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Boumali R, Urli L, Naim M, Soualmia F, Kinugawa K, Petropoulos I, El Amri C. Kallikrein-related peptidase's significance in Alzheimer's disease pathogenesis: A comprehensive survey. Biochimie 2024:S0300-9084(24)00076-2. [PMID: 38608749 DOI: 10.1016/j.biochi.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/19/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024]
Abstract
Alzheimer's disease (AD) and related dementias constitute an important global health challenge. Detailed understanding of the multiple molecular mechanisms underlying their pathogenesis constitutes a clue for the management of the disease. Kallikrein-related peptidases (KLKs), a lead family of serine proteases, have emerged as potential biomarkers and therapeutic targets in the context of AD and associated cognitive decline. Hence, KLKs were proposed to display multifaceted impacts influencing various aspects of neurodegeneration, including amyloid-beta aggregation, tau pathology, neuroinflammation, and synaptic dysfunction. We propose here a comprehensive survey to summarize recent findings, providing an overview of the main kallikreins implicated in AD pathophysiology namely KLK8, KLK6 and KLK7. We explore the interplay between KLKs and key AD molecular pathways, shedding light on their significance as potential biomarkers for early disease detection. We also discuss their pertinence as therapeutic targets for disease-modifying interventions to develop innovative therapeutic strategies aimed at halting or ameliorating the progression of AD and associated dementias.
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Affiliation(s)
- Rilès Boumali
- Sorbonne Université, Faculty of Sciences and Engineering, IBPS, UMR 8256, CNRS-SU, ERL INSERM U1164, Biological Adaptation and Ageing, F-75252, Paris, France. Paris, France
| | - Laureline Urli
- Sorbonne Université, Faculty of Sciences and Engineering, IBPS, UMR 8256, CNRS-SU, ERL INSERM U1164, Biological Adaptation and Ageing, F-75252, Paris, France. Paris, France
| | - Meriem Naim
- Sorbonne Université, Faculty of Sciences and Engineering, IBPS, UMR 8256, CNRS-SU, ERL INSERM U1164, Biological Adaptation and Ageing, F-75252, Paris, France. Paris, France
| | - Feryel Soualmia
- Sorbonne Université, Faculty of Sciences and Engineering, IBPS, UMR 8256, CNRS-SU, ERL INSERM U1164, Biological Adaptation and Ageing, F-75252, Paris, France. Paris, France
| | - Kiyoka Kinugawa
- Sorbonne Université, Faculty of Sciences and Engineering, IBPS, UMR 8256, CNRS-SU, ERL INSERM U1164, Biological Adaptation and Ageing, F-75252, Paris, France. Paris, France; AP-HP, Paris, France; Charles-Foix Hospital, Functional Exploration Unit for Older Patients, 94200 Ivry-sur-Seine, France
| | - Isabelle Petropoulos
- Sorbonne Université, Faculty of Sciences and Engineering, IBPS, UMR 8256, CNRS-SU, ERL INSERM U1164, Biological Adaptation and Ageing, F-75252, Paris, France. Paris, France.
| | - Chahrazade El Amri
- Sorbonne Université, Faculty of Sciences and Engineering, IBPS, UMR 8256, CNRS-SU, ERL INSERM U1164, Biological Adaptation and Ageing, F-75252, Paris, France. Paris, France.
