1
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Lin Y, Lubman DM. The role of N-glycosylation in cancer. Acta Pharm Sin B 2024; 14:1098-1110. [PMID: 38486989 PMCID: PMC10935144 DOI: 10.1016/j.apsb.2023.10.014] [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: 07/31/2022] [Revised: 09/26/2023] [Accepted: 10/07/2023] [Indexed: 03/17/2024] Open
Abstract
Despite advances in understanding the development and progression of cancer in recent years, there remains a lack of comprehensive characterization of the cancer glycoproteome. Glycoproteins play an important role in medicine and are involved in various human disease conditions including cancer. Glycan-moieties participate in fundamental cancer processes like cell signaling, invasion, angiogenesis, and metastasis. Aberrant N-glycosylation significantly impacts cancer processes and targeted therapies in clinic. Therefore, understanding N-glycosylation in a tumor is essential for comprehending disease progression and discovering anti-cancer targets and biomarkers for therapy monitoring and diagnosis. This review presents the fundamental process of protein N-glycosylation and summarizes glycosylation changes in tumor cells, including increased terminal sialylation, N-glycan branching, and core-fucosylation. Also, the role of N-glycosylation in tumor signaling pathways, migration, and metabolism are discussed. Glycoproteins and glycopeptides as potential biomarkers for early detection of cancer based on site specificity have been introduced. Collectively, understanding and exploring the cancer glycoproteome, along with its role in medicine, implication in cancer and other human diseases, highlights the significance of N-glycosylation in tumor processes, necessitating further research for potential anti-cancer targets and biomarkers.
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Affiliation(s)
- Yu Lin
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI 48109, USA
| | - David M. Lubman
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI 48109, USA
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2
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An overview of kinin mediated events in cancer progression and therapeutic applications. Biochim Biophys Acta Rev Cancer 2022; 1877:188807. [PMID: 36167271 DOI: 10.1016/j.bbcan.2022.188807] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/12/2022] [Accepted: 09/21/2022] [Indexed: 11/22/2022]
Abstract
Kinins are bioactive peptides generated in the inflammatory milieu of the tissue microenvironment, which is involved in cancer progression and inflammatory response. Kinins signals through activation of two G-protein coupled receptors; inducible Bradykinin Receptor B1 (B1R) and constitutive receptor B2 (B2R). Activation of kinin receptors and its cross-talk with receptor tyrosine kinases activates multiple signaling pathways, including ERK/MAPK, PI3K, PKC, and p38 pathways regulating cancer hallmarks. Perturbations of the kinin-mediated events are implicated in various aspects of cancer invasion, matrix remodeling, and metastasis. In the tumor microenvironment, kinins initiate fibroblast activation, mesenchymal stem cell interactions, and recruitment of immune cells. Albeit the precise nature of kinin function in the metastasis and tumor microenvironment are not completely clear yet, several kinin receptor antagonists show anti-metastatic potential. Here, we showcase an overview of the complex biology of kinins and their role in cancer pathogenesis and therapeutic aspects.
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3
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Circulating levels of hydroxylated bradykinin function as an indicator of tissue HIF-1α expression. Sci Bull (Beijing) 2020; 65:1570-1579. [PMID: 36738075 DOI: 10.1016/j.scib.2020.04.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/27/2020] [Accepted: 04/14/2020] [Indexed: 02/07/2023]
Abstract
The critical roles of oxygen homeostasis in metabolism are indisputable and hypoxic responses are correlated with the pathogenesis of gastrointestinal, pulmonary, renal diseases and cancers. Evaluating tissue hypoxia to predict treatment outcome is challenging, however, due to the lack of rapid, accurate and non-invasive methods. Hypoxia enhances prolyl-4-hydroxylase α1 (P4HA1) expression, which can convert bradykinin (BK) to hydroxyprolyl-BK (Hyp-BK), leading us to hypothesize that circulating Hyp-BK/BK ratios may reflect tissue hypoxia and predict treatment outcomes. Direct quantification of Hyp-BK peptides in serum or plasma by conventional MALDI-TOF MS analysis is technically challenging. In our study, a nanopore-based fractionation and enrichment protocol was utilized to allow the simple workflow for circulating Hyp-BK/BK analysis. Hypoxia is linked to poor prognosis due to its role in promoting pancreatic cancer progression and metastasis. Here we show that P4HA1 expression was increased in pancreatic tumors versus adjacent tissue, associated with poor survival, and corresponded with tumor expression of the hypoxia inducible factor 1α (HIF-1α) and carbonic anhydrase 9 (CA9). Hypoxia-induced P4HA1 expression and BK conversion to Hyp-BK were found to be HIF-1α dependent, pre-treatment serum Hyp-BK/BK ratios corresponded with tissue HIF-1α and P4HA1 expression, and high Hyp-BK/BK levels corresponded with poor response to therapy. These results suggest that pre-treatment circulating Hyp-BK/BK ratios may have value as a non-invasive, surrogate indicator of tissue hypoxia and tumor responses to therapy.
