines (MCF7, SKBR3, and MDA-MB-231), showing presence of proteoforms only in MCF7. Our approach allows for tailored solubilization, achieving reliable proteoform detection and nuclear retention across different cell types. Proteoform profiling at the single-cell level forms a basis for the exploration of the role of specific CK8 molecular forms in cellular processes.
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Affiliation(s)
| | - Trinh Lam
- University of California, Berkeley, USA
| | - Amy E. Herr
- University of California, Berkeley, USA
- Chan Zuckerberg Biohub, USA
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Zhang M, Zhang J, Teng H, Zhang Q, Xiang Z, Chang Q, Tao Y, Chu T, Ying W. Decreased green autofluorescence of lung parenchyma is a biomarker for lung cancer tissues. JOURNAL OF BIOPHOTONICS 2022; 15:e202200072. [PMID: 35429151 DOI: 10.1002/jbio.202200072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/04/2022] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
It is highly valuable to discover novel biomarkers for differentiating noninvasively the cancerous tissues from the nonneoplastic tissues of lung cancer. In current study, we determined the green autofluorescence (AF) of the pulmonary parenchyma of lung cancer patients, indicating that decreased green AF of pulmonary parenchyma may be the biomarker of this type: First, the green AF intensity of the cancerous tissues was significantly lower than that of the nonneoplastic tissues of the lung cancer patients; second, the green AF intensity of the nonneoplastic tissues of the lung squamous cell carcinoma was significantly lower than that of the lung adenocarcinoma; and third, "decreased green AF intensity" could be used for differentiating the nonneoplastic tissues and the cancerous tissues. Collectively, our study has suggested that decreased green AF of lung parenchyma is a biomarker for differentiating the cancerous tissues from the nonneoplastic tissues of lung cancer.
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Affiliation(s)
- Mingchao Zhang
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Zhang
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Haohua Teng
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Qing Zhang
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Zhenzhen Xiang
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Qing Chang
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yue Tao
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Tianqing Chu
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Weihai Ying
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
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4
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Wu X, Yang W, Gou XH, Xu XY, Lu N, Jian SN, Han YJ, Lv TS, Luo LZ. A study of the proteomic expression in patients with complicated parapneumonic pleural effusion. Arch Med Sci 2021; 19:1270-1280. [PMID: 37732066 PMCID: PMC10507766 DOI: 10.5114/aoms/132885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 01/27/2021] [Indexed: 09/22/2023] Open
Abstract
Introduction The present study aimed to investigate the differences in the proteomic expression between uncomplicated parapneumonic pleural effusion (UPPE) and complicated parapneumonic pleural effusion (CPPE). Material and methods There were 10 patients with UPPE and 10 patients with CPPE. These patients were combined due to the complication of pleural effusion and further divided into group A and group B. An LC-MS analysis was conducted with the extraction of high-abundance proteins, and proteins with 1.5-fold or higher difference multiples were identified as differential proteins. Then, gene ontology (GO) and KEGG analyses were conducted on the differential proteins between the groups. Results Compared with the UPPE group, there were 38 upregulated proteins and 29 downregulated proteins in the CPPE group. The GO analysis revealed that the CPPE group had enhanced expressions in monosaccharide biosynthesis, glucose catabolism, fructose-6-phosphate glycolysis, glucose-6-phosphate glycolysis, and NADH regeneration as well as reduced expressions in fibrinogen complexes, protein polymerization, and coagulation. Moreover, the KEGG analysis showed that the CPPE group had enhanced expressions in amino acid synthesis, the HIF-1 signalling pathway, and glycolysis/glycoisogenesis and decreased expressions in platelet activation and complement activation. Conclusions In pleural effusion in patients with CPPE, there are enhanced expressions of proteins concerning glucose and amino acid metabolism, NADH regeneration, and HIF-1 signalling pathways together with decreased expressions of proteins concerning protein polymerization, blood coagulation, platelet activation, and complement activation.
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Affiliation(s)
- Xin Wu
- The Second Department of Respiration, Baoding No.1 Central Hospital, HeBei, China
| | - Wei Yang
- The Second Department of Respiration, Baoding No.1 Central Hospital, HeBei, China
| | - Xiao-Hua Gou
- The Second Department of Respiration, Baoding No.1 Central Hospital, HeBei, China
| | - Xiao-Yun Xu
- The Second Department of Respiration, Baoding No.1 Central Hospital, HeBei, China
| | - Na Lu
- Department of Respiration, Lixian County Hospital, HeBei, China
| | - Shi-Ning Jian
- The Second Department of Respiration, Baoding No.1 Central Hospital, HeBei, China
| | - Yu-Jie Han
- The Second Department of Respiration, Baoding No.1 Central Hospital, HeBei, China
| | - Tong-Shuai Lv
- The Second Department of Respiration, Baoding No.1 Central Hospital, HeBei, China
| | - Li-Zhu Luo
- The Second Department of Respiration, Baoding No.1 Central Hospital, HeBei, China
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Hou WL, Chang M, Liu XF, Hu LS, Hua SC. Proteomic and ultrastructural analysis of Clara cell and type II alveolar epithelial cell-type lung cancer cells. Transl Cancer Res 2020; 9:565-576. [PMID: 35117401 PMCID: PMC8798965 DOI: 10.21037/tcr.2019.12.04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/15/2019] [Indexed: 11/06/2022]
Abstract
BACKGROUND Currently, the identification of Clara cell and type II alveolar epithelial cell-type cancer cells requires electron microscopy, which is a time-consuming and expensive process involving a complicated tissue sampling procedure. The aim of this study was to identify unique biomarkers for Clara cell and type II alveolar epithelial cell-type lung cancer cells, respectively, with proteomic profiling. METHODS Six human lung adenocarcinoma cell lines (A549, NCI-H358, NCI-H1650, HCC827, NCI-H1395, and NCI-H1975) were investigated for their ultrastructural characteristics. The differentially expressed proteins (DEPs) were screened between NCI-H358 cells (Clara cell type) and A549 cells (type II alveolar epithelial cell type) using two-dimensional difference gel electrophoresis (2D-DIGE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS/MS), and then they were validated by western blot. The protein expression levels of endoplasmic reticulum oxidoreductin 1-α (ERO1L), Clara cell 10-kD protein (CC10), and surfactant protein C (SP-C) were also determined in the six cell lines assayed. RESULTS NCI-H358 cells featured Clara cell differentiation; A549, NCI-H1975, and HCC827 cells had characteristics of type II alveolar epithelial cells; and NCI-H1395 and NCI-H1650 cells had no differentiation characteristics of any lung adenocarcinoma cell type. Five DEPs including ubiquitin carboxyl-terminal hydrolase isozyme L1 (UCHL1), cytokeratin 19 (CK19), cytokeratin 8 (CK8), ERO1L, and peroxiredoxin 2 (PRDX2) between NCI-H358 and A549 cells were identified for further validation; however, none of them showed suitability as an effective biomarker. Similarly, CC10 and SP-C were not appropriate biomarkers. CONCLUSIONS Cytological subtypes of NCI-H1975 and HCC827 cells were identified, but no promising biomarker was discovered in the present study.
