51
|
Lu H, Zhang Y, Yang P. Advancements in mass spectrometry-based glycoproteomics and glycomics. Natl Sci Rev 2016. [DOI: 10.1093/nsr/nww019] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Abstract
Protein N-glycosylation plays a crucial role in a considerable number of important biological processes. Research studies on glycoproteomes and glycomes have already characterized many glycoproteins and glycans associated with cell development, life cycle, and disease progression. Mass spectrometry (MS) is the most powerful tool for identifying biomolecules including glycoproteins and glycans, however, utilizing MS-based approaches to identify glycoproteomes and glycomes is challenging due to the technical difficulties associated with glycosylation analysis. In this review, we summarize the most recent developments in MS-based glycoproteomics and glycomics, including a discussion on the development of analytical methodologies and strategies used to explore the glycoproteome and glycome, as well as noteworthy biological discoveries made in glycoproteome and glycome research. This review places special emphasis on China, where scientists have made sizeable contributions to the literature, as advancements in glycoproteomics and glycomincs are occurring quite rapidly.
Collapse
Affiliation(s)
- Haojie Lu
- Department of Systems Biology for Medicine, School of Basic Medicine and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
- Key Lab of Glycoconjugate of Ministry of Health and Birth Control, Fudan University, Shanghai 200032, China
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Ying Zhang
- Department of Systems Biology for Medicine, School of Basic Medicine and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
- Key Lab of Glycoconjugate of Ministry of Health and Birth Control, Fudan University, Shanghai 200032, China
| | - Pengyuan Yang
- Department of Systems Biology for Medicine, School of Basic Medicine and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
- Key Lab of Glycoconjugate of Ministry of Health and Birth Control, Fudan University, Shanghai 200032, China
- Department of Chemistry, Fudan University, Shanghai 200433, China
| |
Collapse
|
52
|
Ruhaak LR, Kim K, Stroble C, Taylor SL, Hong Q, Miyamoto S, Lebrilla CB, Leiserowitz G. Protein-Specific Differential Glycosylation of Immunoglobulins in Serum of Ovarian Cancer Patients. J Proteome Res 2016; 15:1002-10. [PMID: 26813784 DOI: 10.1021/acs.jproteome.5b01071] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Previous studies indicated that glycans in serum may serve as biomarkers for diagnosis of ovarian cancer; however, it was unclear to which proteins these glycans belong. We hypothesize that protein-specific glycosylation profiles of the glycans may be more informative of ovarian cancer and can provide insight into biological mechanisms underlying glycan aberration in serum of diseased individuals. Serum samples from women diagnosed with epithelial ovarian cancer (EOC, n = 84) and matched healthy controls (n = 84) were obtained from the Gynecologic Oncology Group. Immunoglobulin (IgG, IgA, and IgM) concentrations and glycosylation profiles were quantified using multiple reaction monitoring mass spectrometry. Differential and classification analyses were performed to identify aberrant protein-specific glycopeptides using a training set. All findings were validated in an independent test set. Multiple glycopeptides from immunoglubins IgA, IgG, and IgM were found to be differentially expressed in serum of EOC patients compared with controls. The protein-specific glycosylation profiles showed their potential in the diagnosis of EOC. In particular, IgG-specific glycosylation profiles are the most powerful in discriminating between EOC case and controls. Additional studies of protein- and site-specific glycosylation profiles of immunoglobulins and other proteins will allow further elaboration on the characteristics of biological functionality and causality of the differential glycosylation in ovarian cancer and thus ultimately lead to increased sensitivity and specificity of diagnosis.
