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Wei D, Sun J, Luo Z, Zhang G, Liu Y, Zhang H, Xie Z, Gu Z, Tao WA. Targeted Phosphoproteomics of Human Saliva Extracellular Vesicles via Multiple Reaction Monitoring Cubed (MRM 3). Anal Chem 2024; 96:1223-1231. [PMID: 38205554 DOI: 10.1021/acs.analchem.3c04464] [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: 01/12/2024]
Abstract
Oral squamous cell carcinoma (OSCC) has become a global health problem due to its increasing incidence and high mortality rate. Early intervention through monitoring of the diagnostic biomarker levels during OSCC treatment is critical. Extracellular vesicles (EVs) are emerging surrogates in intercellular communication through transporting biomolecule cargo and have recently been identified as a potential source of biomarkers such as phosphoproteins for many diseases. Here, we developed a multiple reaction monitoring cubed (MRM3) method coupled with a novel sample preparation strategy, extracellular vesicles to phosphoproteins (EVTOP), to quantify phosphoproteins using a minimal amount of saliva (50 μL) samples from OSCC patients with high specificity and sensitivity. Our results established differential patterns in the phosphopeptide content of healthy, presurgery, and postsurgery OSCC patient groups. Notably, we discovered significantly increased salivary phosphorylated alpha-amylase (AMY) in the postsurgery group compared to the presurgery group. We hereby present the first targeted MS method with extremely high sensitivity for measuring endogenous phosphoproteins in human saliva EVs.
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Affiliation(s)
- Dong Wei
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - Jie Sun
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - Zhuojun Luo
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Guiyuan Zhang
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - Yufeng Liu
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - Hao Zhang
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - Zhuoying Xie
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - Zhongze Gu
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - W Andy Tao
- Department of Chemistry and Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
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2
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Nickerson JL, Baghalabadi V, Rajendran SRCK, Jakubec PJ, Said H, McMillen TS, Dang Z, Doucette AA. Recent advances in top-down proteome sample processing ahead of MS analysis. MASS SPECTROMETRY REVIEWS 2023; 42:457-495. [PMID: 34047392 DOI: 10.1002/mas.21706] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/21/2021] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
Abstract
Top-down proteomics is emerging as a preferred approach to investigate biological systems, with objectives ranging from the detailed assessment of a single protein therapeutic, to the complete characterization of every possible protein including their modifications, which define the human proteoform. Given the controlling influence of protein modifications on their biological function, understanding how gene products manifest or respond to disease is most precisely achieved by characterization at the intact protein level. Top-down mass spectrometry (MS) analysis of proteins entails unique challenges associated with processing whole proteins while maintaining their integrity throughout the processes of extraction, enrichment, purification, and fractionation. Recent advances in each of these critical front-end preparation processes, including minimalistic workflows, have greatly expanded the capacity of MS for top-down proteome analysis. Acknowledging the many contributions in MS technology and sample processing, the present review aims to highlight the diverse strategies that have forged a pathway for top-down proteomics. We comprehensively discuss the evolution of front-end workflows that today facilitate optimal characterization of proteoform-driven biology, including a brief description of the clinical applications that have motivated these impactful contributions.
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Affiliation(s)
| | - Venus Baghalabadi
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Subin R C K Rajendran
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
- Verschuren Centre for Sustainability in Energy and the Environment, Sydney, Nova Scotia, Canada
| | - Philip J Jakubec
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Hammam Said
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Teresa S McMillen
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ziheng Dang
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Alan A Doucette
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
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3
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Hadisurya M, Lee ZC, Luo Z, Zhang G, Ding Y, Zhang H, Iliuk AB, Pili R, Boris RS, Tao WA. Data-independent acquisition phosphoproteomics of urinary extracellular vesicles enables renal cell carcinoma grade differentiation. Mol Cell Proteomics 2023; 22:100536. [PMID: 36997065 PMCID: PMC10165457 DOI: 10.1016/j.mcpro.2023.100536] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 03/01/2023] [Accepted: 03/24/2023] [Indexed: 03/31/2023] Open
Abstract
Translating the research capability and knowledge in cancer signaling into clinical settings has been slow and ineffective. Recently, extracellular vesicles (EVs) have emerged as a promising source for developing disease phosphoprotein markers to monitor disease status. This study focuses on the development of a robust data-independent acquisition (DIA) using mass spectrometry to profile urinary EV phosphoproteomics for renal cell cancer (RCC) grades differentiation. We examined gas-phase fractionated (GPF) library, direct DIA (library-free), forbidden zones, and several different windowing schemes. After the development of a DIA mass spectrometry method for EV phosphoproteomics, we applied the strategy to identify and quantify urinary EV phosphoproteomes from 57 individuals representing low-grade clear cell RCC, high-grade clear cell RCC, chronic kidney disease (CKD), and healthy control (HC) individuals. Urinary EVs were efficiently isolated by functional magnetic beads, and EV phosphopeptides were subsequently enriched by PolyMAC. We quantified 2,584 unique phosphosites and observed that multiple prominent cancer-related pathways, such as ErbB signaling, renal cell carcinoma, and regulation of actin cytoskeleton, were only upregulated in high-grade clear cell RCC. These results show that EV phosphoproteome analysis utilizing our optimized procedure of EV isolation, phosphopeptide enrichment, and DIA method provides a powerful tool for future clinical applications.