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Affiliation(s)
- Wen-Li Hou
- Department of Cadre Ward, The First Hospital of Jilin University, Changchun 130021, China
| | - Ming Chang
- Translational Medicine Research Institute, The First Hospital of Jilin University, Changchun 130021, China
| | - Xiao-Feng Liu
- Translational Medicine Research Institute, The First Hospital of Jilin University, Changchun 130021, China
| | - Lin-Sen Hu
- Translational Medicine Research Institute, The First Hospital of Jilin University, Changchun 130021, China
| | - Shu-Cheng Hua
- Department of Respiration, The First Hospital of Jilin University, Changchun 130021, China
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Perzanowska A, Fatalska A, Wojtas G, Lewandowicz A, Michalak A, Krasowski G, Borchers CH, Dadlez M, Domanski D. An MRM-Based Cytokeratin Marker Assay as a Tool for Cancer Studies: Application to Lung Cancer Pleural Effusions. Proteomics Clin Appl 2018; 12. [DOI: 10.1002/prca.201700084] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 01/03/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Anna Perzanowska
- Mass Spectrometry Laboratory; Institute of Biochemistry and Biophysics-Polish Academy of Sciences; Warsaw Poland
| | - Agnieszka Fatalska
- Mass Spectrometry Laboratory; Institute of Biochemistry and Biophysics-Polish Academy of Sciences; Warsaw Poland
| | - Grzegorz Wojtas
- Mazovian Center of Pulmonary Disease and Tuberculosis Treatment; Otwock Poland
| | - Andrzej Lewandowicz
- Department of Geriatrics; National Institute of Geriatrics, Rheumatology and Rehabilitation; Warsaw Poland
| | - Agata Michalak
- Mazovian Center of Pulmonary Disease and Tuberculosis Treatment; Otwock Poland
| | - Grzegorz Krasowski
- Mazovian Center of Pulmonary Disease and Tuberculosis Treatment; Otwock Poland
| | - Christoph H. Borchers
- Proteomics Centre; Segal Cancer Centre; Lady Davis Institute; Jewish General Hospital; McGill University; Montreal Quebec Canada
- Gerald Bronfman Department of Oncology; Jewish General Hospital; McGill University; Montreal Quebec Canada
- Genome British Columbia Proteomics Centre; University of Victoria; Victoria British Columbia Canada
- Department of Biochemistry and Microbiology; University of Victoria; Victoria British Columbia Canada
| | - Michal Dadlez
- Mass Spectrometry Laboratory; Institute of Biochemistry and Biophysics-Polish Academy of Sciences; Warsaw Poland
| | - Dominik Domanski
- Mass Spectrometry Laboratory; Institute of Biochemistry and Biophysics-Polish Academy of Sciences; Warsaw Poland
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Tan HW, Xu YM, Wu DD, Lau ATY. Recent insights into human bronchial proteomics - how are we progressing and what is next? Expert Rev Proteomics 2018; 15:113-130. [PMID: 29260600 DOI: 10.1080/14789450.2017.1417847] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The human respiratory system is highly prone to diseases and complications. Many lung diseases, including lung cancer (LC), tuberculosis (TB), and chronic obstructive pulmonary disease (COPD) have been among the most common causes of death worldwide. Cystic fibrosis (CF), the most common genetic disease in Caucasians, has adverse impacts on the lungs. Bronchial proteomics plays a significant role in understanding the underlying mechanisms and pathogenicity of lung diseases and provides insights for biomarker and therapeutic target discoveries. Areas covered: We overview the recent achievements and discoveries in human bronchial proteomics by outlining how some of the different proteomic techniques/strategies are developed and applied in LC, TB, COPD, and CF. Also, the future roles of bronchial proteomics in predictive proteomics and precision medicine are discussed. Expert commentary: Much progress has been made in bronchial proteomics. Owing to the advances in proteomics, we now have better ability to isolate proteins from desired cellular compartments, greater protein separation methods, more powerful protein detection technologies, and more sophisticated bioinformatic techniques. These all contributed to our further understanding of lung diseases and for biomarker and therapeutic target discoveries.
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Affiliation(s)
- Heng Wee Tan
- a Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics , Shantou University Medical College , Shantou , People's Republic of China
| | - Yan-Ming Xu
- a Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics , Shantou University Medical College , Shantou , People's Republic of China
| | - Dan-Dan Wu
- a Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics , Shantou University Medical College , Shantou , People's Republic of China
| | - Andy T Y Lau
- a Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics , Shantou University Medical College , Shantou , People's Republic of China
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8
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Domanski D, Perzanowska A, Kistowski M, Wojtas G, Michalak A, Krasowski G, Dadlez M. A Multiplexed Cytokeratin Analysis Using Targeted Mass Spectrometry Reveals Specific Profiles in Cancer-Related Pleural Effusions. Neoplasia 2016; 18:399-412. [PMID: 27435923 PMCID: PMC4954941 DOI: 10.1016/j.neo.2016.06.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 06/03/2016] [Indexed: 12/11/2022] Open
Abstract
Pleural effusion (PE), excess fluid in the pleural space, is often observed in lung cancer patients and also forms due to many benign ailments. Classifying it quickly is critical, but this remains an analytical challenge often lengthening the diagnosis process or exposing patients to unnecessary risky invasive procedures. We tested the analysis of PE using a multiplexed cytokeratin (CK) panel with targeted mass spectrometry–based quantitation for its rapid classification. CK markers are often assessed in pathological examinations for cancer diagnosis and guiding treatment course. We developed methods to simultaneously quantify 33 CKs in PE using peptide standards for increased analytical specificity and a simple CK enrichment method to detect their low amounts. Analyzing 121 PEs associated with a variety of lung cancers and noncancerous causes, we show that abundance levels of 10 CKs can be related to PE etiology. CK-6, CK-7, CK-8, CK-18, and CK-19 were found at significantly higher levels in cancer-related PEs. Additionally, elevated levels of vimentin and actin differentiated PEs associated with bacterial infections. A classifier algorithm effectively grouped PEs into cancer-related or benign PEs with 81% sensitivity and 79% specificity. A set of undiagnosed PEs showed that our method has potential to shorten PE diagnosis time. For the first time, we show that a cancer-relevant panel of simple-epithelial CK markers currently used in clinical assessment can also be quantitated in PEs. Additionally, while requiring less invasive sampling, our methodology demonstrated a significant ability to identify cancer-related PEs in clinical samples and thus could improve patient care in the future.
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Affiliation(s)
- Dominik Domanski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland.
| | - Anna Perzanowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Michal Kistowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Grzegorz Wojtas
- Mazovian Center of Pulmonary Disease and Tuberculosis Treatment, Gabriela Narutowicza 80, Otwock, Poland
| | - Agata Michalak
- Mazovian Center of Pulmonary Disease and Tuberculosis Treatment, Gabriela Narutowicza 80, Otwock, Poland
| | - Grzegorz Krasowski
- Mazovian Center of Pulmonary Disease and Tuberculosis Treatment, Gabriela Narutowicza 80, Otwock, Poland
| | - Michal Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland.
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Lu N, Gao A, Dai P, Mao H, Zuo X, Fan C, Wang Y, Li T. Ultrasensitive Detection of Dual Cancer Biomarkers with Integrated CMOS-Compatible Nanowire Arrays. Anal Chem 2015; 87:11203-8. [PMID: 26473941 DOI: 10.1021/acs.analchem.5b01729] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A direct, rapid, highly sensitive and specific biosensor for detection of cancer biomarkers is desirable in early diagnosis and prognosis of cancer. However, the existing methods of detecting cancer biomarkers suffer from poor sensitivity as well as the requirement of enzymatic labeling or nanoparticle conjugations. Here, we proposed a two-channel PDMS microfluidic integrated CMOS-compatible silicon nanowire (SiNW) field-effect transistor arrays with potentially single use for label-free and ultrasensitive electrical detection of cancer biomarkers. The integrated nanowire arrays showed not only ultrahigh sensitivity of cytokeratin 19 fragment (CYFRA21-1) and prostate specific antigen (PSA) with detection to at least 1 fg/mL in buffer solution but also highly selectivity of discrimination from other similar cancer biomarkers. In addition, this method was used to detect both CYFRA21-1 and PSA real samples as low as 10 fg/mL in undiluted human serums. With its excellent properties and miniaturization, the integrated SiNW-FET device opens up great opportunities for a point-of-care test (POCT) for quick screening and early diagnosis of cancer and other complex diseases.
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Affiliation(s)
- Na Lu
- Science and Technology on Microsystem Laboratory, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences , Shanghai 200050, China
| | - Anran Gao
- Science and Technology on Microsystem Laboratory, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences , Shanghai 200050, China
| | - Pengfei Dai
- Science and Technology on Microsystem Laboratory, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences , Shanghai 200050, China
| | - Hongju Mao
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences , Shanghai 200050, China
| | - Xiaolei Zuo
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Yuelin Wang
- Science and Technology on Microsystem Laboratory, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences , Shanghai 200050, China
| | - Tie Li
- Science and Technology on Microsystem Laboratory, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences , Shanghai 200050, China
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10
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Pøhl M, Olsen KE, Holst R, Donnem T, Busund LT, Bremnes RM, Al-Saad S, Andersen S, Richardsen E, Ditzel HJ, Hansen O. Keratin 34betaE12/keratin7 expression is a prognostic factor of cancer-specific and overall survival in patients with early stage non-small cell lung cancer. Acta Oncol 2015; 55:167-77. [PMID: 26057535 DOI: 10.3109/0284186x.2015.1049291] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
BACKGROUND Carcinomas and their metastases often retain the keratin patterns of their epithelial origin, and are therefore useful as lineage-specific markers in diagnostic pathology. Recently, it has become clear that intermediate filaments composed by keratins play a role in modulation of cell proliferation, migration, and possibly cancer invasion, factors impacting prognosis in early stage non-small cell lung cancer (NSCLC). MATERIAL AND METHODS Tumor tissue from a retrospective Danish cohort of 177 patients with completely resected NSCLC, stage I-IIIA tumors, were analyzed for keratin 7 (K7) and keratin 34βE12 expression by immunohistochemistry and validated in a comparable independent Norwegian cohort of 276 stage I-IIIA NSCLC patients. RESULTS Based on keratin 34βE12/K7 expression, three subgroups with significantly different median cancer-specific survival rates were identified (34βE12+/K7+, 168 months vs. 34βE12+/K7+, 73 months vs. 34βE12-/K7+, 30 months; p = 0.0004). In multivariate analysis, stage II-IIIA (HR 2.9), 34βE12+/K7+ (HR 1.90) and 34βE12-/K7+ (HR 3.7), were prognostic factors of poor cancer-specific survival (CSS) (p < 0.001). Validation in the Norwegian cohort confirmed that stage II-IIIA (HR 2.3), 34βE12+/K7+ (HR 1.6), and 34βE12-/K7+ (HR 2.0) were prognostic factors of poor CSS (p < 0.05). Multivariate Cox proportional-hazard analysis demonstrated that 34βE12+/K7 + and 34βE12+/K7 + status was significantly associated with poor overall survival (p < 0.05). CONCLUSION Keratin 34βE12/K7 expression is a prognostic parameter in resected early stage NSCLC that allows identification of high-risk NSCLC patients with poor cancer-specific and overall survival.