Collapse
Affiliation(s)
- L Renee Ruhaak
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Kyoungmi Kim
- Division of Biostatistics, Department of Public Health Sciences, University of California , Davis, California 95616, United States
| | - Carol Stroble
- Department of Chemistry, University of California , Davis, California 95616, United States.,University of California Davis Medical Center , Sacramento, California 95817, United States
| | - Sandra L Taylor
- Division of Biostatistics, Department of Public Health Sciences, University of California , Davis, California 95616, United States
| | - Qiuting Hong
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Suzanne Miyamoto
- University of California Davis Medical Center , Sacramento, California 95817, United States
| | - Carlito B Lebrilla
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Gary Leiserowitz
- University of California Davis Medical Center , Sacramento, California 95817, United States.,Division of Gynecologic Oncology, University of California Davis Medical Center , Sacramento, California 98517, United States
| |
Collapse
|
53
|
Ruhaak LR, Stroble C, Dai J, Barnett M, Taguchi A, Goodman GE, Miyamoto S, Gandara D, Feng Z, Lebrilla CB, Hanash S. Serum Glycans as Risk Markers for Non-Small Cell Lung Cancer. Cancer Prev Res (Phila) 2016; 9:317-23. [PMID: 26813970 DOI: 10.1158/1940-6207.capr-15-0033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 01/18/2016] [Indexed: 11/16/2022]
Abstract
Previous studies have suggested occurrence of altered serum glycan profiles in patients with lung cancer. Here, we aimed to determine the predictive value of serum glycans to distinguish non-small cell lung cancer (NSCLC) cases from controls in prediagnostic samples using a previously validated predictive protein marker pro-SFTPB, as anchor. Blinded prediagnostic serum samples were obtained from the Carotene and Retinol Efficacy Trial (CARET), and included a discovery set of 100 NSCLC cases and 199 healthy controls. A second test set consisted of 108 cases and 216 controls. Cases and controls were matched for age at baseline (5-year groups), sex, smoking status (current vs. former), study enrollment cohort, and date of blood draw. Serum glycan profiles were determined by mass spectrometry. Twelve glycan variables were identified to have significant discriminatory power between cases and controls in the discovery set (AUC > 0.6). Of these, four were confirmed in the independent validation set. A combination marker yielded AUCs of 0.74 and 0.64 in the discovery and test set, respectively. Four glycan variables exhibited significant incremental value when combined with pro-SFTPB compared with pro-SFTPB alone with AUCs of 0.73, 0.72, 0.72, and 0.72 in the test set, indicating that serum glycan signatures have relevance to risk assessment for NSCLC.
Collapse
Affiliation(s)
- L Renee Ruhaak
- Department of Chemistry, University of California Davis, Davis, California. Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Carol Stroble
- Department of Chemistry, University of California Davis, Davis, California. Division of Hematology and Oncology, University of California Davis Comprehensive Cancer Center, Sacramento, California
| | - Jianliang Dai
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Matt Barnett
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington
| | - Ayumu Taguchi
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gary E Goodman
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, Washington
| | - Suzanne Miyamoto
- Division of Hematology and Oncology, University of California Davis Comprehensive Cancer Center, Sacramento, California
| | - David Gandara
- Division of Hematology and Oncology, University of California Davis Comprehensive Cancer Center, Sacramento, California
| | - Ziding Feng
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Carlito B Lebrilla
- Department of Chemistry, University of California Davis, Davis, California
| | - Samir Hanash
- Department of Clinical Cancer Prevention - Research, Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, Texas
| |
Collapse
|
54
|
Cao L, Zhang Y, Chen L, Shen A, Zhang X, Ren S, Gu J, Yu L, Liang X. Sample preparation for mass spectrometric analysis of human serum N-glycans using hydrophilic interaction chromatography-based solid phase extraction. Analyst 2015; 139:4538-46. [PMID: 25068150 DOI: 10.1039/c4an00660g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Expression levels of N-linked glycans derived from human serum glycoproteins have been shown to change during the progression of many diseases. Generally, N-glycans released from human serum proteins co-exist with endogenous serum peptides, salts, and other contaminants. Effective removal of these contaminants is essential to obtain the glycan profile of human serum proteins. Here, we developed a sample preparation method for mass spectrometry (MS) analysis of N-linked glycans derived from human serum glycoproteins based on a zwitterionic hydrophilic material named Click TE-Cys. The high hydrophilicity of Click TE-Cys, resulting from its unique surface structure and charge distribution, facilitated removal of co-existing salts and endogenous serum peptides. Furthermore, the present enrichment approach was handled in parallel, thus saving time. Using this method, a total of 47 unique N-glycans released from human serum proteins were identified. The intrabatch and interbatch coefficients of variation for the 47 N-linked glycans were 8.57% ± 0.96% and 9.22% ± 1.03%, respectively. These results demonstrate that the present method is suitable for fast purification of N-linked glycans derived from human serum glycoproteins, and has potential for clinical application.