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Li N, Zhou Y, Wang J, Niu L, Zhang Q, Sun L, Ding X, Guo X, Xie Z, Zhu N, Zhang M, Chen X, Cai T, Yang F. Sequential Precipitation and Delipidation Enables Efficient Enrichment of Low-Molecular Weight Proteins and Peptides from Human Plasma. J Proteome Res 2020; 19:3340-3351. [DOI: 10.1021/acs.jproteome.0c00232] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Na Li
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yue Zhou
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Thermo Fisher Scientific, Shanghai 200000, China
| | - Jifeng Wang
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Lili Niu
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qing Zhang
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lang Sun
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiang Ding
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaojing Guo
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhensheng Xie
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Nali Zhu
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Mengmeng Zhang
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiulan Chen
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tanxi Cai
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fuquan Yang
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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5
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Greening DW, Kapp EA, Simpson RJ. The Peptidome Comes of Age: Mass Spectrometry-Based Characterization of the Circulating Cancer Peptidome. Enzymes 2017; 42:27-64. [PMID: 29054270 DOI: 10.1016/bs.enz.2017.08.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Peptides play a seminal role in most physiological processes acting as neurotransmitters, hormones, antibiotics, and immune regulation. In the context of tumor biology, it is hypothesized that endogenous peptides, hormones, cytokines, growth factors, and aberrant degradation of select protein networks (e.g., enzymatic activities, protein shedding, and extracellular matrix remodeling) are fundamental in mediating cancer progression. Analysis of peptides in biological fluids by mass spectrometry holds promise of providing sensitive and specific diagnostic and prognostic information for cancer and other diseases. The identification of circulating peptides in the context of disease constitutes a hitherto source of new clinical biomarkers. The field of peptidomics can be defined as the identification and comprehensive analysis of physiological and pathological peptides. Like proteomics, peptidomics has been advanced by the development of new separation strategies, analytical detection methods such as mass spectrometry, and bioinformatic technologies. Unlike proteomics, peptidomics is targeted toward identifying endogenous protein and peptide fragments, defining proteolytic enzyme substrate specificity, as well as protease cleavage recognition (degradome). Peptidomics employs "top-down proteomics" strategies where mass spectrometry is applied at the proteoform level to analyze intact proteins and large endogenous peptide fragments. With recent advances in prefractionation workflows for separating peptides, mass spectrometry instrumentation, and informatics, peptidomics is an important field that promises to impact on translational medicine. This review covers the current advances in peptidomics, including top-down and imaging mass spectrometry, comprehensive quantitative peptidome analyses (developments in reproducibility and coverage), peptide prefractionation and enrichment workflows, peptidomic data analyses, and informatic tools. The application of peptidomics in cancer biomarker discovery will be discussed.
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Affiliation(s)
- David W Greening
- La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria, Australia.
| | - Eugene A Kapp
- Systems Biology & Personalised Medicine Division, Walter & Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Florey Institute of Neuroscience, Parkville, Victoria, Australia; University of Melbourne, Parkville, Victoria, Australia
| | - Richard J Simpson
- La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria, Australia.