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Affiliation(s)
- Mette Pøhl
- a Department of Oncology , Odense University Hospital , Odense , Denmark
- b Institute of Clinical Research, University of Southern Denmark , Odense , Denmark
- f Department of Oncology , Rigshospitalet , Copenhagen , Denmark
| | - Karen Ege Olsen
- b Institute of Clinical Research, University of Southern Denmark , Odense , Denmark
- c Department of Pathology , Odense University Hospital , Odense , Denmark
| | - Rene Holst
- d Department of Statistics , University of Southern Denmark , Odense , Denmark
| | - Tom Donnem
- g Institute of Clinical Medicine, University of Tromso , Tromso , Norway
- h Department of Oncology , University Hospital of North Norway , Tromso , Norway
| | - Lill-Tove Busund
- i Institute of Medical Biology, University of Tromso , Tromso , Norway
- j Department of Clinical Pathology , University Hospital of North Norway , Tromso , Norway
| | - Roy M Bremnes
- g Institute of Clinical Medicine, University of Tromso , Tromso , Norway
- h Department of Oncology , University Hospital of North Norway , Tromso , Norway
| | - Samer Al-Saad
- i Institute of Medical Biology, University of Tromso , Tromso , Norway
- j Department of Clinical Pathology , University Hospital of North Norway , Tromso , Norway
| | - Sigve Andersen
- g Institute of Clinical Medicine, University of Tromso , Tromso , Norway
- h Department of Oncology , University Hospital of North Norway , Tromso , Norway
| | - Elin Richardsen
- i Institute of Medical Biology, University of Tromso , Tromso , Norway
- j Department of Clinical Pathology , University Hospital of North Norway , Tromso , Norway
| | - Henrik J Ditzel
- a Department of Oncology , Odense University Hospital , Odense , Denmark
- e Department of Cancer and Inflammation Research , Institute of Molecular Medicine, University of Southern Denmark , Odense , Denmark
| | - Olfred Hansen
- a Department of Oncology , Odense University Hospital , Odense , Denmark
- b Institute of Clinical Research, University of Southern Denmark , Odense , Denmark
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11
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Kisluk J, Ciborowski M, Niemira M, Kretowski A, Niklinski J. Proteomics biomarkers for non-small cell lung cancer. J Pharm Biomed Anal 2014; 101:40-9. [DOI: 10.1016/j.jpba.2014.07.038] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 07/29/2014] [Accepted: 07/31/2014] [Indexed: 01/07/2023]
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12
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Ma Y, Fan M, Chen K. [Significance of immunohistochemical indicators in diagnosis and prognosis of
squamous cell carcinoma and adenocarcinoma of lung]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2014; 17:506-10. [PMID: 24949694 PMCID: PMC6000096 DOI: 10.3779/j.issn.1009-3419.2014.06.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Yunfan Ma
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department I of Thoracic Surgery,
Peking University Cancer Hospital, Beijing 100142, China
| | - Mengying Fan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department I of Thoracic Surgery,
Peking University Cancer Hospital, Beijing 100142, China
| | - Keneng Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department I of Thoracic Surgery,
Peking University Cancer Hospital, Beijing 100142, China
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13
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miR-9 is an essential oncogenic microRNA specifically overexpressed in mixed lineage leukemia-rearranged leukemia. Proc Natl Acad Sci U S A 2013; 110:11511-6. [PMID: 23798388 DOI: 10.1073/pnas.1310144110] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs (miRNAs), small noncoding RNAs that regulate target gene mRNAs, are known to contribute to pathogenesis of cancers. Acute myeloid leukemia (AML) is a group of heterogeneous hematopoietic malignancies with various chromosomal and/or molecular abnormalities. AML with chromosomal translocations involving the mixed lineage leukemia (MLL) gene are usually associated with poor survival. In the present study, through a large-scale, genomewide miRNA expression assay, we show that microRNA-9 (miR-9) is the most specifically up-regulated miRNA in MLL-rearranged AML compared with both normal control and non-MLL-rearranged AML. We demonstrate that miR-9 is a direct target of MLL fusion proteins and can be significantly up-regulated in expression by the latter in human and mouse hematopoietic stem/progenitor cells. Depletion of endogenous miR-9 expression by an appropriate antagomiR can significantly inhibit cell growth/viability and promote apoptosis in human MLL-rearranged AML cells, and the opposite is true when expression of miR-9 is forced. Blocking endogenous miR-9 function by anti-miRNA sponge can significantly inhibit, whereas forced expression of miR-9 can significantly promote, MLL fusion-induced immortalization/transformation of normal mouse bone marrow progenitor cells in vitro. Furthermore, forced expression of miR-9 can significantly promote MLL fusion-mediated leukemogenesis in vivo. In addition, a group of putative target genes of miR-9 exhibited a significant inverse correlation of expression with miR-9 in a series of leukemia sample sets, suggesting that they are potential targets of miR-9 in MLL-rearranged AML. Collectively, our data demonstrate that miR-9 is a critical oncomiR in MLL-rearranged AML and can serve as a potential therapeutic target to treat this dismal disease.
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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: 1.8] [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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15
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Ceruti P, Principe M, Capello M, Cappello P, Novelli F. Three are better than one: plasminogen receptors as cancer theranostic targets. Exp Hematol Oncol 2013; 2:12. [PMID: 23594883 PMCID: PMC3640925 DOI: 10.1186/2162-3619-2-12] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 03/28/2013] [Indexed: 12/22/2022] Open
Abstract
Activation of plasminogen on the cell surface initiates a cascade of protease activity with important implications for several physiological and pathological events. In particular, components of the plasminogen system participate in tumor growth, invasion and metastasis. Plasminogen receptors are in fact expressed on the cell surface of most tumors, and their expression frequently correlates with cancer diagnosis, survival and prognosis. Notably, they can trigger multiple specific immune responses in cancer patients, highlighting their role as tumor-associated antigens. In this review, three of the most characterized plasminogen receptors involved in tumorigenesis, namely Annexin 2 (ANX2), Cytokeratin 8 (CK8) and alpha-Enolase (ENOA), are analyzed to ascertain an overall view of their role in the most common cancers. This analysis emphasizes the possibility of delineating new personalized therapeutic strategies to counteract tumor growth and metastasis by targeting plasminogen receptors, as well as their potential application as cancer predictors.
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Affiliation(s)
- Patrizia Ceruti
- Center for Experimental Research and Medical Studies (CeRMS), Azienda Ospedaliera Città della Salute e della Scienza, Via Cherasco 15, Turin, 10126, Italy.,Department of Molecular Biotechnology and Health Science, University of Turin, Turin, Italy
| | - Moitza Principe
- Center for Experimental Research and Medical Studies (CeRMS), Azienda Ospedaliera Città della Salute e della Scienza, Via Cherasco 15, Turin, 10126, Italy.,Department of Molecular Biotechnology and Health Science, University of Turin, Turin, Italy
| | - Michela Capello
- Center for Experimental Research and Medical Studies (CeRMS), Azienda Ospedaliera Città della Salute e della Scienza, Via Cherasco 15, Turin, 10126, Italy.,Department of Molecular Biotechnology and Health Science, University of Turin, Turin, Italy
| | - Paola Cappello
- Center for Experimental Research and Medical Studies (CeRMS), Azienda Ospedaliera Città della Salute e della Scienza, Via Cherasco 15, Turin, 10126, Italy.,Department of Molecular Biotechnology and Health Science, University of Turin, Turin, Italy
| | - Francesco Novelli
- Center for Experimental Research and Medical Studies (CeRMS), Azienda Ospedaliera Città della Salute e della Scienza, Via Cherasco 15, Turin, 10126, Italy.,Department of Molecular Biotechnology and Health Science, University of Turin, Turin, Italy
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16
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Abstract
Ovine pulmonary adenocarcinoma (OPA) is a transmissible lung cancer of sheep caused by jaagsiekte sheep retrovirus (JSRV). In the present study the protein profiles of five neoplastic and three non-neoplastic sheep lung tissues were examined for the identification of proteins overexpressed in ovine pulmonary adenocarcinoma. Lung sections of the experimental group of sheep were collected during necropsies for proteomic and immunohistochemical examination. Two dimensional electrophoresis (2DE) was performed using gel strips with immobilized pH gradient 3-10. As a result of 2DE gel analysis 14 spots characterized by over 2-fold higher expression in tumour proteomes were selected for mass spectrometry. In eleven spots more than one polypeptide was identified indicating overlapping of proteins in gels. In two spots demonstrating over 3-fold higher expression in OPA proteomes, single proteins: cytokerarin 19 (CK19) and aldolase A were identified. Immunohistochemical studies revealed that CK19 and aldolase A were expressed in the cytoplasm of epithelial cells of bronchioles in non-neoplastic lung sections, as well as epithelial cells of bronchioles and neoplastic cells in lung sections of OPA affected sheep. The results indicate that the overexpression of the two proteins reflects the presence of neoplastic cells in the lungs of OPA affected sheep.