Collapse
Affiliation(s)
- Liwei Cao
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | | | | | | | | | | | | | | | | |
Collapse
|
55
|
Lindheim SR, Gagneux P. A sweet view of reproduction. Fertil Steril 2015; 104:533. [PMID: 26149356 DOI: 10.1016/j.fertnstert.2015.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 06/05/2015] [Indexed: 10/23/2022]
Affiliation(s)
- Steven R Lindheim
- Department of Obstetrics and Gynecology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio
| | - Pascal Gagneux
- Division of Comparative Pathology and Medicine, Department of Pathology, University of California, San Diego, California
| |
Collapse
|
56
|
Yi CH, Weng HL, Zhou FG, Fang M, Ji J, Cheng C, Wang H, Liebe R, Dooley S, Gao CF. Elevated core-fucosylated IgG is a new marker for hepatitis B virus-related hepatocellular carcinoma. Oncoimmunology 2015; 4:e1011503. [PMID: 26587313 DOI: 10.1080/2162402x.2015.1011503] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 01/18/2015] [Accepted: 01/21/2015] [Indexed: 01/11/2023] Open
Abstract
Immunoglubulin G (IgG) and its abnormal glycosylations are associated with carcinogenesis. The present study investigates the relationship between cancer-derived IgG and clinicopathological characteristics in hepatocellular carcinoma (HCC) and assesses the value of serum N-glycosylated IgG in diagnosing and monitoring hepatitis B virus (HBV)-related HCC. Tissue microarray analysis of 90 HCC tissues showed that HCC patients with IgG immunopositivity had higher levels of core-fucosylated α fetoprotein (AFP-L3), larger tumors, and a higher incidence of portal vein tumor thrombus. HCC-derived IgG stimulated the growth of liver cancer cells in vitro. HCC patients presented a significantly increased fraction of Lens culinaris agglutinin binding IgG (core-fucosylated IgG, IgG-L3) among total serum IgG. The clinical diagnostic performance of serum IgG-L3% was evaluated in 3 case-control studies (1 training set and 2 validation cohorts), including 293 patients with HCC, 131 with liver cirrhosis, 132 HBV carriers, and 151 healthy controls. IgG-L3% had better general diagnostic performance than AFP in the training set and validation cohort 1 (accuracy: 81.33-85.11% versus 63.33-78.61%). In validation cohort 2, where we aimed to assess the efficiency of IgG-L3% in patients with AFP-negative HCC, the diagnostic accuracy of IgG-L3% was 72.54-73.60%. Finally, a longitudinal evaluation based on 31 HCC patients demonstrated that IgG-L3% decreased in 24 patients after curative surgery. The remaining 7 patients showed elevated IgG-L3% and post-operative recurrence. HCC patients with higher IgG-L3% had poor survival during a 3-year follow up. We conclude that HCC-derived IgG is correlated with progressive behavior of HCC. Therefore, elevated core-fucosylated IgG is a new diagnostic and prognostic marker in HBV-related HCC.
Collapse
Affiliation(s)
- Chang-Hong Yi
- Department of Laboratory Medicine; Eastern Hepatobiliary Surgery Hospital; Second Military Medical University ; Shanghai, China
| | - Hong-Lei Weng
- Molecular Alcohol Research in Gastroenterology, Department of Medicine II; Germany Faculty of Medicine at Mannheim; University of Heidelberg , Heidelberg, Germany
| | - Fei-Guo Zhou
- Department of Hepatic Surgery VI; Eastern Hepatobiliary Surgery Hospital; Second Military Medical University ; Shanghai, China
| | - Meng Fang
- Department of Laboratory Medicine; Eastern Hepatobiliary Surgery Hospital; Second Military Medical University ; Shanghai, China
| | - Jun Ji
- Department of Laboratory Medicine; Eastern Hepatobiliary Surgery Hospital; Second Military Medical University ; Shanghai, China
| | - Cheng Cheng
- Department of Laboratory Medicine; Eastern Hepatobiliary Surgery Hospital; Second Military Medical University ; Shanghai, China
| | - Hao Wang
- Department of Laboratory Medicine; Changzheng Hospital; Second Military Medical University ; Shanghai, China
| | - Roman Liebe
- Molecular Alcohol Research in Gastroenterology, Department of Medicine II; Germany Faculty of Medicine at Mannheim; University of Heidelberg , Heidelberg, Germany
| | - Steven Dooley
- Molecular Alcohol Research in Gastroenterology, Department of Medicine II; Germany Faculty of Medicine at Mannheim; University of Heidelberg , Heidelberg, Germany
| | - Chun-Fang Gao
- Department of Laboratory Medicine; Eastern Hepatobiliary Surgery Hospital; Second Military Medical University ; Shanghai, China
| |
Collapse
|
57
|
Ruhaak LR, Barkauskas DA, Torres J, Cooke CL, Wu LD, Stroble C, Ozcan S, Williams CC, Camorlinga M, Rocke DM, Lebrilla CB, Solnick JV. The Serum Immunoglobulin G Glycosylation Signature of Gastric Cancer. EUPA OPEN PROTEOMICS 2015; 6:1-9. [PMID: 25685702 DOI: 10.1016/j.euprot.2014.11.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Biomarkers may facilitate detection of gastric cancer at an earlier stage and reduce mortality. Here we sought to determine if the glycosylation profile of serum immunoglobulin G (IgG) could distinguish patients with non-atrophic gastritis (NAG), duodenal ulcer (DU) and gastric cancer (GC). Serum IgG was released and analyzed using nano-LC-TOF mass spectrometry. Statistically significant false discovery rate (FDR)-adjusted p-values were observed for 18 glycans, eight that differed significantly between NAG and GC, three that distinguished NAG from DU, and eight that differed between DU and GC. The IgG glycosylation signature may be useful as a predictive marker for gastric cancer.