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Zhang Y, Wang Q, Liang J, Liu L, Liu P, Zhao H. Serum proteomic analysis of differentially expressed proteins and pathways involved in the mechanism of endemic osteoarthritis. Mol Omics 2022; 18:745-753. [PMID: 35820143 DOI: 10.1039/d2mo00154c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Kashin-Beck disease (KBD) is a chronic and endemic osteochondral disease and the etiology and pathogenic mechanism of KBD are still unknown. This study aimed to elucidate and screen KBD-associated proteins, which were differentially expressed between KBD patients and healthy controls. We combined protein fractionation and liquid chromatography-tandem mass spectrometry (LC-MS/MS) with a high-resolution mass spectrometer coupled with tandem mass tags (TMTs) to quantitatively analyze and screen KBD-associated proteins, which were differentially expressed between KBD patients and healthy controls. In addition, we used parallel reaction monitoring (PRM) to quantify proteins in serum from patients with KBD and healthy controls in order to verify the differentially expressed proteins in patients with KBD. We identified 224 differentially expressed proteins, including 11 up-regulated and 213 down-regulated proteins. Catalase (CAT) was observed to be significantly elevated in patients with KBD compared with control patients. Further, the fold difference of CAT is significantly elevated in PRM compared with label-free quantification. The results in this study suggest that CAT may be the reflection of the dynamic nature of KBD and could be considered as a novel pathogenic indicator for patients with KBD.
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Affiliation(s)
- Yan Zhang
- Foot and ankle surgery department, Honghui Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
| | - Qiong Wang
- Foot and ankle surgery department, Honghui Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
| | - Jingqi Liang
- Foot and ankle surgery department, Honghui Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
| | - Liang Liu
- Foot and ankle surgery department, Honghui Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
| | - Peilong Liu
- Foot and ankle surgery department, Honghui Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
| | - Hongmou Zhao
- Foot and ankle surgery department, Honghui Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
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Cheng J, Wang X, Yuan X, Liu G, Chu Q. Emerging roles of exosome-derived biomarkers in cancer theranostics: messages from novel protein targets. Am J Cancer Res 2022; 12:2226-2248. [PMID: 35693088 PMCID: PMC9185602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 04/14/2022] [Indexed: 06/15/2023] Open
Abstract
Effective biomarkers that guide therapeutics with limited adverse effects, have emerged as attractive research topics in cancer diagnosis and treatment. Cancer-derived exosomes, a type of extracellular vesicles representing molecular signatures of cells of origin, could serve as stable reservoirs for potential biomarkers (i.e., proteins, nucleic acids) in non-invasive cancer diagnosis and prognosis. In this review, the physiological and pathological roles of exosomes and their protein components in facilitating tumorigenesis are highlighted. Exosomes carrying proteins can participate in tumor development and progression through multiple signaling pathways, including EMT, invasion and metastasis. Meanwhile, the practical applications of exosomal proteins in detecting and monitoring several solid-tumor cancers (including lung, breast, pancreatic, colorectal and prostate cancers) were also summarized. More clinically relevant, exosomal proteins play pivotal roles in transmitting oncogenic potential or resistance to therapies in recipient cells, which might further support therapeutic strategy determinations.
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Affiliation(s)
- Jiongjia Cheng
- Key Laboratory of Advanced Functional Materials of Nanjing, Nanjing Xiaozhuang UniversityNanjing 211171, Jiangsu, China
| | - Xiaofeng Wang
- Key Laboratory of Advanced Functional Materials of Nanjing, Nanjing Xiaozhuang UniversityNanjing 211171, Jiangsu, China
| | - Xuechun Yuan
- Department of Medicinal Chemistry, China Pharmaceutical UniversityNanjing 211198, Jiangsu, China
| | - Guangxiang Liu
- Key Laboratory of Advanced Functional Materials of Nanjing, Nanjing Xiaozhuang UniversityNanjing 211171, Jiangsu, China
| | - Qian Chu
- Department of Medicinal Chemistry, China Pharmaceutical UniversityNanjing 211198, Jiangsu, China
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He Y, Zhang S, Zhong C, Yang Y, Li G, Ji Y, Lin Z. Facile synthesis of Ti 4+-immobilized magnetic covalent organic frameworks for enhanced phosphopeptide enrichment. Talanta 2021; 235:122789. [PMID: 34517647 DOI: 10.1016/j.talanta.2021.122789] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/31/2021] [Accepted: 08/04/2021] [Indexed: 10/20/2022]
Abstract
In this work, core-shell structured Ti4+-immobilized magnetic covalent organic frameworks (denoted as Fe3O4@TAPTDHTA-Ti4+ composites) were prepared for enhanced phosphopeptide enrichment by one-pot synthesis of COFs shell with inherent bifunctional groups on Fe3O4 NPs and further Ti4+ immobilization. The widely distributed bifunctional groups could provide abundant chelating sites for Ti4+ immobilizing. Combining with the high specific surface area and mesoporous structure, the Fe3O4@TAPTDHTA-Ti4+ composites exhibited excellent enrichment efficiency for phosphopeptides, such as low detection limit (0.05 fmol μL-1), high selectivity (1:5000 of molar ratio of β-casein/bovine serum albumin (BSA) tryptic digests), high adsorption capacity (62.9 μg mg-1) and strong size-exclusive effect (1:250:250 of molar ratio of β-casein tryptic digest/β-casein/BSA). In addition, this method was general for immobilizing other metal ions (Zr4+ and Fe3+). Notably, the Fe3O4@TAPTDHTA-Fe3+ composites exhibited controllable affinity towards mono-phosphopeptides and multi-phosphopeptides. Furthermore, the Fe3O4@TAPTDHTA-Ti4+ composites were successfully applied to selectively capture phosphopeptides from complex biological samples including the tryptic digest of nonfat milk, human serum and human saliva. More significantly, 3333 phosphopeptides derived from 1409 phosphoproteins with 3492 phosphorylation sites were clearly identified from the tryptic digest of HeLa cell lysate. In addition to providing a potential excellent enrichment probe for comprehensive phosphoproteomic analysis, this study also offers a new perspective for the functionalization of COFs.
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Affiliation(s)
- Yanting He
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Shasha Zhang
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Chao Zhong
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Yixin Yang
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Guorong Li
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Yin Ji
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Zian Lin
- Ministry of Education Key Laboratory of Analytical Science for Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China.