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17
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Nagaraj NS, Singh OV. Integrating genomics and proteomics-oriented biomarkers to comprehend lung cancer. ACTA ACUST UNITED AC 2013; 3:167-80. [PMID: 23485163 DOI: 10.1517/17530050902725125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Lung cancer is the leading cause of cancer deaths worldwide. Recent years have brought tremendous progress in the development of genomic and proteomic platforms to study lung cancer progression and biomarker identification. OBJECTIVE To evaluate and integrate potential innovations of 'omics' (e.g., genomics and proteomics) technologies in dissecting biomarkers for lung cancer. METHODS Omics technologies permit simultaneous monitoring of many hundreds or thousands of macro and small molecules, as well as functional monitoring of multiple pivotal cellular pathways. Discussion follows to explore the principal challenges in the development of cancer biomarkers integrating genomics with proteomics data sets with their functional counterparts in conjunction with clinical data. RESULTS/CONCLUSION Sets of genes and gene interactions affecting different subsets of cancers can be determined using genomics in lung cancer. Proteomic studies have generated numerous functional data sets of potential diagnostic, prognostic and therapeutic significance in lung cancer. It is likely that omics will take a central place in the understanding, diagnosis, monitoring and treatment of lung cancer. Here the potential benefits and pitfalls of these methodologies are reviewed for the faster discovery of therapeutically valuable biomarkers for lung cancer.
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Affiliation(s)
- Nagathihalli S Nagaraj
- Vanderbilt University School of Medicine, Division of Surgical Oncology, Department of Surgery, 1161 21st Ave S., D2300 MCN, Nashville, TN 37232, USA +1 615 509 1565 , +1 615 322 6174 ,
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18
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Indovina P, Marcelli E, Pentimalli F, Tanganelli P, Tarro G, Giordano A. Mass spectrometry-based proteomics: the road to lung cancer biomarker discovery. MASS SPECTROMETRY REVIEWS 2013; 32:129-142. [PMID: 22829143 DOI: 10.1002/mas.21355] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2011] [Revised: 04/18/2012] [Accepted: 04/18/2012] [Indexed: 06/01/2023]
Abstract
Lung cancer is the leading cause of cancer death in men and women in Western nations, and is among the deadliest cancers with a 5-year survival rate of 15%. The high mortality caused by lung cancer is attributable to a late-stage diagnosis and the lack of effective treatments. So, it is crucial to identify new biomarkers that could function not only to detect lung cancer at an early stage but also to shed light on the molecular mechanisms that underlie cancer development and serve as the basis for the development of novel therapeutic strategies. Considering that DNA-based biomarkers for lung cancer showed inadequate sensitivity, specificity, and reproducibility, proteomics could represent a better tool for the identification of useful biomarkers and therapeutic targets for this cancer type. Among the proteomics technologies, the most powerful tool is mass spectrometry. In this review, we describe studies that use mass spectrometry-based proteomics technologies to analyze tumor proteins and peptides, which might represent new diagnostic, prognostic, and predictive markers for lung cancer. We focus in particular on those findings that hold promise to impact significantly on the clinical management of this disease.
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MESH Headings
- Animals
- Antineoplastic Agents/therapeutic use
- Biomarkers/blood
- Biomarkers/metabolism
- Biomarkers, Tumor/blood
- Biomarkers, Tumor/chemistry
- Biomarkers, Tumor/metabolism
- Chromatography, High Pressure Liquid
- Glycosylation/drug effects
- Humans
- Lung Neoplasms/blood
- Lung Neoplasms/diagnosis
- Lung Neoplasms/drug therapy
- Lung Neoplasms/metabolism
- Pleural Effusion, Malignant/blood
- Pleural Effusion, Malignant/drug therapy
- Pleural Effusion, Malignant/metabolism
- Prognosis
- Protein Processing, Post-Translational/drug effects
- Proteomics/methods
- Saliva/chemistry
- Saliva/drug effects
- Spectrometry, Mass, Electrospray Ionization
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Tandem Mass Spectrometry
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Affiliation(s)
- Paola Indovina
- Department of Human Pathology and Oncology, University of Siena, Siena, Italy
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19
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Ha ES, Choi S, In KH, Lee SH, Lee EJ, Lee SY, Kim JH, Shin C, Shim JJ, Kang KH, Phark S, Sul D. Identification of proteins expressed differently among surgically resected stage I lung adenocarcinomas. Clin Biochem 2012. [PMID: 23200884 DOI: 10.1016/j.clinbiochem.2012.11.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
RATIONALE Among patients with surgically resected stage I lung adenocarcinoma, some succumb to early recurrence, while others survive for more than 5 years. Few markers to predict prognoses in these patients have been accepted. Recent advances in proteomic methodologies offer a unique chance to identify new candidate biomarkers. The aim of this study is to find differences in protein expression in resected lung cancer tissue of stage I adenocarcinoma from patients with no recurrence for more than 5 years and from those with early recurrence. METHODS Lung cancer tissues were obtained from 15 patients with pathologically confirmed stage I adenocarcinoma. The patients were divided into two groups, those with recurrence within 36 months (early recurrence group, n=9) and those that were disease-free for over 5 years (disease free group, n=6). Tissue proteins were separated by a two-dimensional electrophoresis long gel system (30 × 40 cm) with set ranges (3-10 NL) and examined by nano-LC-ESI-MS/MS. Western blot assays were performed to validate these proteins. RESULTS Twelve protein spots were up-regulated and 8 were down-regulated in the disease-free group as compared with the recurrence group. Of the 12 up-regulated proteins, haptoglubin, tau-tubulin kinase-2 (TTBK2), thymidine phosphorylase, annexin-1, PIN1, CAPG, and SEC23 were validated by Western blot. Among the 8 down-regulated proteins, serpinB6 and trangelin-2 were validated. CONCLUSIONS A total of 9 differentially expressed proteins were successfully extracted, identified, and confirmed from stage I lung adenocarcinoma tissues. The increased or decreased expression of these proteins according to prognosis may be the basis for further studies of proteomics in developing prognostic biomarkers.
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Affiliation(s)
- Eun Sil Ha
- Division of Respiratory and Critical Care Medicine, Department of Internal Medicine, College of Medicine, Korea University, Seoul, Korea
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20
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Brouillard F, Fritsch J, Edelman A, Ollero M. Contribution of proteomics to the study of the role of cytokeratins in disease and physiopathology. Proteomics Clin Appl 2012; 2:264-85. [PMID: 21136830 DOI: 10.1002/prca.200780018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Cytokeratins (CKs), the most abundant group of cytoskeletal intermediate filaments, and proteomics are strongly connected. On the one hand, proteomics has been extremely useful to uncover new features and functions of CKs, on the other, the highly abundant CKs serve as an exceptional tool to test new technological developments in proteomics. As a result, proteomics has contributed to finding valuable associations of CKs with diseases as diverse as cancer, cystic fibrosis, steatohepatitis, viral and bacterial infection, keratoconus, vitreoretinopathy, preeclampsia or the chronic fatigue syndrome, as well as to characterizing their participation in a number of physiopathological processes, including drug resistance, response to toxicants, inflammation, stem cell differentiation, embryo development, and tissue repair. In some cases, like in cystic fibrosis, CKs have been described as potential therapeutic targets. The development of a specific field of proteomics where CKs become the main subject of research aims and hypotheses is suggested.
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Affiliation(s)
- Franck Brouillard
- INSERM, Unité 845, Paris, France; Faculté de Médecine René Descartes, Université Paris-Descartes, Plateau Protéomes IFR94, Paris, France
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21
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Lung cancer proteomics: recent advances in biomarker discovery. INTERNATIONAL JOURNAL OF PROTEOMICS 2011; 2011:726869. [PMID: 22229091 PMCID: PMC3196861 DOI: 10.1155/2011/726869] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 07/16/2011] [Indexed: 12/21/2022]
Abstract
Lung cancer is the most common cause of cancer death in both men and women in Western countries, with a 5-year survival rate of 15%, which is among the lowest of all cancers. The high mortality from lung cancer is due not only to the late stage diagnosis but also to the lack of effective treatments even for patients diagnosed with stage I lung cancer. Therefore, there is an urgent need to identify new markers for early diagnosis and prognosis that could serve to open novel therapeutic avenues. Proteomics can represent an important tool for the identification of biomarkers and therapeutic targets for lung cancer since DNA-based biomarkers did not prove to have adequate sensitivity, specificity, and reproducibility. In this paper we will describe studies focused on the identification of new diagnostic, prognostic, and predictive markers for lung cancer, using proteomics technologies.