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Zhang L, Lovell S, De Vita E, Jagtap PKA, Lucy D, Goya Grocin A, Kjær S, Borg A, Hennig J, Miller AK, Tate EW. A KLK6 Activity-Based Probe Reveals a Role for KLK6 Activity in Pancreatic Cancer Cell Invasion. J Am Chem Soc 2022; 144:22493-22504. [PMID: 36413626 DOI: 10.1021/jacs.2c07378] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Pancreatic cancer has the lowest survival rate of all common cancers due to late diagnosis and limited treatment options. Serine hydrolases are known to mediate cancer progression and metastasis through initiation of signaling cascades and cleavage of extracellular matrix proteins, and the kallikrein-related peptidase (KLK) family of secreted serine proteases have emerging roles in pancreatic ductal adenocarcinoma (PDAC). However, the lack of reliable activity-based probes (ABPs) to profile KLK activity has hindered progress in validation of these enzymes as potential targets or biomarkers. Here, we developed potent and selective ABPs for KLK6 by using a positional scanning combinatorial substrate library and characterized their binding mode and interactions by X-ray crystallography. The optimized KLK6 probe IMP-2352 (kobs/I = 11,000 M-1 s-1) enabled selective detection of KLK6 activity in a variety of PDAC cell lines, and we observed that KLK6 inhibition reduced the invasiveness of PDAC cells that secrete active KLK6. KLK6 inhibitors were combined with N-terminomics to identify potential secreted protein substrates of KLK6 in PDAC cells, providing insights into KLK6-mediated invasion pathways. These novel KLK6 ABPs offer a toolset to validate KLK6 and associated signaling partners as targets or biomarkers across a range of diseases.
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Affiliation(s)
- Leran Zhang
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K
| | - Scott Lovell
- Department of Life Sciences, University of Bath, Bath BA2 7AX, U.K
| | - Elena De Vita
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K
| | - Pravin Kumar Ankush Jagtap
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany.,Chair of Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Bayreuth 95447, Germany
| | - Daniel Lucy
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K
| | - Andrea Goya Grocin
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K
| | - Svend Kjær
- Structural Biology Science Technology Platform, The Francis Crick Institute, London NW1 1AT, U.K
| | - Annabel Borg
- Structural Biology Science Technology Platform, The Francis Crick Institute, London NW1 1AT, U.K
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany.,Chair of Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Bayreuth 95447, Germany
| | - Aubry K Miller
- Cancer Drug Development Group, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Edward W Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K
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In Situ N-glycosylation Signatures of Epithelial Ovarian Cancer Tissue as Defined by MALDI Mass Spectrometry Imaging. Cancers (Basel) 2022; 14:cancers14041021. [PMID: 35205768 PMCID: PMC8870006 DOI: 10.3390/cancers14041021] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 01/14/2022] [Indexed: 12/31/2022] Open
Abstract
The particularly high mortality of epithelial ovarian cancer (EOC) is in part linked to limited understanding of its molecular signatures. Although there are data available on in situ N-glycosylation in EOC tissue, previous studies focused primarily on neutral N-glycan species and, hence, still little is known regarding EOC tissue-specific sialylation. In this proof-of-concept study, we implemented MALDI mass spectrometry imaging (MALDI-MSI) in combination with sialic acid derivatization to simultaneously investigate neutral and sialylated N-glycans in formalin-fixed paraffin-embedded tissue microarray specimens of less common EOC histotypes and non-malignant borderline ovarian tumor (BOT). The applied protocol allowed detecting over 50 m/z species, many of which showed differential tissue distribution. Most importantly, it could be demonstrated that α2,6- and α2,3-sialylated N-glycans are enriched in tissue regions corresponding to tumor and adjacent tumor-stroma, respectively. Interestingly, analogous N-glycosylation patterns were observed in tissue cores of BOT, suggesting that regio-specific N-glycan distribution might occur already in non-malignant ovarian pathologies. All in all, our data provide proof that the combination of MALDI-MSI and sialic acid derivatization is suitable for delineating regio-specific N-glycan distribution in EOC and BOT tissues and might serve as a promising strategy for future glycosylation-based biomarker discovery studies.