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7
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Hydrophilic polydopamine-derived mesoporous channels for loading Ti(IV) ions for salivary phosphoproteome research. Anal Chim Acta 2020; 1146:53-60. [PMID: 33461719 DOI: 10.1016/j.aca.2020.12.038] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/21/2020] [Accepted: 12/18/2020] [Indexed: 11/20/2022]
Abstract
Salivary phosphoproteome holds great promise in clinic diagnosis. For profiling of salivary phosphoproteome, it is essential to develop efficient enrichment methods prior to mass spectrum (MS). Among developed enrichment strategies, immobilized metal ions affinity chromatography (IMAC) has exhibited outstanding performance. In this work, we report a coherent approach where polydopamine (PDA) is first utilized to form mesoporous structure through soft templating method, then chelated with Ti4+ to construct hydrophilic polydopamine-derived magnetic mesoporous nanocomposite (denoted Fe3O4@mPDA@Ti4+). In virtue of the merits including ordered mesoporous channels, appropriate superparamagnetism, and abundant Ti4+, the enrichment strategy based on Fe3O4@mPDA@Ti4+ combined with MS is employed for accurate identification of phosphopeptides in β-casein digest and human saliva. As expected, Fe3O4@mPDA@Ti4+ revealed a great selectivity (1:200) and a low detection limit (0.1 fmol μL-1) toward phosphopeptides. More importantly, the further successful capture of phosphopeptides from human saliva indicated the prominent potential of this method for seeking phosphopeptide biomarkers in further analysis.
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8
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Zheng X, Xu K, Zhou B, Chen T, Huang Y, Li Q, Wen F, Ge W, Wang J, Yu S, Sun L, Zhu L, Liu W, Gao H, Yue L, Cai X, Zhang Q, Ruan G, Zhu T, Wu Z, Zhu Y, Shao Y, Guo T, Zheng S. A circulating extracellular vesicles-based novel screening tool for colorectal cancer revealed by shotgun and data-independent acquisition mass spectrometry. J Extracell Vesicles 2020; 9:1750202. [PMID: 32363013 PMCID: PMC7178829 DOI: 10.1080/20013078.2020.1750202] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 03/03/2020] [Accepted: 03/16/2020] [Indexed: 01/06/2023] Open
Abstract
Background: Early screening for colorectal cancer (CRC) is essential to improve its prognosis. Liquid biopsies are increasingly being considered for diagnosing cancer due to low invasiveness and high reproducibility. In addition, circulating extracellular vesicles (crEVs, extracellular vesicles isolated from plasma) expressing tumour-specific proteins are potential biomarkers for various cancers. Here, we present a data-independent acquisition (DIA)-mass spectrometry (MS)-based diagnostic method for liquid biopsies. Methods: Extracellular vesicles (EVs) were isolated from culture supernatants of human CRC cell lines, and plasma of patients with CRC at different tumour stages, by overnight ultracentrifugation coupled with sucrose density gradient centrifugation. Tumour-specific EV proteins were prioritized using Tandem Mass Tag (TMT)-based shotgun proteomics and phosphoproteomics. The results were verified in a second independent cohort and a mouse tumour-bearing model using Western blotting (WB). The candidate biomarkers were further validated in a third cohort by DIA-MS. Finally, the DIA-MS methodology was accelerated to permit high-throughput detection of EV biomarkers in another independent cohort of patients with CRC and healthy controls. Results: High levels of total and phosphorylated fibronectin 1 (FN1) in crEVs, haptoglobin (HP), S100A9 and fibrinogen α chain (FGA) were significantly associated with cancer progression. FGA was the most dominant biomarker candidate. Analysis of the human CRC cell lines and the mouse model indicated that FGA+ crEVs were likely released by CRC cells. Furthermore, fast DIA-MS and parallel reaction monitoring (PRM)-MS both confirmed that FGA+ crEVs could distinguish colon adenoma with an area of curve (AUC) in the receiver operating characteristic (ROC) curve of 0.949 and patients with CRC (AUC of ROC is 1.000) from healthy individuals. The performance outperformed conventional tumour biomarkers. The DIA-MS quantification of FGA+ crEVs among three groups agreed with that from PRM-MS. Conclusion: DIA-MS detection of FGA+ crEVs is a potential rapid and non-invasive screening tool to identify early stage CRC. Abbreviations: FGA: fibrinogen α chain; CRC: colorectal cancer; crEVs: circulating extracellular vesicles; EV: extracellular vesicles;MS: mass spectrometry; WB: Western blotting; ROC: receiver operating characteristic; PRM: Parallel Reaction Monitoring; GPC1: Glypican-1; GO: Gene ontology; TEM: transmission electron microscopy; FN1: Fibronectin 1; HP: haptoglobin; TMT: Tandem Mass Tag; LC-MS/MS: liquid chromatography coupled to tandem mass spectrometry; DIA: data-independent acquisition; DDA: data-dependent acquisition; CiRT: Common internal Retention Time standards;AGC: Automatic gain control; AUC: area under curve.
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Affiliation(s)
- Xi Zheng
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Kailun Xu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Biting Zhou
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ting Chen
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yanqin Huang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qilong Li
- Institute of Cancer Research and Prevention of Jiashan County, Jiashan, Zhejiang, China
| | - Fei Wen
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Weiting Ge
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jian Wang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Department of Surgical Oncology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, People's Republic of China
| | - Shaojun Yu
- Department of Surgical Oncology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, People's Republic of China
| | - Lifeng Sun
- Department of Surgical Oncology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, People's Republic of China
| | - Liang Zhu
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
| | - Wei Liu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Huanhuan Gao
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Liang Yue
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Xue Cai
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Qiushi Zhang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Guan Ruan
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Tiansheng Zhu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Zhicheng Wu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Yi Zhu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Yingkuan Shao
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Tiannan Guo
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Shu Zheng
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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Dong S, Wang Y, Liu Z, Zhang W, Yi K, Zhang X, Zhang X, Jiang C, Yang S, Wang F, Xiao X. Beehive-Inspired Macroporous SERS Probe for Cancer Detection through Capturing and Analyzing Exosomes in Plasma. ACS APPLIED MATERIALS & INTERFACES 2020; 12:5136-5146. [PMID: 31894690 DOI: 10.1021/acsami.9b21333] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The protein phosphorylation status of exosomes can regulate the activity and function of proteins related to cancer development, and it is highly possible to diagnose cancers through analyzing the protein phosphorylation status. However, monitoring the protein phosphorylation status with a simple and label-free method is still clinically challenging. Here, inspired by beehives, we developed an Au-coated TiO2 macroporous inverse opal (MIO) structure with an engineered "slow light effect" and thus with outstanding surface-enhanced Raman scattering (SERS) performance. The MIO structure can capture and analyze the exosomes from plasma of cancer patients without any labeling processes. It was found that the SERS intensity of exosomes at 1087 cm-1 arising from the P-O bond within the phosphoproteins can be used as a criterion for tumor liquid biopsies. The intensity of the 1087 cm-1 SERS peak from exosomes extracted from the plasma of cancer patients (prostate, lung, liver, and colon) is at least two times of that from healthy people. This indicates the simplicity and versatility of this method in cancer diagnostics. Our method has obvious advantages (noninvasive and time-saving) over currently clinically used tumor liquid biopsy techniques (such as western blot), which has great potentials to make vitro cancer diagnostics/monitoring as simple as diagnostics/monitoring of common diseases.