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22
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Perluigi M, Giorgi A, Blarzino C, De Marco F, Foppoli C, Di Domenico F, Butterfield DA, Schininà ME, Cini C, Coccia R. Proteomics analysis of protein expression and specific protein oxidation in human papillomavirus transformed keratinocytes upon UVB irradiation. J Cell Mol Med 2010; 13:1809-1822. [PMID: 19267883 DOI: 10.1111/j.1582-4934.2008.00465.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Increasing evidence supports the role of oxidative stress in cancer development. Ultraviolet (UV) irradiation is one of the major sources of oxidative stress through the generation of reactive oxygen species (ROS). Besides the physiological function of ROS in cellular homeostasis, accumulating reports suggest that ROS are involved in all stages of multistep cancer development. In order to investigate the involvement of oxidative damage into the mechanisms of tumour progression, we used a parallel proteomic approach to analyse the protein expression profile and to identify oxidatively modified proteins in human papillomavirus (HPV)-transformed keratinocytes (HK-168 cells) upon ultraviolet B (UVB) exposure. The HK-168 cells were obtained from normal human epidermal keratinocytes transfected with the whole genome of the high-risk HPV type 16, unanimously recognized as an etiological agent of cervical carcinoma. Because of its year-long latency, this tumour offers a convenient model to study the role of environmental concurring agents in the multistep malignant progression. By the protein expression profile, we identified 21 proteins that showed different expression levels in HK-168 cells treated with UVB in comparison with untreated cells. Focusing on the oxidative modifications occurring at the protein level, we identified five proteins that showed elevated protein carbonyls levels: alpha-enolase, heat shock protein 75, annexin 2, elongation factor Tu and elongation factor gamma. Our results indicate that UVB-induced oxidative stress perturbs the normal redox balance and shifts HPV-transformed keratinocytes into a state in which the carbonylation of specific proteins is systematically induced. We suggest that UVB-induced modulation of protein expression combined with oxidative modification lead to protein dysfunction that might contribute to the malignant progression of transformed cells.
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Affiliation(s)
- Marzia Perluigi
- Department of Biochemical Sciences, "Sapienza" University of Rome, Rome, Italy
| | - Alessandra Giorgi
- Department of Biochemical Sciences, "Sapienza" University of Rome, Rome, Italy
| | - Carla Blarzino
- Department of Biochemical Sciences, "Sapienza" University of Rome, Rome, Italy
| | - Federico De Marco
- Laboratory of Virology, "Regina Elena Institute for Cancer Research", Rome, Italy
| | - Cesira Foppoli
- CNR Institute of Molecular Biology and Pathology, Rome, Italy
| | - Fabio Di Domenico
- Department of Biochemical Sciences, "Sapienza" University of Rome, Rome, Italy
| | - D Allan Butterfield
- Department of Chemistry, Center of Membrane Science, and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - M Eugenia Schininà
- Department of Biochemical Sciences, "Sapienza" University of Rome, Rome, Italy
| | - Chiara Cini
- Department of Biochemical Sciences, "Sapienza" University of Rome, Rome, Italy
| | - Raffaella Coccia
- Department of Biochemical Sciences, "Sapienza" University of Rome, Rome, Italy
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Lung cancer proteomics, clinical and technological considerations. J Proteomics 2010; 73:1851-63. [PMID: 20685322 DOI: 10.1016/j.jprot.2010.05.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Revised: 05/21/2010] [Accepted: 05/25/2010] [Indexed: 11/23/2022]
Abstract
The overall survival of lung cancer patients is disappointingly low. This is due to several factors, including the lack of an effective screening strategy to detect tumors at a potentially curable early stage, a marked resistance of lung cancer cells to drug treatment and a still superficial knowledge about the multifactorial cellular networks that are activated or suppressed during cancer progression. Furthermore, the armamentarium of clinicians and researchers in the field does not yet include reliable biomarkers to predict tumor response to treatment and foresee the natural history of the disease. In the present situation, a potential breakthrough is presented by proteomics technologies with the potential to discover relevant biomarkers which can be accurately quantified in multiplexed assays. Proteomics field can also contribute greatly in the understanding of mechanisms in tumor progression and treatment response. In this review we will describe the work that is being done in the field of lung cancer proteomics, focusing on clinically relevant questions that need to be addressed and on the possible applications of novel technologies.
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De Petris L, Pernemalm M, Elmberger G, Bergman P, Orre L, Lewensohn R, Lehtiö J. A novel method for sample preparation of fresh lung cancer tissue for proteomics analysis by tumor cell enrichment and removal of blood contaminants. Proteome Sci 2010; 8:9. [PMID: 20187940 PMCID: PMC2847553 DOI: 10.1186/1477-5956-8-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Accepted: 02/26/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In-depth proteomics analyses of tumors are frequently biased by the presence of blood components and stromal contamination, which leads to large experimental variation and decreases the proteome coverage. We have established a reproducible method to prepare freshly collected lung tumors for proteomics analysis, aiming at tumor cell enrichment and reduction of plasma protein contamination. We obtained enriched tumor-cell suspensions (ETS) from six lung cancer cases (two adenocarcinomas, two squamous-cell carcinomas, two large-cell carcinomas) and from two normal lung samples. The cell content of resulting ETS was evaluated with immunocytological stainings and compared with the histologic pattern of the original specimens. By means of a quantitative mass spectrometry-based method we evaluated the reproducibility of the sample preparation protocol and we assessed the proteome coverage by comparing lysates from ETS samples with the direct lysate of corresponding fresh-frozen samples. RESULTS Cytological analyses on cytospin specimens showed that the percentage of tumoral cells in the ETS samples ranged from 20% to 70%. In the normal lung samples the percentage of epithelial cells was less then 10%. The reproducibility of the sample preparation protocol was very good, with coefficient of variation at the peptide level and at the protein level of 13% and 7%, respectively. Proteomics analysis led to the identification of a significantly higher number of proteins in the ETS samples than in the FF samples (244 vs 109, respectively). Albumin and hemoglobin were among the top 5 most abundant proteins identified in the FF samples, showing a high contamination with blood and plasma proteins, whereas ubiquitin and the mitochondrial ATP synthase 5A1 where among the top 5 most abundant proteins in the ETS samples. CONCLUSION The method is feasible and reproducible. We could obtain a fair enrichment of cells but the major benefit of the method was an effective removal of contaminants from red blood cells and plasma proteins resulting in larger proteome coverage compared to the direct lysis of frozen samples. This sample preparation method may be successfully implemented for the discovery of lung cancer biomarkers on tissue samples using mass spectrometry-based proteomics.
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Affiliation(s)
- Luigi De Petris
- Karolinska Biomics Center, Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden.
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Lau ATY, Chiu JF. Biomarkers of lung-related diseases: current knowledge by proteomic approaches. J Cell Physiol 2009; 221:535-43. [PMID: 19681054 PMCID: PMC7166618 DOI: 10.1002/jcp.21893] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The lung epithelial surface is one of the vital barriers or sensors in the body responding to the external atmosphere and thereby always subjecting to direct toxicological exposure, stress, stimulus, or infection. Due to its relatively higher sensitivity in response to toxicants, the use of lung epithelial cell culture and lung tissue from animal models or patients has facilitated our learning to lung physiopathology and toxicopharmacology. The recent advancement of proteomics has made it possible to investigate the cellular response at a global level. In this review, the potential applications of proteomic approach in studying lung-related diseases and biomarker discovery will be discussed.
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Affiliation(s)
- Andy T Y Lau
- Department of Anatomy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China
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Abstract
In an effort to further our understanding of lung cancer biology and to identify new candidate biomarkers to be used in the management of lung cancer, we need to probe these tissues and biological fluids with tools that address the biology of lung cancer directly at the protein level. Proteins are responsible of the function and phenotype of cells. Cancer cells express proteins that distinguish them from normal cells. Proteomics is defined as the study of the proteome, the complete set of proteins produced by a species, using the technologies of large-scale protein separation and identification. As a result, new technologies are being developed to allow the rapid and systematic analysis of thousands of proteins. The analytical advantages of mass spectrometry (MS), including sensitivity and high-throughput, promise to make it a mainstay of novel biomarker discovery to differentiate cancer from normal cells and to predict individuals likely to develop or recur with lung cancer. In this review, we summarize the progress made in clinical proteomics as it applies to the management of lung cancer. We will focus our discussion on how MS approaches may advance the areas of early detection, response to therapy, and prognostic evaluation.