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Colomb F, Giron LB, Kuri-Cervantes L, Adeniji OS, Ma T, Dweep H, Battivelli E, Verdin E, Palmer CS, Tateno H, Kossenkov AV, Roan NR, Betts MR, Abdel-Mohsen M. Sialyl-Lewis X Glycoantigen Is Enriched on Cells with Persistent HIV Transcription during Therapy. Cell Rep 2020; 32:107991. [PMID: 32755584 PMCID: PMC7432956 DOI: 10.1016/j.celrep.2020.107991] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 05/30/2020] [Accepted: 07/14/2020] [Indexed: 12/30/2022] Open
Abstract
A comprehensive understanding of the phenotype of persistent HIV-infected cells, transcriptionally active and/or transcriptionally inactive, is imperative for developing a cure. The relevance of cell-surface glycosylation to HIV persistence has never been explored. We characterize the relationship between cell-surface glycomic signatures and persistent HIV transcription in vivo. We find that the cell surface of CD4+ T cells actively transcribing HIV, despite suppressive therapy, harbors high levels of fucosylated carbohydrate ligands, including the cell extravasation mediator Sialyl-LewisX (SLeX), compared with HIV-infected transcriptionally inactive cells. These high levels of SLeX are induced by HIV transcription in vitro and are maintained after therapy in vivo. Cells with high-SLeX are enriched with markers associated with HIV susceptibility, signaling pathways that drive HIV transcription, and pathways involved in leukocyte extravasation. We describe a glycomic feature of HIV-infected transcriptionally active cells that not only differentiates them from their transcriptionally inactive counterparts but also may affect their trafficking abilities.
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Affiliation(s)
- Florent Colomb
- The Wistar Institute, Philadelphia, PA 19104, USA; Penn Center for AIDS Research (Penn CFAR), University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Leila B Giron
- The Wistar Institute, Philadelphia, PA 19104, USA; Penn Center for AIDS Research (Penn CFAR), University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Leticia Kuri-Cervantes
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Center for AIDS Research (Penn CFAR), University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Opeyemi S Adeniji
- The Wistar Institute, Philadelphia, PA 19104, USA; Penn Center for AIDS Research (Penn CFAR), University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tongcui Ma
- University of California, San Francisco, San Francisco, CA 94158, USA; Gladstone Institutes, San Francisco, CA 94158, USA
| | - Harsh Dweep
- The Wistar Institute, Philadelphia, PA 19104, USA
| | | | - Eric Verdin
- The Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Clovis S Palmer
- The Burnet Institute, Melbourne, VIC 3004, Australia; Department of Infectious Diseases, Monash University, Melbourne, VIC 3004, Australia
| | - Hiroaki Tateno
- National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | | | - Nadia R Roan
- University of California, San Francisco, San Francisco, CA 94158, USA; Gladstone Institutes, San Francisco, CA 94158, USA
| | - Michael R Betts
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Center for AIDS Research (Penn CFAR), University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mohamed Abdel-Mohsen
- The Wistar Institute, Philadelphia, PA 19104, USA; Penn Center for AIDS Research (Penn CFAR), University of Pennsylvania, Philadelphia, PA 19104, USA.
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Abstract
Alternative splicing of precursor mRNA is a key mediator of gene expression regulation leading to greater diversity of the proteome in complex organisms. Systematic sequencing of the human genome and transcriptome has led to our understanding of how alternative splicing of critical genes leads to multiple pathological conditions such as cancer. For many years, proteases were known only for their roles as proteolytic enzymes, acting to regulate/process proteins associated with diverse cellular functions. However, the differential expression and altered function of various protease isoforms, such as (i) anti-apoptotic activities, (ii) mediating intercellular adhesion, and (iii) modifying the extracellular matrix, are evidence of their specific contribution towards shaping the tumor microenvironment. Revealing the alternative splicing of protease genes and characterization of their protein products/isoforms with distinct and opposing functions creates a platform to understand how protease isoforms contribute to specific cancer hallmarks. Here, in this review, we address cancer-specific isoforms produced by the alternative splicing of proteases and their distinctive roles in the tumor microenvironment.
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Affiliation(s)
- Chamikara Liyanage
- School of Biomedical Sciences, Faculty of Health, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
- Australian Prostate Cancer Research Centre-Queensland (APCRC-Q), Translational Research Institute, Queensland University of Technology, Brisbane, Australia
| | - Achala Fernando
- School of Biomedical Sciences, Faculty of Health, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
- Australian Prostate Cancer Research Centre-Queensland (APCRC-Q), Translational Research Institute, Queensland University of Technology, Brisbane, Australia
| | - Jyotsna Batra
- School of Biomedical Sciences, Faculty of Health, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia.