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Affiliation(s)
- Shilian Dong
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, Hubei Nuclear Solid Physics Key Laboratory , Wuhan University , Wuhan 430072 , P. R. China
| | - Yuhui Wang
- Department of Clinical Laboratory Medicine and Center for Gene Diagnosis , Zhongnan Hospital of Wuhan University , Wuhan 430071 , P. R. China
- Department of Clinical Laboratory , The Third Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan 450072 , P.R. China
| | - Zhengqi Liu
- Institute of Optoelectronic Materials and Technology, College of Physics and Communication Electronics , Jiangxi Normal University , Nanchang 330022 , P. R. China
| | - Wuwen Zhang
- Department of Clinical Laboratory Medicine and Center for Gene Diagnosis , Zhongnan Hospital of Wuhan University , Wuhan 430071 , P. R. China
| | - Kezhen Yi
- Department of Clinical Laboratory Medicine and Center for Gene Diagnosis , Zhongnan Hospital of Wuhan University , Wuhan 430071 , P. R. China
| | - Xingang Zhang
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, Hubei Nuclear Solid Physics Key Laboratory , Wuhan University , Wuhan 430072 , P. R. China
| | - Xiaolei Zhang
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, Hubei Nuclear Solid Physics Key Laboratory , Wuhan University , Wuhan 430072 , P. R. China
| | - Changzhong Jiang
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, Hubei Nuclear Solid Physics Key Laboratory , Wuhan University , Wuhan 430072 , P. R. China
| | - Shikuan Yang
- School of Materials Science and Engineering , Zhejiang University , Hangzhou 310027 , P. R. China
| | - Fubing Wang
- Department of Clinical Laboratory Medicine and Center for Gene Diagnosis , Zhongnan Hospital of Wuhan University , Wuhan 430071 , P. R. China
| | - Xiangheng Xiao
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, Hubei Nuclear Solid Physics Key Laboratory , Wuhan University , Wuhan 430072 , P. R. China
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10
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Zhang G, Jiang L, Zhou J, Hu L, Feng S. Epitope-imprinted mesoporous silica nanoparticles for specific recognition of tyrosine phosphorylation. Chem Commun (Camb) 2019; 55:9927-9930. [PMID: 31334708 DOI: 10.1039/c9cc03950c] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Tyrosine phosphorylation regulates the upstream signaling pathway but accounts for less than 0.1% of total phosphorylation in human cells. Herein, molecularly imprinted mesoporous materials were first synthesized to recognize the phosphorylated tyrosine residue from other phosphorylated residues.
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Affiliation(s)
- Guiyuan Zhang
- Key Laboratory Molecular Enzymology and Engineering, the Ministry of Education, National Engineering Laboratory of AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130023, China.
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11
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Dou M, Tsai CF, Piehowski PD, Wang Y, Fillmore TL, Zhao R, Moore RJ, Zhang P, Qian WJ, Smith RD, Liu T, Kelly RT, Shi T, Zhu Y. Automated Nanoflow Two-Dimensional Reversed-Phase Liquid Chromatography System Enables In-Depth Proteome and Phosphoproteome Profiling of Nanoscale Samples. Anal Chem 2019; 91:9707-9715. [PMID: 31241912 DOI: 10.1021/acs.analchem.9b01248] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Two-dimensional reversed-phase capillary liquid chromatography (2D RPLC) separations have enabled comprehensive proteome profiling of biological systems. However, milligram sample quantities of proteins are typically required due to significant losses during offline fractionation. Such a large sample requirement generally precludes the application samples in the nanogram to low-microgram range. To achieve in-depth proteomic analysis of such small-sized samples, we have developed the nanoFAC (nanoflow Fractionation and Automated Concatenation) 2D RPLC platform, in which the first dimension high-pH fractionation was performed on a 75-μm i.d. capillary column at a 300 nL/min flow rate with automated fraction concatenation, instead of on a typically used 2.1 mm column at a 200 μL/min flow rate with manual concatenation. Each fraction was then fully transferred to the second-dimension low-pH nanoLC separation using an autosampler equipped with a custom-machined syringe. We have found that using a polypropylene 96-well plate as collection device as well as the addition of n-Dodecyl β-d-maltoside (0.01%) in the collection buffer can significantly improve sample recovery. We have demonstrated the nanoFAC 2D RPLC platform can achieve confident identifications of ∼49,000-94,000 unique peptides, corresponding to ∼6,700-8,300 protein groups using only 100-1000 ng of HeLa tryptic digest (equivalent to ∼500-5,000 cells). Furthermore, by integrating with phosphopeptide enrichment, the nanoFAC 2D RPLC platform can identify ∼20,000 phosphopeptides from 100 μg of MCF-7 cell lysate.