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Jagannathan J, Li J, Szerlip N, Vortmeyer AO, Lonser RR, Oldfield EH, Zhuang Z. Application and implementation of selective tissue microdissection and proteomic profiling in neurological disease. Neurosurgery 2009; 64:4-14; discussion 14. [PMID: 19145153 DOI: 10.1227/01.neu.0000335776.93176.83] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE Proteins are the primary components of cells and are vital constituents of any living organism. The proteins that make up an organism (proteome) are constantly changing and are intricately linked to neurological disease processes. The study of proteins, or proteomics, is a relatively new but rapidly expanding field with increasing relevance to neurosurgery. METHODS We present a review of the state-of-the-art proteomic technology and its applications in central nervous system diseases. RESULTS The technique of "selective microdissection" allows an investigator to selectively isolate and study a pathological tissue of interest. By evaluating protein expression in a variety of central nervous system disorders, it is clear that proteins are differentially expressed across disease states, and protein expression changes markedly during disease progression. CONCLUSION Understanding the patterns of protein expression in the nervous system has critical implications for the diagnosis and treatment of neurological disease. As gatekeepers in the diagnosis, evaluation, and treatment of central nervous system diseases, it is important for neurosurgeons to develop an appreciation for proteomic techniques and their utility.
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Affiliation(s)
- Jay Jagannathan
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892-1414, USA
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Kondo T, Hirohashi S. Application of 2D-DIGE in cancer proteomics toward personalized medicine. Methods Mol Biol 2009; 577:135-54. [PMID: 19718514 DOI: 10.1007/978-1-60761-232-2_11] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Two-dimensional difference gel electrophoresis (2D-DIGE) is an advanced variation of two-dimensional polyacrylamide gel electrophoresis (2D-PAGE); protein samples are labeled with different fluorescent dyes, mixed and separated by 2D-PAGE. 2D-DIGE solves major inherent drawbacks of 2D-PAGE, demonstrating great utility in biomarker studies. Biomarker development requires quantitative, reproducible, highly sensitive and high-throughput experimental platforms, and 2D-DIGE meets these criteria. Here we demonstrate the advantages of 2D-DIGE and discuss the possibilities 2D-DIGE offers for further, more comprehensive proteome studies.
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Affiliation(s)
- Tadashi Kondo
- National Cancer Center Research Institute, Proteome Bioinformatics Project, Tokyo, Japan
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Abstract
Profiling of differentially expressed proteins is perhaps the most important and useful approach in developing tools for risk assessment in a population, diagnostic screening, and therapeutics. Proteomic markers have potential for identifying individuals at high risk of developing cancer; however, these markers have not been extensively used in cancer epidemiologic studies. Several markers have to be clinically validated. In this chapter, methods used in proteomic analysis of clinical samples, challenges in the proteomics and cancer epidemiology, and their potential solutions are discussed.
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Eberini I, Gianazza E, Pastorino U, Sirtori C. Assessment of individual lung cancer risk by the proteomic analysis of exhaled breath condensate. ACTA ACUST UNITED AC 2008; 2:1309-15. [PMID: 23496779 DOI: 10.1517/17530050802600675] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Lung cancer is one of the leading causes of cancer-related deaths. Several diagnostic strategies are available but these are frequently ineffective, either because of their cost and organizational difficulty or because of the involvement of high radiations. As recent data from spiral computerized axial tomography have shown limited sensitivity and limited impact on cancer-related fatality, several options have been proposed in order to identify biological fluid-based biomarkers. OBJECTIVE Evaluating whether proteomic analysis of alveolar fluid obtained in the form of exhaled breath condensate (EBC) can be valuable for detecting and effectively diagnosing lung cancer. METHODS Careful review of recently published papers on proteomic EBC analysis, together with experience in the authors' laboratory, allows the discussion of benefits, pitfalls and possible future development of this approach. RESULTS/CONCLUSIONS The rapid advancements of proteomics are expected to validate EBC protein(s) as lung pathology biomarker(s). Accessibility of an early marker of lung cancer will be a great advantage for potentially early treatment by surgical procedures with limited tissue removal, possibly preceding metastasis development.
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Affiliation(s)
- I Eberini
- University of Milano, Department of Pharmacological Sciences, via Balzaretti 9-I-20133, Milano, Italy +39 02 5031 8311 ; +39 02 5031 8284 ;
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Matthias C, Mack B, Berghaus A, Gires O. Keratin 8 expression in head and neck epithelia. BMC Cancer 2008; 8:267. [PMID: 18803884 PMCID: PMC2556347 DOI: 10.1186/1471-2407-8-267] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2008] [Accepted: 09/22/2008] [Indexed: 12/19/2022] Open
Abstract
Background The intermediate filament forming protein keratin 8 (K8) is a tumour-associated antigen, which was shown to be over-expressed in a variety of malignancies. Here, we present a study of K8 expression in squamous epithelia of the head and neck area, including normal mucosa, hyperplastic and dysplastic leukoplakia, carcinomas of different sub-localisations, and lymph node metastases. Methods K8 expression was assessed upon immunohistochemistry with specific antibodies in cryosections of primary tumours of the head and neck area. Results K8 expression was characteristic of transformed tissue and marked early stages of disease, i.e. dysplastic oral leukoplakia, but not normal or hyperplastic epithelium. With the exception of carcinomas of the larynx and the tongue, K8 expression also strictly differentiated carcinomas from normal epithelium of the same origin. Furthermore, K8high was characteristic of cells, which had detached from the sites of primary tumours and had been invading the surrounding tissue at the time point of surgery. Conclusion K8 is an excellent marker for head and neck malignancies, which allows for early detection as well as for visualisation of potentially disseminating tumour cells in vivo.
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Affiliation(s)
- Christoph Matthias
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Goettingen Medical School, Robert-Kochstr. 40, 37075 Göttingen, Germany.
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Parikh AA, Johnson JC, Merchant NB. Genomics and Proteomics in Predicting Cancer Outcomes. Surg Oncol Clin N Am 2008; 17:257-77, vii. [DOI: 10.1016/j.soc.2007.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Abstract
Proteomic studies have generated numerous datasets of potential diagnostic, prognostic, and therapeutic significance in human cancer. Two key technologies underpinning these studies in cancer tissue are two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry (MS). Although surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF)-MS is the mainstay for serum or plasma analysis, other methods including isotope-coded affinity tag technology, reverse-phase protein arrays, and antibody microarrays are emerging as alternative proteomic technologies. Because there is little overlap between studies conducted with these approaches, confirmation of these advanced technologies remains an elusive goal. This problem is further exacerbated by lack of uniform patient inclusion and exclusion criteria, low patient numbers, poor supporting clinical data, absence of standardized sample preparation, and limited analytical reproducibility (in particular of 2D-PAGE). Despite these problems, there is little doubt that the proteomic approach has the potential to identify novel diagnostic biomarkers in cancer. In therapeutic proteomics, the challenge is significant due to the complexity systems under investigation (i.e., cells generate over 10(5) different polypeptides). However, the most significant contribution of therapeutic proteomics research is expected to derive not from single experiments, but from the synthesis and comparison of large datasets obtained under different conditions (e.g., normal, inflammation, cancer) and in different tissues and organs. Thus, standardized processes for storing and retrieving data obtained with different technologies by different research groups will have to be developed. Shifting the emphasis of cancer proteomics from technology development and data generation to careful study design, data organization, formatting, and mining is crucial to answer clinical questions in cancer research.
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Affiliation(s)
- M A Reymond
- Department of Surgery, University of Magdeburg, Germany
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Wang S, Nan B, Zhu J, Beer DG. Doubly Penalized Buckley-James Method for Survival Data with High-Dimensional Covariates. Biometrics 2007; 64:132-40. [PMID: 17680828 DOI: 10.1111/j.1541-0420.2007.00877.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Recent interest in cancer research focuses on predicting patients' survival by investigating gene expression profiles based on microarray analysis. We propose a doubly penalized Buckley-James method for the semiparametric accelerated failure time model to relate high-dimensional genomic data to censored survival outcomes, which uses the elastic-net penalty that is a mixture of L1- and L2-norm penalties. Similar to the elastic-net method for a linear regression model with uncensored data, the proposed method performs automatic gene selection and parameter estimation, where highly correlated genes are able to be selected (or removed) together. The two-dimensional tuning parameter is determined by generalized crossvalidation. The proposed method is evaluated by simulations and applied to the Michigan squamous cell lung carcinoma study.
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Affiliation(s)
- Sijian Wang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
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Plowman JE. The proteomics of keratin proteins. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 849:181-9. [PMID: 16931191 DOI: 10.1016/j.jchromb.2006.07.055] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2006] [Revised: 07/18/2006] [Accepted: 07/26/2006] [Indexed: 10/24/2022]
Abstract
Keratin proteins are widespread in nature, being found in the nuclei and cytoplasm of almost all differentiated eukaryote cells. However, they are best known as the principal structural proteins in hair, wool and skin. Because of difficulties associated with their extraction from biological samples, high sequence homology and the presence of numerous post-translational modifications, they have been less well studied than other protein families. Thanks to the advent of modern proteomic techniques we now have available a good suite of tools to study this neglected family of proteins.