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Fan J, Ning B, Lyon CJ, Hu TY. Circulating Peptidome and Tumor-Resident Proteolysis. PEPTIDOMICS OF CANCER-DERIVED ENZYME PRODUCTS 2017; 42:1-25. [DOI: 10.1016/bs.enz.2017.08.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Fan J, Tea MKM, Yang C, Ma L, Meng QH, Hu TY, Singer CF, Ferrari M. Profiling of Cross-Functional Peptidases Regulated Circulating Peptides in BRCA1 Mutant Breast Cancer. J Proteome Res 2016; 15:1534-45. [PMID: 27058005 PMCID: PMC5124559 DOI: 10.1021/acs.jproteome.6b00010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Women with inherited BRCA1 mutations are more likely to develop breast cancer (BC); however, not every carrier will progress to BC. The aim of this study was to identify and characterize circulating peptides that correlate with BC patients carrying BRCA1 mutations. Circulating peptides were enriched using our well-designed nanoporous silica thin films (NanoTraps) and profiled by mass spectrometry to identify among four clinical groups. To determine the corresponding proteolytic processes and their sites of activity, purified candidate peptidases and synthesized substrates were assayed to verify the processes predicted by the MERPOS database. Proteolytic processes were validated using patient serum samples. The peptides, KNG1K438-R457 and C 3fS1304-R1320, were identified as putative peptide candidates to differentiate BRCA1 mutant BC from sporadic BC and cancer-free BRCA1 mutant carriers. Kallikrein-2 (KLK2) is the major peptidase that cleaves KNG1K438-R457 from kininogen-1, and its expressions and activities were also found to be dependent on BRCA1 status. We further determined that KNG1K438-R457 is cleaved at its C-terminal arginine by carboxypeptidase N1 (CPN1). Increased KLK2 activity, with decreased CPN1 activity, results in the accumulation of KNG1K438-R457 in BRCA1-associated BC. Our work outlined a useful strategy for determining the peptide-petidase relationship and thus establishing a biological mechanism for changes in the peptidome in BRCA1-associated BC.
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Affiliation(s)
- Jia Fan
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, Texas 77030, United States
| | - Muy-Kheng M. Tea
- Department of Obstetrics and Gynecology and Comprehensive Cancer Center, Division of Senology, Medical University of Vienna, Vienna 1090, Austria
| | - Chuan Yang
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, Texas 77030, United States
| | - Li Ma
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Qing H. Meng
- Department of Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Tony Y. Hu
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, Texas 77030, United States
- Department of Cell and Developmental Biology, Weill Cornell Medical College of Cornell University, New York, New York 10021, United States
| | - Christian F. Singer
- Department of Obstetrics and Gynecology and Comprehensive Cancer Center, Division of Senology, Medical University of Vienna, Vienna 1090, Austria
| | - Mauro Ferrari
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, Texas 77030, United States
- Department of Internal Medicine, Weill Cornell Medical College of Cornell University, New York, New York 10021, United States
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8
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Du YM, Hu Y, Xia Y, Ouyang Z. Power Normalization for Mass Spectrometry Data Analysis and Analytical Method Assessment. Anal Chem 2016; 88:3156-63. [PMID: 26882462 PMCID: PMC8135100 DOI: 10.1021/acs.analchem.5b04418] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Biomarker profiling using mass spectrometry plays an essential role in biological studies and is highly dependent on the data analysis for sample classification. In this study, we introduced power nomination of the mass spectra as a method for systematically altering the weights of peaks at different intensity levels. In combination with the use of support vector machine method (SVM), the impact on the sample classification has been characterized using data in four studies previously reported, including the distinctions of anomeric configurations of sugars, types of bacteria, stages of melanoma, and the types of breast cancer. Comprehensive analysis of the data with normalization at different power normalization index (PNI) was developed and analysis tools, including error-PNI plots, reference profiles, and error source profiles, were used to assess the potential of the analytical methods as well as to find the proper approaches to classify the samples.
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Affiliation(s)
- Y. Melodie Du
- Weldon School of Biomedical Engineering, Purdue University, 206 South Martin Jischke Drive, West Lafayette, Indiana 47907, United States
| | - Ye Hu
- Department of Nanomedicine, Houston Methodist Research Institute, 6565 Fannin Street, Houston, Texas 77030, United States
| | - Yu Xia
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Zheng Ouyang
- Weldon School of Biomedical Engineering, Purdue University, 206 South Martin Jischke Drive, West Lafayette, Indiana 47907, United States
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
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9
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Bergman N, Bergquist J. Recent developments in proteomic methods and disease biomarkers. Analyst 2015; 139:3836-51. [PMID: 24975697 DOI: 10.1039/c4an00627e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Proteomic methodologies for identification and analysis of biomarkers have gained more attention during recent years and have evolved rapidly. Identification and detection of disease biomarkers are important to foresee outbreaks of certain diseases thereby avoiding surgery and other invasive and expensive medical treatments for patients. Thus, more research into discovering new biomarkers and new methods for faster and more accurate detection is needed. It is often difficult to detect and measure biomarkers because of their low concentrations and the complexity of their respective matrices. Therefore it is hard to find and validate methods for accurate screening methods suitable for clinical use. The most recent developments during the last three years and also some historical considerations of proteomic methodologies for identification and validation of disease biomarkers are presented in this review.