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Affiliation(s)
- Maowei Dou
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Chia-Feng Tsai
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Paul D Piehowski
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Yang Wang
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Thomas L Fillmore
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Ronald J Moore
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Pengfei Zhang
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Wei-Jun Qian
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Richard D Smith
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Tao Liu
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Ryan T Kelly
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States.,Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84604 , United States
| | - Tujin Shi
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
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12
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Phosphoproteins Involved in the Inhibition of Apoptosis and in Cell Survival in the Leiomyoma. J Clin Med 2019; 8:jcm8050691. [PMID: 31100862 PMCID: PMC6572112 DOI: 10.3390/jcm8050691] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 05/01/2019] [Accepted: 05/13/2019] [Indexed: 12/24/2022] Open
Abstract
Uterine leiomyomas are benign smooth muscle cell tumors originating from the myometrium. In this study we focus on leiomyoma and normal myometrium phosphoproteome, to identify differentially phosphorylated proteins involved in tumorigenic signaling pathways, and in anti-apoptotic processes and cell survival. We obtained paired tissue samples of seven leiomyomas and adjacent myometria and analyzed the phosphoproteome by two-dimensional gel electrophoresis (2-DE) combined with immobilized metal affinity chromatography (IMAC) and Pro-Q Diamond phosphoprotein gel stain. We used mass spectrometry for protein identification and Western blotting for 2-DE data validation. Quantities of 33 proteins enriched by the IMAC approach were significantly different in the leiomyoma if compared to the myometrium. Bioinformatic analysis revealed ten tumorigenic signaling pathways and four phosphoproteins involved in both the inhibition of apoptosis and cell survival. Our study highlights the involvement of the phosphoproteome in leiomyoma growth. Further studies are needed to understand the role of phosphorylation in leiomyoma. Our data shed light on mechanisms that still need to be ascertained, but could open the path to a new class of drugs that not only can block the growth, but could also lead to a significant reduction in tumor size.
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13
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Núñez C. Blood-based protein biomarkers in breast cancer. Clin Chim Acta 2018; 490:113-127. [PMID: 30597138 DOI: 10.1016/j.cca.2018.12.028] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/26/2018] [Accepted: 12/27/2018] [Indexed: 02/07/2023]
Abstract
Breast cancer (BCa) is a significant healthcare problem on women worldwide. Thus, early detection is very important to reduce mortality. Furthermore, better BCa prognosis could improve selection of patients eligible for adjuvant therapy. New markers for early diagnosis, accurate prognosis and prediction of response to treatment are necessary to improve BCa care. The present review summarizes important aspects of the potential usefulness of modern technologies, strategies, and scientific findings in proteomic research for discovery of breast cancer-associated blood-based protein biomarkers in the clinic.
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Affiliation(s)
- Cristina Núñez
- Research Unit, Hospital Universitario Lucus Augusti (HULA), Servizo Galego de Saúde (SERGAS), 27002 Lugo, Spain.
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14
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Arrington JV, Hsu CC, Elder SG, Andy Tao W. Recent advances in phosphoproteomics and application to neurological diseases. Analyst 2018; 142:4373-4387. [PMID: 29094114 DOI: 10.1039/c7an00985b] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Phosphorylation has an incredible impact on the biological behavior of proteins, altering everything from intrinsic activity to cellular localization and complex formation. It is no surprise then that this post-translational modification has been the subject of intense study and that, with the advent of faster, more accurate instrumentation, the number of large-scale mass spectrometry-based phosphoproteomic studies has swelled over the past decade. Recent developments in sample preparation, phosphorylation enrichment, quantification, and data analysis strategies permit both targeted and ultra-deep phosphoproteome profiling, but challenges remain in pinpointing biologically relevant phosphorylation events. We describe here technological advances that have facilitated phosphoproteomic analysis of cells, tissues, and biofluids and note applications to neuropathologies in which the phosphorylation machinery may be dysregulated, much as it is in cancer.
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15
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Peng J, Niu H, Zhang H, Yao Y, Zhao X, Zhou X, Wan L, Kang X, Wu R. Highly Specific Enrichment of Multi-phosphopeptides by the Diphosphorylated Fructose-Modified Dual-Metal-Centered Zirconium-Organic Framework. ACS APPLIED MATERIALS & INTERFACES 2018; 10:32613-32621. [PMID: 30156824 DOI: 10.1021/acsami.8b11138] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Multisite phosphorylation of a protein, generally occurring in biological processes, plays important roles in the regulation of cellular functions. However, the identification of multi-phosphopeptides especially at low abundance is a big challenge as the extreme hydrophilicity and poor ionization efficiency of the multiphosphorylated peptides restrict the deep inspection of multisite phosphorylation processes. In this study, the highly specific enrichment of multiphosphorylated peptides was achieved via the modification of the dual-metal-centered zirconium-organic framework with the diphosphorylated fructose. The diphosphorylated fructose-modified dual-metal-centered zirconium-organic framework (DZMOF-FDP) demonstrated the highly specific affinity to the multiple phosphorylated peptides, with the density functional theory calculations explaining the plausible mechanism for multi-phosphopeptides on the DZMOF-FDP. The selective capture of multi-phosphopeptides from mimic samples confirmed the superior performance of the DZMOF-FDP, with comprehensive comparisons to other modification agents, such as orthophosphate and pyrophosphate. A number of 1871 multiphosphorylated peptides captured by DZMOF-FDP from tryptic digests of HeLa cell lysate could be identified, significantly higher than that by the pristine DZMOF. The deliberately designed modification with diphosphorylated fructose for the dual-zirconium-centered metal-organic framework materials suggests an efficient strategy to develop new enrichment methods in the selective capture of target analytes by judiciously optimizing specific modifiers for adsorbents.