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Abstract
Recent technological developments in proteomic analysis are bringing us new insights into the molecular classification of tumours. Although proteomic analysis in cancer profiling is still under development both in terms of the instruments used and the data analytical tools, this method has great potential advantages for the analysis of biospecimens of many types. Direct measurement of abnormally expressed or modified proteins in the tumour tissue and/or patient blood may be an effective approach for discovering new biomarkers. Proteomics has the significant advantage of being able to discern not only changes in expression levels but also in post-translational modifications. Thus, the proteomics approach to protein profiling and biomarker discovery uncovers biomarkers from a different viewpoint than microarray analysis. This review summarizes the range of proteomics technologies employed for cancer profiling, and how they have been used to derive new classification models for human lung cancer.
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Affiliation(s)
- Takefumi Kikuchi
- Vanderbilt Ingram Cancer Center, Nashville, Tennessee 37232, USA
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Harpole DH, Meyerson SL. Lung cancer staging: proteomics. Thorac Surg Clin 2007; 16:339-43. [PMID: 17240821 DOI: 10.1016/j.thorsurg.2006.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The results of ACOSOG Z4031 may provide landmark information for the use of proteomic profiling to diagnose lung cancer noninvasively and to provide more accurate predictions of survival. Although the technological developments allowing generalized use of proteomic and genomic analyses are relatively recent, major progress in understanding the molecular basis of lung cancer has been made. Predicting survival is only the first step in the use of proteomics. If a reliable protein profile can be identified that is associated with poor prognosis, these proteins can then be identified and become therapeutic targets. It is not difficult to envision a day when a simple blood test will diagnose a lung cancer, perhaps even before it is clinically apparent, and, at the same time, identify the chemotherapeutic agents to which the tumor is sensitive, allowing individually directed treatment.
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Affiliation(s)
- David H Harpole
- Department of Surgery, Duke University Medical Center, Box 8627, 2400 Pratt Street, Room 0311, Durham, NC 27710, USA.
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Massion PP, Caprioli RM. Proteomic Strategies for the Characterization and the Early Detection of Lung Cancer. J Thorac Oncol 2006. [DOI: 10.1016/s1556-0864(15)31639-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Raponi M, Zhang Y, Yu J, Chen G, Lee G, Taylor JMG, Macdonald J, Thomas D, Moskaluk C, Wang Y, Beer DG. Gene expression signatures for predicting prognosis of squamous cell and adenocarcinomas of the lung. Cancer Res 2006; 66:7466-72. [PMID: 16885343 DOI: 10.1158/0008-5472.can-06-1191] [Citation(s) in RCA: 312] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Non-small-cell lung cancers (NSCLC) compose 80% of all lung carcinomas with squamous cell carcinomas (SCC) and adenocarcinoma representing the majority of these tumors. Although patients with early-stage NSCLC typically have a better outcome, 35% to 50% will relapse within 5 years after surgical treatment. We have profiled primary squamous cell lung carcinomas from 129 patients using Affymetrix U133A gene chips. Unsupervised analysis revealed two clusters of SCC that had no correlation with tumor stage but had significantly different overall patient survival (P = 0.036). The high-risk cluster was most significantly associated with down-regulation of epidermal development genes. Cox proportional hazard models identified an optimal set of 50 prognostic mRNA transcripts using a 5-fold cross-validation procedure. Quantitative reverse transcription-PCR and immunohistochemistry using tissue microarrays were used to validate individual gene candidates. This signature was tested in an independent set of 36 SCC samples and achieved 84% specificity and 41% sensitivity with an overall predictive accuracy of 68%. Kaplan-Meier analysis showed clear stratification of high-risk and low-risk patients [log-rank P = 0.04; hazard ratio (HR), 2.66; 95% confidence interval (95% CI), 1.01-7.05]. Finally, we combined the SCC classifier with our previously identified adenocarcinoma prognostic signature and showed that the combined classifier had a predictive accuracy of 71% in 72 NSCLC samples also showing significant differences in overall survival (log-rank P = 0.0002; HR, 3.54; 95% CI, 1.74-7.19). This prognostic signature could be used to identify patients with early-stage high-risk NSCLC who might benefit from adjuvant therapy following surgery.
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Affiliation(s)
- Mitch Raponi
- Molecular Diagnostics, Veridex LLC-a Johnson & Johnson Company, 3210 Merryfriend Row, San Diego, CA 92121, USA.
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Abstract
Human cancer is caused by multiple factors, such as genetic predisposition, chronic persistent inflammation, environmental factors, life style, and aging. Dysregulated proliferation, dysregulated adhesion, resistance to apoptosis, resistance to senescence, and resistance to anti-cancer drugs are features of cancer cells. Accumulation of multiple epigenetic changes and genetic alterations of cancer-associated genes during multi-stage carcinogenesis results in more malignant phenotypes. Post-genome science is characterized by omics data related to genome, transcriptome, proteome, metabolome, interactome, and epigenome as well as by high-throughput technology, such as whole-genome tiling oligonucleotide array, array CGH with 32,433 overlapping BAC clones, transcriptome microarray, mass spectrometry, tissue-based expression array, and cell-based transfection array. Benchtop oncology supplies Desktop oncology with large amounts of omics data produced by high-throughput technology. Desktop oncology establishes knowledge on cancer-related biomarkers, such as predisposition markers, diagnostic markers, prognostic markers, and therapeutic markers, by using bioinformatics and human intelligence of experts for data mining and text mining. Bedside oncology applies the knowledge established by Desktop oncology to determine therapeutics for cancer patients. Antibody drugs (Trastuzumab/Herceptin, Cetuximab/Erbitux, Bevacizumab/Avastin, et cetera), small molecule inhibitors for tyrosine kinases (Gefitinib/Iressa, Erlotinib/Tarceva, Imatinib/Gleevec, et cetera), conventional cytotoxic drugs, and anti-hormonal drugs are used for cancer chemotherapy. Biomarker monitoring contributes to therapeutic optional choice and drug dosage determination for cancer patients. Knowledge on biomarkers is feedforwarded from desktop to bedside in the translational research, and then biomarker monitoring is feedbacked from bedside to desktop in the reverse translational research. Desktop oncology is indispensable for cancer research in the post-genome era. Combination of genetic screening for cancer predisposition in the general population and precise selection of therapeutic options during cancer management could contribute to the realization of personalized prevention and to dramatically improve the prognosis of cancer patients in the future.
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Affiliation(s)
- Masuko Katoh
- M & M Medical BioInformatics, Hongo 113-0033, Japan
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Zhan X, Desiderio DM. Comparative proteomics analysis of human pituitary adenomas: current status and future perspectives. MASS SPECTROMETRY REVIEWS 2005; 24:783-813. [PMID: 15495141 DOI: 10.1002/mas.20039] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
This article will review the published research on the elucidation of the mechanisms of pituitary adenoma formation. Mass spectrometry (MS) plays a key role in those studies. Comparative proteomics has been used with the long-term goal to locate, detect, and characterize the differentially expressed proteins (DEPs) in human pituitary adenomas; to identify tumor-related and -specific biomarkers; and to clarify the basic molecular mechanisms of pituitary adenoma formation. The methodology used for comparative proteomics, the current status of human pituitary proteomics studies, and future perspectives are reviewed. The methodologies that are used in comparative proteomics studies of human pituitary adenomas are readily exportable to other different areas of cancer research.
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Affiliation(s)
- Xianquan Zhan
- Charles B. Stout Neuroscience Mass Spectrometry Laboratory, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
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Seike M, Kondo T, Fujii K, Okano T, Yamada T, Matsuno Y, Gemma A, Kudoh S, Hirohashi S. Proteomic signatures for histological types of lung cancer. Proteomics 2005; 5:2939-48. [PMID: 15996008 DOI: 10.1002/pmic.200401166] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We performed proteomic studies on lung cancer cells to elucidate the mechanisms that determine histological phenotype. Thirty lung cancer cell lines with three different histological backgrounds (squamous cell carcinoma, small cell lung carcinoma and adenocarcinoma) were subjected to two-dimensional difference gel electrophoresis (2-D DIGE) and grouped by multivariate analyses on the basis of their protein expression profiles. 2-D DIGE achieves more accurate quantification of protein expression by using highly sensitive fluorescence dyes to label the cysteine residues of proteins prior to two-dimensional polyacrylamide gel electrophoresis. We found that hierarchical clustering analysis and principal component analysis divided the cell lines according to their original histology. Spot ranking analysis using a support vector machine algorithm and unsupervised classification methods identified 32 protein spots essential for the classification. The proteins corresponding to the spots were identified by mass spectrometry. Next, lung cancer cells isolated from tumor tissue by laser microdissection were classified on the basis of the expression pattern of these 32 protein spots. Based on the expression profile of the 32 spots, the isolated cancer cells were categorized into three histological groups: the squamous cell carcinoma group, the adenocarcinoma group, and a group of carcinomas with other histological types. In conclusion, our results demonstrate the utility of quantitative proteomic analysis for molecular diagnosis and classification of lung cancer cells.