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Affiliation(s)
- Nina Bergman
- Analytical Chemistry, BMC, Department of Chemistry, Uppsala University, Sweden.
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10
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Yang X, Du T, Wang X, Zhang Y, Hu W, Du X, Miao L, Han C. IDH1, a CHOP and C/EBPβ-responsive gene under ER stress, sensitizes human melanoma cells to hypoxia-induced apoptosis. Cancer Lett 2015; 365:201-10. [PMID: 26049021 DOI: 10.1016/j.canlet.2015.05.027] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 05/22/2015] [Accepted: 05/29/2015] [Indexed: 01/07/2023]
Abstract
Isocitrate dehydrogenase1 (IDH1) is of great importance in cell metabolism and energy conversion. However, alterations in IDH1 in response to stress and excise-regulated mechanisms are not well described. Here we investigated gene expression profiles under ER stress in melanoma cells and found that IDH1 was dramatically increased with ER stress induced by tunicamycin. Elevated IDH1 subsequently sensitized human melanoma cells to hypoxia-induced apoptosis and promoted HIF-1α degradation. In addition, we revealed that CHOP and C/EBPβ were involved in hypoxia-induced apoptosis via transcriptional regulation of IDH1 expression. Our data indicate that IDH1, regulated by CHOP and C/EBPβ in response to ER stress treatment, inhibits survival of melanoma cells under hypoxia and promotes HIF-1α degradation. Therefore, we propose that IDH1 may serve as a valuable target for melanoma therapy.
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Affiliation(s)
- Xuejun Yang
- Institute of Cancer Stem Cell, Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Tongde Du
- Institute of Cancer Stem Cell, Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Xiang Wang
- Institute of Cancer Stem Cell, Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Yingqiu Zhang
- Institute of Cancer Stem Cell, Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Wanglai Hu
- Department of Immunology, Anhui Medical University, Hefei, Anhui 230601, China
| | - Xiaofeng Du
- Institute of Cancer Stem Cell, Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Lin Miao
- Oncology Department, The Second Hospital of Anhui Medical University, Hefei, Anhui 230601, China.
| | - Chuanchun Han
- Institute of Cancer Stem Cell, Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China.
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11
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Deng Z, Li Y, Fan J, Wang G, Li Y, Zhang Y, Cai G, Shen H, Ferrari M, Hu TY. Circulating peptidome to indicate the tumor-resident proteolysis. Sci Rep 2015; 5:9327. [PMID: 25788424 PMCID: PMC4365414 DOI: 10.1038/srep09327] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 02/05/2015] [Indexed: 01/02/2023] Open
Abstract
Tumor-resident proteases (TRPs) are regarded as informative biomarkers for staging cancer progression and evaluating therapeutic efficacy. Currently in the clinic, measurement of TRP is dependent on invasive biopsies, limiting their usefulness as monitoring tools. Here we identified circulating peptides naturally produced by TRPs, and evaluated their potential to monitor the efficacy of anti-tumor treatments. We established a mouse model for ovarian cancer development and treatment by orthotopic implantation of the human drug-resistant ovarian cancer cell line HeyA8-MDR, followed by porous silicon particle- or multistage vector (MSV) - enabled EphA2 siRNA therapy. Immunohistochemistry staining of tumor tissue revealed decreased expression of matrix metallopeptidase 9 (MMP-9) in mice exhibiting positive responses to MSV-EphA2 siRNA treatment. We demonstrated, via an ex vivo proteolysis assay, that C3f peptides can act as substrates of MMP-9, which cleaves C3f at L1311-L1312 into two peptides (SSATTFRL and LWENGNLLR). Importantly, we showed that these two C3f-derived fragments detected in serum were primarily generated by tumor-resident, but not blood-circulating, MMP-9. Our results suggested that the presence of the circulating fragments specially derived from the localized cleavage in tumor microenvironment can be used to evaluate therapeutic efficacy of anti-cancer treatment, assessed through a relatively noninvasive and user-friendly proteomics approach.
