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Tang J, Wang Y, Li Y, Zhang Y, Zhang R, Xiao Z, Luo Y, Guo X, Tao L, Lou Y, Xue W, Zhu F. Recent Technological Advances in the Mass Spectrometry-based Nanomedicine Studies: An Insight from Nanoproteomics. Curr Pharm Des 2019; 25:1536-1553. [PMID: 31258068 DOI: 10.2174/1381612825666190618123306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 06/11/2019] [Indexed: 11/22/2022]
Abstract
Nanoscience becomes one of the most cutting-edge research directions in recent years since it is gradually matured from basic to applied science. Nanoparticles (NPs) and nanomaterials (NMs) play important roles in various aspects of biomedicine science, and their influences on the environment have caused a whole range of uncertainties which require extensive attention. Due to the quantitative and dynamic information provided for human proteome, mass spectrometry (MS)-based quantitative proteomic technique has been a powerful tool for nanomedicine study. In this article, recent trends of progress and development in the nanomedicine of proteomics were discussed from quantification techniques and publicly available resources or tools. First, a variety of popular protein quantification techniques including labeling and label-free strategies applied to nanomedicine studies are overviewed and systematically discussed. Then, numerous protein profiling tools for data processing and postbiological statistical analysis and publicly available data repositories for providing enrichment MS raw data information sources are also discussed.
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Affiliation(s)
- Jing Tang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Yunxia Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China
| | - Yi Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China
| | - Yang Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Runyuan Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China
| | - Ziyu Xiao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China
| | - Yongchao Luo
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China
| | - Xueying Guo
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China
| | - Lin Tao
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicine of Zhejiang Province, School of Medicine, Hangzhou Normal University, Hangzhou 310036, China
| | - Yan Lou
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, 79 QingChun Road, Hangzhou, Zhejiang 310000, China
| | - Weiwei Xue
- School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
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2
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Bohnenberger H, Kaderali L, Ströbel P, Yepes D, Plessmann U, Dharia NV, Yao S, Heydt C, Merkelbach-Bruse S, Emmert A, Hoffmann J, Bodemeyer J, Reuter-Jessen K, Lois AM, Dröge LH, Baumeister P, Walz C, Biggemann L, Walter R, Häupl B, Comoglio F, Pan KT, Scheich S, Lenz C, Küffer S, Bremmer F, Kitz J, Sitte M, Beißbarth T, Hinterthaner M, Sebastian M, Lotz J, Schildhaus HU, Wolff H, Danner BC, Brandts C, Büttner R, Canis M, Stegmaier K, Serve H, Urlaub H, Oellerich T. Comparative proteomics reveals a diagnostic signature for pulmonary head-and-neck cancer metastasis. EMBO Mol Med 2019; 10:emmm.201708428. [PMID: 30097507 PMCID: PMC6127892 DOI: 10.15252/emmm.201708428] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Patients with head‐and‐neck cancer can develop both lung metastasis and primary lung cancer during the course of their disease. Despite the clinical importance of discrimination, reliable diagnostic biomarkers are still lacking. Here, we have characterised a cohort of squamous cell lung (SQCLC) and head‐and‐neck (HNSCC) carcinomas by quantitative proteomics. In a training cohort, we quantified 4,957 proteins in 44 SQCLC and 30 HNSCC tumours. A total of 518 proteins were found to be differentially expressed between SQCLC and HNSCC, and some of these were identified as genetic dependencies in either of the two tumour types. Using supervised machine learning, we inferred a proteomic signature for the classification of squamous cell carcinomas as either SQCLC or HNSCC, with diagnostic accuracies of 90.5% and 86.8% in cross‐ and independent validations, respectively. Furthermore, application of this signature to a cohort of pulmonary squamous cell carcinomas of unknown origin leads to a significant prognostic separation. This study not only provides a diagnostic proteomic signature for classification of secondary lung tumours in HNSCC patients, but also represents a proteomic resource for HNSCC and SQCLC.