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Affiliation(s)
- Masahiro Seike
- Cancer Proteomics Project, National Cancer Center Research Institute, Tokyo, Japan
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Meyerson M, Carbone D. Genomic and Proteomic Profiling of Lung Cancers: Lung Cancer Classification in the Age of Targeted Therapy. J Clin Oncol 2005; 23:3219-26. [PMID: 15886309 DOI: 10.1200/jco.2005.15.511] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Both proteomic and genomic methods offer promise for the classification of human lung carcinomas. This review summarizes the range of proteomic methods in development for lung cancer classification, and describes a number of recent analyses of messenger RNA expression in lung cancer. Multiple independent studies of mRNA expression profiles in lung adenocarcinoma have proven highly reproducible. Analyses of the relationship between expression profiles and tumor development and differentiation, the presence or absence of specific pathogenic mutations, patient prognosis and survival after surgical treatment, and specific histopathology all appear to be promising.
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Affiliation(s)
- Matthew Meyerson
- Vanderbilt Cancer Center, 2220 Pierce Ave, 685 PRB, Nashville, TN 37232-6863, USA
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Zhang DH, Tai LK, Wong LL, Sethi SK, Koay ESC. Proteomics of breast cancer: Enhanced expression of cytokeratin19 in human epidermal growth factor receptor type 2 positive breast tumors. Proteomics 2005; 5:1797-805. [PMID: 15825149 DOI: 10.1002/pmic.200401069] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The human epidermal growth factor receptor, type 2 (HER-2/neu or c-erbB-2) is a 185 kDa transmembrane protein that is phosphorylated upon ligand binding and dimerization with members of the HER/c-erbB family and regulates cell growth and differentiation. Its overexpression is strongly associated with advanced disease, metastasis and poor clinical outcome. To better understand the mechanisms underlying the poor prognosis of breast tumors with HER-2/neu-positive status, parallel proteomic analyses were performed on estrogen receptor-negative and node-positive breast tumors with or without overexpression of the HER-2/neu oncogene, using laser capture microdissection and two-dimensional gel electrophoresis. The differentially expressed proteins were identified by peptide mass fingerprinting using matrix-assisted laser desorption/ionization-time of flight mass spectrometry. Cytokeratin 19 (CK19), one of the identified proteins, was highly expressed in the HER-2/neu-positive breast tumors when compared with HER-2/neu-negative breast tumors. The enhanced overexpression of CK19 in HER-2/neu-positive tumors was further analyzed using semiquantitative reverse-transcription polymerase chain reaction, Western blotting and reverse-phase protein arrays. Immunohistochemical staining of sections from a breast tumor tissue microarray of 97 tumors showed moderate to strong staining against anti-CK19 antibody in 20 (5 with moderate and 15 with strong staining) of the 26 HER-2/neu-positive tumors (76.9%) and in 22 (12 with moderate and 10 with strong staining) of 52 HER-2/neu-negative tumors (48%) (p = 0.002). Our results indicate that CK19, an intermediate fragment of the cytoskeleton, and other proteins showing differential expression, are likely to be intricately involved in intra- and intercellular molecular events driving the more aggressive tumor proliferation, invasion and metastasis associated with HER-2/neu-positive tumors.
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Affiliation(s)
- Dao-Hai Zhang
- Department of Pathology, National University of Singapore
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Cheng YL, Zhang GY, Xiao ZQ, Tang FQ. Two-dimensional polyacrylamide gel electrophoresis analysis of indomethacin-treated human colon cancer cells. World J Gastroenterol 2005; 11:2420-5. [PMID: 15832411 PMCID: PMC4305628 DOI: 10.3748/wjg.v11.i16.2420] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To establish the two-dimensional gel electrophoresis (2-DE) profiles of indomethacin (IN)-treated human colon cancer cell line HCT116, and to provide a new way to study its anti-tumor molecular mechanism through analyzing a variety of protein maps.
METHODS: Two-DE profiles of HCT116 were established in IN-treated and untreated groups. Total proteins were separated by immobilized pH gradient-based 2-DE. The gels were stained by silver, scanned by ImageScanner, and analyzed with Image Master software.
RESULTS: Clear background, well-resolved and reproducible 2-DE patterns of HCT116 cells were acquired in IN-treated and untreated group. The average deviation of spot position was 0.896±0.177 mm in IEF direction and 1.106±0.289 mm in SDS-PAGE direction respectively. In IN-treated group, 1169±36 spots were detected and 1061±32 spots were matched, the average matching rate was 90.6% in three gels. In untreated group, 1256±50 spots were detected and 1168±46 spots were matched, the average matching rate was 93.0% in three gels. Forty-five differential protein spots were displayed between IN-treated and untreated groups. Of which, 34 protein spots decreased and 9 showed higher expression in IN-treated group, and only two protein spots showed an expression in untreated cells.
CONCLUSION: Two-DE profiles of IN-treated and untreated HCT116 cells were established. Apparent 45 different protein spots were detected in IN-treated and untreated HCT116 cells. The analysis on differential protein spots may serve as a new way to study the molecule mechanism of IN-treated colon cancer.
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Affiliation(s)
- Yan-Li Cheng
- Department of Gastroenterology, Xiangya Hospital, Central South University, Xiangya Road, Changsha 410008, Hunan Province, China
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Li LS, Kim H, Rhee H, Kim SH, Shin DH, Chung KY, Park KS, Paik YK, Chang J, Kim H. Proteomic analysis distinguishes basaloid carcinoma as a distinct subtype of nonsmall cell lung carcinoma. Proteomics 2005; 4:3394-400. [PMID: 15378762 DOI: 10.1002/pmic.200400901] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The histopathologic type of lung cancer is known to be correlated with tumor behavior and prognosis. However, this classification is subjective and no specific molecular markers have been identified. The aim of this study was to identify protein markers in different types of nonsmall cell lung cancers. Two-dimensional polyacrylamide gel electrophoresis analysis was performed with paired samples of three squamous cell carcinomas, three adenocarcinomas, four large cell carcinomas, and four basaloid carcinomas. We found that 25 proteins in 14 cases of lung cancer were differentially expressed compared to matched nontumorous lung tissues. Among these 25 proteins, 11 proteins were down-regulated and 14 were up-regulated in these four types of lung cancer. Alloalbumin venezia, selenium-binding protein 1, carbonic dehydratase, heat shock 20KD-like protein, and SM22 alpha protein were down-regulated in all 14 cases of lung cancer examined, whereas alpha enolase was consistently up-regulated. Supervised hierarchical cluster analysis based on the 25 differentially expressed proteins showed that basaloid carcinoma formed one independent group, whereas the other three cancer types were not uniquely classifiable. Our findings suggest that basaloid carcinoma is a unique subtype of nonsmall cell lung carcinoma.
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Affiliation(s)
- Long Shan Li
- Department of Pathology, Brain Korea 21 Projects for Medical Sciences, Yonsei University College of Medicine, Seoul, Korea
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Mouat MF, Kolli K, Orlando R, Hargrove JL, Grider A. The effects of quercetin on SW480 human colon carcinoma cells: a proteomic study. Nutr J 2005; 4:11. [PMID: 15748282 PMCID: PMC555539 DOI: 10.1186/1475-2891-4-11] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2005] [Accepted: 03/04/2005] [Indexed: 12/02/2022] Open
Abstract
Background High fruit and vegetable intake is known to reduce the risk of colon cancer. To improve understanding of this phenomenon the action of different phytochemicals on colon cells has been examined. One such compound is quercetin that belongs to the group known as flavonoids. The purpose of this study was to determine the influence of quercetin on the proteome of the SW480 human colon adenocarcinoma cell line, specifically to identify proteins that could be the molecular targets of quercetin in its amelioration of the progression of colon cancer. To this end, two-dimensional gel electrophoresis and mass spectrometry were used to identify proteins that underwent a change in expression following treatment of the cells with 20 μM quercetin. This could elucidate how quercetin may reduce the progression of colon cancer. Results Quercetin treatment of the SW480 human colon cancer cells was found to result in the decreased expression of three proteins and the increased expression of one protein. The identified proteins with decreased expression were type II cytoskeletal 8 keratin and NADH dehydrogenase Fe-S protein 3. The other protein with decreased expression was not identified. The protein with increased expression belonged to the annexin family. Conclusion Several proteins were determined to have altered expression following treatment with quercetin. Such changes in the levels of these particular proteins could underlie the chemo-protective action of quercetin towards colon cancer.
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Affiliation(s)
- Michael F Mouat
- Department of Foods and Nutrition, University of Georgia, Athens, Georgia 30602, USA
| | - Kumar Kolli
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA
| | - Ronald Orlando
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA
| | - James L Hargrove
- Department of Foods and Nutrition, University of Georgia, Athens, Georgia 30602, USA
| | - Arthur Grider
- Department of Foods and Nutrition, University of Georgia, Athens, Georgia 30602, USA
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Coming of Age in the Life of Neoplasia. Neoplasia 2004. [DOI: 10.1593/neo.6-6ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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