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Affiliation(s)
- Zaian Deng
- 1] School of Life Science, Tsinghua University, Beijing 100084, China [2] Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Avenue R8-213, Houston, TX 77030, United States [3] Life Science Division, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
| | - Yaojun Li
- Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Avenue R8-213, Houston, TX 77030, United States
| | - Jia Fan
- Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Avenue R8-213, Houston, TX 77030, United States
| | - Guohui Wang
- Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Avenue R8-213, Houston, TX 77030, United States
| | - Yan Li
- Institute of Biophysics, Chinese Academy Of Sciences, 15 Datum Road, Chaoyang District, Beijing 100101, China
| | - Yaou Zhang
- 1] School of Life Science, Tsinghua University, Beijing 100084, China [2] Life Science Division, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
| | - Guoping Cai
- 1] School of Life Science, Tsinghua University, Beijing 100084, China [2] Life Science Division, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
| | - Haifa Shen
- 1] Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Avenue R8-213, Houston, TX 77030, United States [2] Department of Cell and Developmental Biology, Weill Cornell Medical College of Cornell University, 445 E. 69th Street, New York, New York 10021, United States
| | - Mauro Ferrari
- 1] Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Avenue R8-213, Houston, TX 77030, United States [2] Department of Internal Medicine, Weill Cornell Medical College of Cornell University, 445 E. 69th Street, New York, New York 10021, United States
| | - Tony Y Hu
- 1] Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Avenue R8-213, Houston, TX 77030, United States [2] Department of Cell and Developmental Biology, Weill Cornell Medical College of Cornell University, 445 E. 69th Street, New York, New York 10021, United States
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Zhao H, Li Y, Hu Y. Nanotechnologies in glycoproteomics. Clin Proteomics 2014; 11:21. [PMID: 24940182 PMCID: PMC4040410 DOI: 10.1186/1559-0275-11-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 03/17/2014] [Indexed: 12/25/2022] Open
Abstract
Protein glycosylation, as an important post-translational modification, is implicated in a number of ailments. Applying proteomic approaches, including mass spectrometry (MS) analyses that have played a significant role in biomarker detection and early diagnosis of diseases, to the study of glycoproteins or glycopeptides will facilitate a deeper understanding of many physiological functions and biological pathways involved in cancer, inflammatory and degenerative diseases. The abundance of glycopeptides and their ionization potential are relatively lower compared to those of non-glycopeptides; therefore, sample enrichment is necessary for glycopeptides prior to MS analysis. The application of nanotechnology in the past decade has been rapidly penetrating into many diverse scientific research disciplines. Particularly in what we now refer to as the “glycoproteomics area”, nanotechnologies have enabled enhanced sensitivity and specificity of glycopeptide detection in complex biological fluids, which are critical for disease diagnosis and monitoring. In this review, we highlight some recent studies that combine the capabilities of specific nanotechnologies with the comprehensive features of glycoproteomics. In particular, we focus on the ways in which nanotechnology has facilitated the detection of glycopeptides in complex biological samples and enhanced their characterization by MS, in terms of intensity and resolution. These studies reveal an increasingly important role for nanotechnology in helping to overcome certain technical challenges in biomarker discovery, in general, and glycoproteomics research, in particular.
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Affiliation(s)
- Hu Zhao
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Yaojun Li
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Ye Hu
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA ; Department of Cell and Developmental Biology, Weill Cornell Medical College, New York City, NY 10021, USA
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13
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Wu HJ, Li Y, Fan J, Deng Z, Hu Z, Liu X, Graviss EA, Ferrari M, Ma X, Hu Y. Antibody-free detection of Mycobacterium tuberculosis antigen using customized nanotraps. Anal Chem 2014; 86:1988-96. [PMID: 24446580 PMCID: PMC3983014 DOI: 10.1021/ac4027669] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Rapid
screening and diagnosis of tuberculosis disease (TB) is still
challenging and critically needed for global TB control efforts. In
this study, we present a rapid and streamlined technology, using precisely
engineered silica nanopore thin films, which are optimized for pore
size, structure, capillary force, and film thickness, to isolate Mycobacterium tuberculosis (MTB) antigens in laboratory
and clinical samples for rapid TB screening. This technology, referred
to here as on-chip fractionation, is integrated with high-throughput
matrix-assisted laser desorption/ionization time-of flight mass spectrometry
to screen and identify fragments of the MTB antigen, CFP-10, from
complex biological samples, without use of immunoaffinity agents.
With the use of this comprehensive approach, we were able to clearly
distinguish a clinical isolate of MTB from a nonTB species of the
genus Mycobacterium avium grown in
liquid culture media. This assay can reach a detection limit of 10
fmol and an isolation rate of 90% for the antigen CFP-10. Our strategy
has significant potential to fill the conceptual and technical gaps
in rapid diagnosis of active TB disease.