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Affiliation(s)
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Philipp Ströbel
- Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Diego Yepes
- Department of Medicine II, Hematology/Oncology, Goethe University, Frankfurt, Germany.,German Cancer Research Center, German Cancer Consortium, Heidelberg, Germany
| | - Uwe Plessmann
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Neekesh V Dharia
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Division of Pediatric Hematology/Oncology, Boston Childrens Hospital, Boston, MA, USA.,The Broad Institute, Cambridge, MA, USA
| | - Sha Yao
- Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Carina Heydt
- Institute of Pathology, University Hospital Cologne, University of Cologne, Köln, Germany
| | | | - Alexander Emmert
- Department of Thoracic and Cardiovascular Surgery, University Medical Center, Göttingen, Germany
| | - Jonatan Hoffmann
- Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Julius Bodemeyer
- Institute of Pathology, University Medical Center, Göttingen, Germany
| | | | - Anna-Maria Lois
- Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Leif Hendrik Dröge
- Department of Radiooncology, University Medical Center, Göttingen, Germany
| | - Philipp Baumeister
- Department of Otorhinolaryngology, University Hospital Munich, Ludwig-Maximilian-University München, München, Germany
| | - Christoph Walz
- Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Lorenz Biggemann
- Institute for Diagnostic and Interventional Radiology, University Medical Center, Göttingen, Germany
| | - Roland Walter
- Department of Medicine II, Hematology/Oncology, Goethe University, Frankfurt, Germany
| | - Björn Häupl
- Department of Medicine II, Hematology/Oncology, Goethe University, Frankfurt, Germany.,German Cancer Research Center, German Cancer Consortium, Heidelberg, Germany
| | - Federico Comoglio
- Department of Haematology, University of Cambridge, Cambridge, UK.,Cambridge Institute for Medical Research, Wellcome Trust/MRC Stem Cell Institute, Cambridge, UK
| | - Kuan-Ting Pan
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Sebastian Scheich
- Department of Medicine II, Hematology/Oncology, Goethe University, Frankfurt, Germany
| | - Christof Lenz
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Bioanalytics, University Medical Center, Göttingen, Germany
| | - Stefan Küffer
- Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Felix Bremmer
- Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Julia Kitz
- Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Maren Sitte
- Institute of Medical Statistics, University Medical Center, Göttingen, Germany
| | - Tim Beißbarth
- Institute of Medical Statistics, University Medical Center, Göttingen, Germany
| | - Marc Hinterthaner
- Department of Thoracic and Cardiovascular Surgery, University Medical Center, Göttingen, Germany
| | - Martin Sebastian
- Department of Medicine II, Hematology/Oncology, Goethe University, Frankfurt, Germany
| | - Joachim Lotz
- Institute for Diagnostic and Interventional Radiology, University Medical Center, Göttingen, Germany.,German Cardiovascular Research Center, Deutsches Zentrum für Herz-Kreislaufforschung (DZHK), Partnersite Göttingen, Germany
| | | | - Hendrik Wolff
- University Medical Center, Göttingen, Germany.,Department of Radiooncology, University Medical Center, Regensburg, Germany
| | - Bernhard C Danner
- Department of Thoracic and Cardiovascular Surgery, University Medical Center, Göttingen, Germany
| | - Christian Brandts
- Department of Medicine II, Hematology/Oncology, Goethe University, Frankfurt, Germany.,German Cancer Research Center, German Cancer Consortium, Heidelberg, Germany
| | - Reinhard Büttner
- Institute of Pathology, University Hospital Cologne, University of Cologne, Köln, Germany
| | - Martin Canis
- Department of Otorhinolaryngology, University Hospital Munich, Ludwig-Maximilian-University München, München, Germany
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Division of Pediatric Hematology/Oncology, Boston Childrens Hospital, Boston, MA, USA.,The Broad Institute, Cambridge, MA, USA
| | - Hubert Serve
- Department of Medicine II, Hematology/Oncology, Goethe University, Frankfurt, Germany.,German Cancer Research Center, German Cancer Consortium, Heidelberg, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Institute for Diagnostic and Interventional Radiology, University Medical Center, Göttingen, Germany
| | - Thomas Oellerich
- Department of Medicine II, Hematology/Oncology, Goethe University, Frankfurt, Germany .,German Cancer Research Center, German Cancer Consortium, Heidelberg, Germany
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Garabedian A, Benigni P, Ramirez CE, Baker ES, Liu T, Smith RD, Fernandez-Lima F. Towards Discovery and Targeted Peptide Biomarker Detection Using nanoESI-TIMS-TOF MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:817-826. [PMID: 28889248 PMCID: PMC5844780 DOI: 10.1007/s13361-017-1787-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/29/2017] [Accepted: 08/10/2017] [Indexed: 05/12/2023]
Abstract
In the present work, the potential of trapped ion mobility spectrometry coupled to TOF mass spectrometry (TIMS-TOF MS) for discovery and targeted monitoring of peptide biomarkers from human-in-mouse xenograft tumor tissue was evaluated. In particular, a TIMS-MS workflow was developed for the detection and quantification of peptide biomarkers using internal heavy analogs, taking advantage of the high mobility resolution (R = 150-250) prior to mass analysis. Five peptide biomarkers were separated, identified, and quantified using offline nanoESI-TIMS-CID-TOF MS; the results were in good agreement with measurements using a traditional LC-ESI-MS/MS proteomics workflow. The TIMS-TOF MS analysis permitted peptide biomarker detection based on accurate mobility, mass measurements, and high sequence coverage for concentrations in the 10-200 nM range, while simultaneously achieving discovery measurements of not initially targeted peptides as markers from the same proteins and, eventually, other proteins. Graphical Abstract ᅟ.