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Affiliation(s)
- Jiaxi Peng
- Laboratory of High-Resolution Mass Spectrometry Technologies, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Sciences (CAS) , Dalian 116023 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Huan Niu
- Laboratory of High-Resolution Mass Spectrometry Technologies, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Sciences (CAS) , Dalian 116023 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Hongyan Zhang
- Laboratory of High-Resolution Mass Spectrometry Technologies, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Sciences (CAS) , Dalian 116023 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Yating Yao
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Xingyun Zhao
- Laboratory of High-Resolution Mass Spectrometry Technologies, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Sciences (CAS) , Dalian 116023 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Xiaoyu Zhou
- Laboratory of High-Resolution Mass Spectrometry Technologies, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Sciences (CAS) , Dalian 116023 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Lihong Wan
- Laboratory of High-Resolution Mass Spectrometry Technologies, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Sciences (CAS) , Dalian 116023 , China
| | - Xiaohui Kang
- College of Pharmacy , Dalian Medical University , Dalian 116044 , China
| | - Ren'an Wu
- Laboratory of High-Resolution Mass Spectrometry Technologies, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics , Chinese Academy of Sciences (CAS) , Dalian 116023 , China
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16
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Exploration of variations in proteome and metabolome for predictive diagnostics and personalized treatment algorithms: Innovative approach and examples for potential clinical application. J Proteomics 2018; 188:30-40. [DOI: 10.1016/j.jprot.2017.08.020] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/06/2017] [Accepted: 08/25/2017] [Indexed: 12/20/2022]
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17
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Li A, Zhang T, Zheng M, Liu Y, Chen Z. Exosomal proteins as potential markers of tumor diagnosis. J Hematol Oncol 2017; 10:175. [PMID: 29282096 PMCID: PMC5745959 DOI: 10.1186/s13045-017-0542-8] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 12/08/2017] [Indexed: 12/12/2022] Open
Abstract
Liquid biopsy especially that of exosomes carries tumor-specific molecules and provides useful information during tumor development and progression in "real time." Exosomes are membrane-encapsulated vesicles, constantly released by multiple cells, including cancer cells, in large quantities, and are widely present in body fluids. Tumor exosomes can remodel a tumor-supportive microenvironment via cross-talk with target cells. Recent research has mainly focused on exosomal miRNAs and to a small degree on proteins. However, detecting the genome output (active proteins such as phosphoproteins) can provide more direct information about disease progression, such as in the early discovery and monitoring of cancers. This review highlights the unique features of exosomal proteins over traditional serological markers and summarizes their recent use in cancer diagnosis and prognosis. Furthermore, we describe the general protocols of research on exosome proteomics with an emphasis on their clinical use.
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Affiliation(s)
- Aichun Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79# Qingchun Road, 6A-17, Hangzhou, 310003, China
| | - Tianbao Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79# Qingchun Road, 6A-17, Hangzhou, 310003, China
| | - Min Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79# Qingchun Road, 6A-17, Hangzhou, 310003, China
| | - Yanning Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79# Qingchun Road, 6A-17, Hangzhou, 310003, China.
| | - Zhi Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79# Qingchun Road, 6A-17, Hangzhou, 310003, China.
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18
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Carrera M, Cañas B, Lopez-Ferrer D. Fast Global Phosphoproteome Profiling of Jurkat T Cells by HIFU-TiO 2-SCX-LC-MS/MS. Anal Chem 2017; 89:8853-8862. [PMID: 28787133 DOI: 10.1021/acs.analchem.7b01321] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We propose a new workflow for fast phosphoproteome profiling. The workflow is based on the use of accelerated in-solution trypsin digestion under an ultrasonic field provided by high-intensity focused ultrasound (HIFU) combined with an inverse strategy based on TiO2 selective phosphopeptide enrichment, fractionation by strong cation exchange chromatography (SCX) and analysis by liquid chromatography tandem mass spectrometry (LC-MS/MS) using a high-resolution mass spectrometer. The performance of the method was established for the global phosphoproteome analysis of unstimulated human Jurkat leukemia T cells (E6.1). Using this accelerated workflow, 15367 phosphorylation sites from 13029 different phosphopeptides belonging to 3163 different phosphoproteins were efficiently identified with high-throughput and reproducibility in less than 15 h. The functional analysis revealed significant phosphorylation-based networks that are implicated in immune function and tumor development pathways. The present strategy, HIFU-TiO2-SCX-LC-MS/MS, is the fastest analytical method reported to date for generating large-scale phosphoproteomics data sets (<15 h).
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Affiliation(s)
- Mónica Carrera
- Spanish National Research Council (CSIC), 36208, Vigo, Spain
| | - Benito Cañas
- Complutense University of Madrid (UCM) , 28040, Madrid, Spain
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19
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Labots M, van der Mijn JC, Beekhof R, Piersma SR, de Goeij-de Haas RR, Pham TV, Knol JC, Dekker H, van Grieken NC, Verheul HM, Jiménez CR. Phosphotyrosine-based-phosphoproteomics scaled-down to biopsy level for analysis of individual tumor biology and treatment selection. J Proteomics 2017; 162:99-107. [DOI: 10.1016/j.jprot.2017.04.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 02/28/2017] [Accepted: 04/12/2017] [Indexed: 12/17/2022]
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20
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Hsu CC, Xue L, Arrington JV, Wang P, Paez Paez JS, Zhou Y, Zhu JK, Tao WA. Estimating the Efficiency of Phosphopeptide Identification by Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1127-1135. [PMID: 28283928 PMCID: PMC5438756 DOI: 10.1007/s13361-017-1603-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 01/08/2017] [Accepted: 01/09/2017] [Indexed: 06/06/2023]
Abstract
Mass spectrometry has played a significant role in the identification of unknown phosphoproteins and sites of phosphorylation in biological samples. Analyses of protein phosphorylation, particularly large scale phosphoproteomic experiments, have recently been enhanced by efficient enrichment, fast and accurate instrumentation, and better software, but challenges remain because of the low stoichiometry of phosphorylation and poor phosphopeptide ionization efficiency and fragmentation due to neutral loss. Phosphoproteomics has become an important dimension in systems biology studies, and it is essential to have efficient analytical tools to cover a broad range of signaling events. To evaluate current mass spectrometric performance, we present here a novel method to estimate the efficiency of phosphopeptide identification by tandem mass spectrometry. Phosphopeptides were directly isolated from whole plant cell extracts, dephosphorylated, and then incubated with one of three purified kinases-casein kinase II, mitogen-activated protein kinase 6, and SNF-related protein kinase 2.6-along with 16O4- and 18O4-ATP separately for in vitro kinase reactions. Phosphopeptides were enriched and analyzed by LC-MS. The phosphopeptide identification rate was estimated by comparing phosphopeptides identified by tandem mass spectrometry with phosphopeptide pairs generated by stable isotope labeled kinase reactions. Overall, we found that current high speed and high accuracy mass spectrometers can only identify 20%-40% of total phosphopeptides primarily due to relatively poor fragmentation, additional modifications, and low abundance, highlighting the urgent need for continuous efforts to improve phosphopeptide identification efficiency. Graphical Abstract ᅟ.