Collapse
Affiliation(s)
- L Renee Ruhaak
- Department of Chemistry, University of California, Davis, CA, 95616
| | - Donald A Barkauskas
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, 90089
| | - Javier Torres
- Infectious Diseases Research Unit, Instituto Mexicano del Seguro Social, Mexico
| | - Cara L Cooke
- Departments of Medicine and Microbiology & Immunology; Center for Comparative Medicine, University of California, Davis School of Medicine, Davis, CA, 95616
| | - Lauren D Wu
- Department of Chemistry, University of California, Davis, CA, 95616
| | - Carol Stroble
- Department of Chemistry, University of California, Davis, CA, 95616
| | - Sureyya Ozcan
- Department of Chemistry, University of California, Davis, CA, 95616
| | | | | | - David M Rocke
- Department of Biomedical Engineering, University of California, Davis, CA, 95616 ; Division of Biostatistics, Department of Public Health Sciences, University of California, Davis, CA, 95616
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, CA, 95616 ; Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616
| | - Jay V Solnick
- Departments of Medicine and Microbiology & Immunology; Center for Comparative Medicine, University of California, Davis School of Medicine, Davis, CA, 95616
| |
Collapse
|
58
|
Ning Z, Gan J, Chen C, Zhang D, Zhang H. Molecular functions and significance of the MTA family in hormone-independent cancer. Cancer Metastasis Rev 2014; 33:901-19. [PMID: 25341508 DOI: 10.1007/s10555-014-9517-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The members of the metastasis-associated protein (MTA) family play pivotal roles in both physiological and pathophysiological processes, especially in cancer development and metastasis, and their role as master regulators has come to light. Due to the fact that they were first identified as crucial factors in estrogen receptor-mediated breast cancer metastasis, most of the early studies focused on their hormone-dependent functions. However, the accumulating evidence shows that the members of MTA family are deregulated in most, if not all, the cancers studied so far. Therefore, the levels as well as the activities of the MTA family members are widely accepted as potential biomarkers for diagnosis, prognosis, and predictors of overall survival. They function differently in different cancers with specific mechanisms. p53 and HIF-1α appear to be the respectively common upstream and downstream regulator of the MTA family in both development and metastasis of a wide spectrum of cancers. Here, we review the expression and clinical significance of the MTA family, focusing on hormone-independent cancers. To illustrate the molecular mechanisms, we analyze the MTA family-related signaling pathways in different cancers. Finally, targeting the MTA family directly or the pathways involved in the MTA family indirectly could be invaluable strategies in the development of cancer therapeutics.
Collapse
Affiliation(s)
- Zhifeng Ning
- Laboratory for Translational Oncology, Basic Medicine College, Hubei University of Science and Technology, Xianning, Hubei Province, 437100, China
| | | | | | | | | |
Collapse
|
59
|
Engelberth SA, Hempel N, Bergkvist M. Development of nanoscale approaches for ovarian cancer therapeutics and diagnostics. Crit Rev Oncog 2014; 19:281-315. [PMID: 25271436 DOI: 10.1615/critrevoncog.2014011455] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Ovarian cancer is the deadliest of all gynecological cancers and the fifth leading cause of death due to cancer in women. This is largely due to late-stage diagnosis, poor prognosis related to advanced-stage disease, and the high recurrence rate associated with development of chemoresistance. Survival statistics have not improved significantly over the last three decades, highlighting the fact that improved therapeutic strategies and early detection require substantial improvements. Here, we review and highlight nanotechnology-based approaches that seek to address this need. The success of Doxil, a PEGylated liposomal nanoencapsulation of doxorubicin, which was approved by the FDA for use on recurrent ovarian cancer, has paved the way for the current wave of nanoparticle formulations in drug discovery and clinical trials. We discuss and summarize new nanoformulations that are currently moving into clinical trials and highlight novel nanotherapeutic strategies that have shown promising results in preclinical in vivo studies. Further, the potential for nanomaterials in diagnostic imaging techniques and the ability to leverage nanotechnology for early detection of ovarian cancer are also discussed.
Collapse
Affiliation(s)
| | - Nadine Hempel
- SUNY College of Nanoscale Science and Engineering, Albany NY 12203
| | - Magnus Bergkvist
- SUNY College of Nanoscale Science and Engineering, Albany NY 12203
| |
Collapse
|