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Affiliation(s)
- Alyssa Garabedian
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, 33199, USA
| | - Paolo Benigni
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, 33199, USA
| | - Cesar E Ramirez
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, 33199, USA
| | - Erin S Baker
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Tao Liu
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Richard D Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, 33199, USA.
- Biomolecular Sciences Institute, Florida International University, Miami, FL, 33199, USA.
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5
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Wu Z, Wang C, Zhang Z, Liu W, Xu H, Wang H, Wang Y, Zhang W, Wang SL. High Expression of Derlin-1 Is Associated with the Malignancy of Bladder Cancer in a Chinese Han Population. PLoS One 2016; 11:e0168351. [PMID: 27977784 PMCID: PMC5158059 DOI: 10.1371/journal.pone.0168351] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 11/29/2016] [Indexed: 02/07/2023] Open
Abstract
Derlin-1 is overexpressed in various types of solid tumors and has an important function in cancer progression. However, its expression pattern in and association with the clinicopathological characteristics of human bladder cancer remain unclear. In the present study, 3 pairs of fresh samples of bladder cancer tissue and paracancerous tissue were first detected by liquid chromatography tandem mass spectrometry (UPLC-MS/MS) to screen for differentially expressed proteins. Following bioinformatics analysis and assessments by qRT-PCR and western blotting, Derlin-1 was selected as a candidate protein and was then validated in samples from patients with bladder cancer by immunohistochemistry and western blotting. The results showed that the bladder cancer tissues exhibited higher levels of Derlin-1 expression than the paracancerous tissues (P < 0.05). Positive expression of Derlin-1 was significantly correlated with tumor stage, histological grade, and lymph node metastasis (P < 0.001) but was not correlated with other clinicopathological parameters including patient age (P = 0.758) and gender (P = 0.831). Besides, Derlin-1 was highly expressed in BC cell lines (um-uc-3 and T24), and the interference of Derlin-1 could reverse EMT progression, inhibit the tumor migration and invasion in T24 cells. Further, patients with positive Derlin-1 expression had shorter overall survival than those with negative expression (P < 0.001). Taken together, our results demonstrated that Derlin-1 was overexpressed in bladder cancer and was associated with the malignancy of bladder cancer.
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Affiliation(s)
- Ziyu Wu
- School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, People's Republic of China
- Department of Urology, Huai’an Hospital Affiliated with Xuzhou Medical University, Huai’an, People's Republic of China
| | - Chao Wang
- School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, People's Republic of China
| | - Zhan Zhang
- School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, People's Republic of China
| | - Wenlou Liu
- Department of Oncology, Zhongnan Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Hengsen Xu
- School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, People's Republic of China
| | - Huanqiang Wang
- School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, People's Republic of China
| | - Yun Wang
- School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, People's Republic of China
| | - Wei Zhang
- Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
- * E-mail: (WZ); (SLW)
| | - Shou-Lin Wang
- School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, People's Republic of China
- * E-mail: (WZ); (SLW)
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