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Affiliation(s)
- Chuan-Chih Hsu
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Liang Xue
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
- Celgene Corporation, Cambridge, MA, USA
| | - Justine V Arrington
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Pengcheng Wang
- Department of Horticulture and Landscape, Purdue University, West Lafayette, IN, 47907, USA
| | | | - Yuan Zhou
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Jian-Kang Zhu
- Department of Horticulture and Landscape, Purdue University, West Lafayette, IN, 47907, USA
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA.
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21
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Phosphoproteins in extracellular vesicles as candidate markers for breast cancer. Proc Natl Acad Sci U S A 2017; 114:3175-3180. [PMID: 28270605 DOI: 10.1073/pnas.1618088114] [Citation(s) in RCA: 286] [Impact Index Per Article: 40.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The state of protein phosphorylation can be a key determinant of cellular physiology such as early-stage cancer, but the development of phosphoproteins in biofluids for disease diagnosis remains elusive. Here we demonstrate a strategy to isolate and identify phosphoproteins in extracellular vesicles (EVs) from human plasma as potential markers to differentiate disease from healthy states. We identified close to 10,000 unique phosphopeptides in EVs isolated from small volumes of plasma samples. Using label-free quantitative phosphoproteomics, we identified 144 phosphoproteins in plasma EVs that are significantly higher in patients diagnosed with breast cancer compared with healthy controls. Several biomarkers were validated in individual patients using paralleled reaction monitoring for targeted quantitation. This study demonstrates that the development of phosphoproteins in plasma EV as disease biomarkers is highly feasible and may transform cancer screening and monitoring.
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22
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Thurgood LA, Chataway TK, Lower KM, Kuss BJ. From genome to proteome: Looking beyond DNA and RNA in chronic lymphocytic leukemia. J Proteomics 2017; 155:73-84. [PMID: 28069558 DOI: 10.1016/j.jprot.2017.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 11/11/2016] [Accepted: 01/03/2017] [Indexed: 02/07/2023]
Abstract
Chronic lymphocytic leukemia (CLL) remains the most common leukemia in the Western world. Whilst its disease course is extremely heterogeneous (ranging from indolent to aggressive), current methods are unable to accurately predict the clinical journey of each patient. There is clearly a pressing need for both improved prognostication and treatment options for patients with this disease. Whilst molecular studies have analyzed both genetic mutations and gene expression profiles of these malignant B-cells, and as a result have shed light on the pathogenesis of CLL, proteomic studies have been largely overlooked to date. This review summarizes our current knowledge of the proteomics of CLL, and discusses some of the issues in CLL proteomic research, such as reproducibility and data interpretation. In addition, we look ahead to how proteomics may significantly help in the development of a successful treatment for this currently incurable disease.
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Affiliation(s)
- Lauren A Thurgood
- Department of Haematology and Genetic Pathology, Flinders University, Adelaide, South Australia, Australia.
| | - Tim K Chataway
- Department of Physiology, Flinders University, Adelaide, South Australia, Australia
| | - Karen M Lower
- Department of Haematology and Genetic Pathology, Flinders University, Adelaide, South Australia, Australia
| | - Bryone J Kuss
- Department of Haematology and Genetic Pathology, Flinders University, Adelaide, South Australia, Australia
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23
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Stewart A, Banerji U. Utilizing the Luminex Magnetic Bead-Based Suspension Array for Rapid Multiplexed Phosphoprotein Quantification. Methods Mol Biol 2017; 1636:119-131. [PMID: 28730477 DOI: 10.1007/978-1-4939-7154-1_9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The study of protein phosphorylation is critical for the advancement of our understanding of cellular responses to external and internal stimuli. Phosphorylation, the addition of phosphate groups, most often occurs on serine, threonine, or tyrosine residues due to the action of protein kinases. This structural change causes the protein to become activated (or deactivated) and enables it in turn to initiate the phosphorylation of other proteins in a cascade, eventually causing cell-wide changes such as apoptosis, cell differentiation, and growth (among others). Cellular phosphoprotein pathway dysregulation by mutation or chromosomal instability can often give the cell a selective advantage and lead to cancer. Obviously the understanding of these systems is of huge importance to the field of oncology.This chapter aims to provide a "how to" manual for one such technology, the 96-well plate-based xMAP® platform from Luminex. The system utilizes antibody-bound free-floating magnetic spheres which can easily be removed from suspension via magnetization. There are 100 unique bead sets (moving up to 500 bead sets for the most recent system) identified by the ratio of two dyes coating the microsphere. Each bead set is conjugated to a specific antibody which allows targeted protein extraction from low-concentration lysate solution. Biotinylated secondary antibodies/streptavidin-R-phycoerythrin (SAPE) complexes provide the quantification mechanism for the phosphoprotein of interest.
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Affiliation(s)
- Adam Stewart
- The Institute of Cancer Research, London, UK
- The Royal Marsden, Sycamore House, Downs Road, Sutton, London, SM2 5PT, UK
| | - Udai Banerji
- The Institute of Cancer Research, London, UK.
- The Royal Marsden, Sycamore House, Downs Road, Sutton, London, SM2 5PT, UK.
- Drug Development Unit, Sycamore House, London, UK.