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Affiliation(s)
- Hung-Jen Wu
- Department of Nanomedicine, Houston Methodist Research Institute , 6670 Bertner Avenue R8-213, Houston, TX 77030, United States
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Kobeissy FH, Gulbakan B, Alawieh A, Karam P, Zhang Z, Guingab-Cagmat JD, Mondello S, Tan W, Anagli J, Wang K. Post-genomics nanotechnology is gaining momentum: nanoproteomics and applications in life sciences. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:111-31. [PMID: 24410486 DOI: 10.1089/omi.2013.0074] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The post-genomics era has brought about new Omics biotechnologies, such as proteomics and metabolomics, as well as their novel applications to personal genomics and the quantified self. These advances are now also catalyzing other and newer post-genomics innovations, leading to convergences between Omics and nanotechnology. In this work, we systematically contextualize and exemplify an emerging strand of post-genomics life sciences, namely, nanoproteomics and its applications in health and integrative biological systems. Nanotechnology has been utilized as a complementary component to revolutionize proteomics through different kinds of nanotechnology applications, including nanoporous structures, functionalized nanoparticles, quantum dots, and polymeric nanostructures. Those applications, though still in their infancy, have led to several highly sensitive diagnostics and new methods of drug delivery and targeted therapy for clinical use. The present article differs from previous analyses of nanoproteomics in that it offers an in-depth and comparative evaluation of the attendant biotechnology portfolio and their applications as seen through the lens of post-genomics life sciences and biomedicine. These include: (1) immunosensors for inflammatory, pathogenic, and autoimmune markers for infectious and autoimmune diseases, (2) amplified immunoassays for detection of cancer biomarkers, and (3) methods for targeted therapy and automatically adjusted drug delivery such as in experimental stroke and brain injury studies. As nanoproteomics becomes available both to the clinician at the bedside and the citizens who are increasingly interested in access to novel post-genomics diagnostics through initiatives such as the quantified self, we anticipate further breakthroughs in personalized and targeted medicine.
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Affiliation(s)
- Firas H Kobeissy
- 1 Center for Neuroproteomics and Biomarkers Research, Department of Psychiatry, McKnight Brain Institute, University of Florida , Gainesville, Florida
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Cheng G, Wang Y, Wang ZG, Sui XJ, Zhang JL, Ni JZ. Magnetic mesoporous silica incorporated with TiO2for selective and rapid capture of peptides. RSC Adv 2014. [DOI: 10.1039/c3ra46887a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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16
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Li Y, Li Y, Chen T, Kuklina AS, Bernard P, Esteva FJ, Shen H, Ferrari M, Hu Y. Circulating proteolytic products of carboxypeptidase N for early detection of breast cancer. Clin Chem 2013; 60:233-42. [PMID: 24146311 DOI: 10.1373/clinchem.2013.211953] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Carboxypeptidase N (CPN) is important in regulating vasoactive peptide hormones, growth factors, and cytokines by specifically cleaving their C-terminal basic residues. We investigated whether circulating peptides specifically cleaved by CPN in the tumor microenvironment can be stage-specific indicators of breast cancer. METHODS CPN activity was measured using an ex vivo peptide cleavage assay by incubating synthesized C3f peptide (His6-C3f_S1304-R1320-His6) in interstitial fluids of breast tumors and adjacent normal breast tissues in mice with orthotopic implantation of the human cell line MDA-MB-231. The nature and extent of peptide cleavage by CPN was investigated by fragment profiling using nanopore fractionation and mass spectrometry. The fragment profiles in interstitial fluid correlated with concentrations of CPN-catalyzed peptides in blood samples taken from the tumor-bearing mice, healthy women, and breast cancer patients. CPN expression in the same set of samples was further examined by immunohistochemistry and immunoblotting. RESULTS We showed that generation of C3f_R1310-L1319 specifically correlated with the CPN expression level. In both the mouse and clinical patient samples, CPN was clearly increased in tumor tissues compared with normal breast tissue, whereas corresponding CPN abundance in blood remained constant. Concentrations of 6 CPN-catalyzed peptides predominantly increased in sera taken from the mice (n = 8) at 2 weeks after orthotopic implantation. Six homologous peptides displayed significantly higher expression in the patients' plasma as early as the first pathologic stage of breast cancer. CONCLUSIONS Circulating CPN-catalyzed peptide concentrations reflect the CPN activity in tumors. These biomarkers show strong potential for the noninvasive and early diagnosis of breast cancer.
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Affiliation(s)
- Yaojun Li
- Department of Nanomedicine, The Methodist Hospital Research Institute, Houston, TX
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