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24
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Chen Z, Kim J. Urinary proteomics and metabolomics studies to monitor bladder health and urological diseases. BMC Urol 2016; 16:11. [PMID: 27000794 PMCID: PMC4802825 DOI: 10.1186/s12894-016-0129-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 03/10/2016] [Indexed: 12/16/2022] Open
Abstract
Background Assays of molecular biomarkers in urine are non-invasive compared to other body fluids and can be easily repeated. Based on the hypothesis that the secreted markers from the diseased organs may locally release into the body fluid in the vicinity of the injury, urine-based assays have been considered beneficial to monitoring bladder health and urological diseases. The urine proteome is much less complex than the serum and tissues, but nevertheless can contain biomarkers for diagnosis and prognosis of diseases. The urine metabolome has a much higher number and concentration of low-molecular metabolites than the serum or tissues, with a far lower lipid concentration, yet informs directly about dietary and microbial metabolism. Discussion We here discuss the use of mass spectrometry-based proteomics and metabolomics for urine biomarker assays, specifically with respect to the underlying mechanisms that trigger the pathological condition. Conclusion Molecular biomarker profiles, based on proteomics and metabolomics studies, reliably distinguish patients from healthy controls, stratify sub-populations with respect to treatment options, and predict therapeutic response of patients with urological disease.
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Affiliation(s)
- Zhaohui Chen
- Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jayoung Kim
- Department of Surgery, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA, 90048, USA. .,Department of Biomedical Sciences, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA, 90048, USA. .,Department of Medicine, University of California, Los Angeles, CA, USA.
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25
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Loroch S, Schommartz T, Brune W, Zahedi RP, Sickmann A. Multidimensional electrostatic repulsion–hydrophilic interaction chromatography (ERLIC) for quantitative analysis of the proteome and phosphoproteome in clinical and biomedical research. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:460-8. [DOI: 10.1016/j.bbapap.2015.01.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 01/10/2015] [Accepted: 01/15/2015] [Indexed: 11/29/2022]
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26
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Cutillas PR. Role of phosphoproteomics in the development of personalized cancer therapies. Proteomics Clin Appl 2015; 9:383-95. [PMID: 25488289 DOI: 10.1002/prca.201400104] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 10/20/2014] [Accepted: 11/18/2014] [Indexed: 01/08/2023]
Abstract
Cell signalling pathways driven by protein and lipid kinases contribute to the onset and progression of virtually all cancer types. Consequently, several inhibitors against these enzymes have clinical utility for the treatment of different forms of cancer. A problem that hampers further development is that not all patients respond equally well to kinase inhibitors and a significant proportion of those that initially respond eventually develop resistance. This review considers how an integrative analysis of kinase signalling may be used to address this issue. Advances in the biophysics of mass spectrometry, in biochemical procedures for phosphopeptide enrichment, and in computational approaches for label-free quantification have contributed to the development of phosphoproteomics workflows compatible with the analysis of clinical material. These developments, together with new bioinformatics tools to derive information on signalling circuitry from phosphoproteomics data, allow investigating kinase networks with unprecedented depth. Phosphoproteomics technology is starting to be used in translational research and, with further developments, such methods may also be able to measure the circuitry of cancer signalling networks in routine clinical assays. This review reflects on how this information could be used to accurately predict the best kinase inhibitor for each individual cancer patient.
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Affiliation(s)
- Pedro R Cutillas
- Integrative Cell Signalling and Proteomics, Centre for Haemato-Oncology, John Vane Science Centre, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, UK
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27
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Abstract
Mass spectrometry (MS) is a complex analytical chemistry tool that allows qualitative and quantitative assessments of the components of complex chemical compounds. Applications of MS in medicine include the identification and quantification of drugs and metabolites; identification of proteins, biopolymers and disease markers and investigation of differential protein expression and proteins altered by mutations and/or post-translational changes. A variety of MS methods and technologies now play valuable and expanding roles in the diagnosis and monitoring of acute leukemia, as well as in identification of therapeutic targets and biomarkers, drug discovery, and other important areas of leukemia research. The objective of this review is to present a clinically oriented review of the roles of MS in the research, diagnosis and therapy of acute leukemia.
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Affiliation(s)
- John Roboz
- Department of Medicine, Division of Hematology/Oncology, Icahn School of Medicine of Mount Sinai, New York, NY, 10029, USA
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Searleman AC, Iliuk AB, Collier TS, Chodosh LA, Tao WA, Bose R. Tissue phosphoproteomics with PolyMAC identifies potential therapeutic targets in a transgenic mouse model of HER2 positive breast cancer. Electrophoresis 2014; 35:3463-9. [PMID: 24723360 DOI: 10.1002/elps.201400022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 03/06/2014] [Accepted: 03/24/2014] [Indexed: 12/26/2022]
Abstract
Altered protein phosphorylation is a feature of many human cancers that can be targeted therapeutically. Phosphopeptide enrichment is a critical step for maximizing the depth of phosphoproteome coverage by MS, but remains challenging for tissue specimens because of their high complexity. We describe the first analysis of a tissue phosphoproteome using polymer-based metal ion affinity capture (PolyMAC), a nanopolymer that has excellent yield and specificity for phosphopeptide enrichment, on a transgenic mouse model of HER2-driven breast cancer. By combining phosphotyrosine immunoprecipitation with PolyMAC, 411 unique peptides with 139 phosphotyrosine, 45 phosphoserine, and 29 phosphothreonine sites were identified from five LC-MS/MS runs. Combining reverse phase liquid chromatography fractionation at pH 8.0 with PolyMAC identified 1571 unique peptides with 1279 phosphoserine, 213 phosphothreonine, and 21 phosphotyrosine sites from eight LC-MS/MS runs. Linear motif analysis indicated that many of the phosphosites correspond to well-known phosphorylation motifs. Analysis of the tyrosine phosphoproteome with the Drug Gene Interaction database uncovered a network of potential therapeutic targets centered on Src family kinases with inhibitors that are either FDA-approved or in clinical development. These results demonstrate that PolyMAC is well suited for phosphoproteomic analysis of tissue specimens.
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Affiliation(s)
- Adam C Searleman
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
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