- Australian Prostate Cancer Research Centre-Queensland (APCRC-Q), Translational Research Institute, Queensland University of Technology, Brisbane, Australia.
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Lv X, Song J, Xue K, Li Z, Li M, Zahid D, Cao H, Wang L, Song W, Ma T, Gu J, Li W. Core fucosylation of copper transporter 1 plays a crucial role in cisplatin-resistance of epithelial ovarian cancer by regulating drug uptake. Mol Carcinog 2019; 58:794-807. [PMID: 30614075 DOI: 10.1002/mc.22971] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 12/13/2018] [Accepted: 12/27/2018] [Indexed: 12/13/2022]
Abstract
Core fucosylation catalyzed by core fucosyltransferase (Fut8) contributes to the progressions of epithelial ovarian cancer (EOC). Copper transporter 1 (CTR1), which contains one N-glycan on Asn15 , mediates cellular transport of cisplatin (cDDP), and plays an important role in the process of cDDP-resistance in EOC. In the present study, we found that the core fucosylation level elevated significantly in the sera of cDDP-treated EOC patients. The in vitro assays also indicate that core fucosylation of CTR1 was significantly upregulated in cDDP-resistant A2780CP cells compared to the cDDP-sensitive A2780S cells. Intriguingly, the hyper core fucosylation suppressed the CTR1-cDDP interactions and cDDP-uptake into A2780CP cells. Conversely, contrast to the Fut8+/+ mouse ovarian epithelial cells, the Fut8-deleted (Fut8-/- ) cells obviously showed higher cDDP-uptake. Furthermore, the recovered core fucosylation induced the suppression of cDDP-uptake in Fut8-restored ovarian epithelial cells. In addition, the core fucosylation could regulate the phosphorylation of cDDP-resistance-associated molecules, such as AKT, ERK, JNK, and mTOR. Our findings suggest that the core fucosylation of CTR1 plays an important role in the cellular cDDP-uptake and thus provide new strategies for improving the outcome of cDDP based chemotherapy of EOC.
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Affiliation(s)
- Xiaoxue Lv
- College of Basic Medical Sciences, Dalian Medical University, Liaoning, China
| | - Jiazhe Song
- College of Basic Medical Sciences, Dalian Medical University, Liaoning, China
| | - Kai Xue
- College of Basic Medical Sciences, Dalian Medical University, Liaoning, China
| | - Zhi Li
- Clinical Laboratory, Dalian Municipal Central Hospital, Dalian, Liaoning, China
| | - Ming Li
- College of Basic Medical Sciences, Dalian Medical University, Liaoning, China
| | - Danishi Zahid
- College of Basic Medical Sciences, Dalian Medical University, Liaoning, China
| | - Hongyu Cao
- College of Life Science and Technology, Dalian University, Liaoning, China
| | - Lu Wang
- College of Basic Medical Sciences, Dalian Medical University, Liaoning, China
| | - Wanli Song
- College of Basic Medical Sciences, Dalian Medical University, Liaoning, China
| | - Tonghui Ma
- College of Basic Medical Sciences, Dalian Medical University, Liaoning, China
| | - Jianguo Gu
- Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Miyagi, Japan
| | - Wenzhe Li
- College of Basic Medical Sciences, Dalian Medical University, Liaoning, China
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De Vita E, Schüler P, Lovell S, Lohbeck J, Kullmann S, Rabinovich E, Sananes A, Heßling B, Hamon V, Papo N, Hess J, Tate EW, Gunkel N, Miller AK. Depsipeptides Featuring a Neutral P1 Are Potent Inhibitors of Kallikrein-Related Peptidase 6 with On-Target Cellular Activity. J Med Chem 2018; 61:8859-8874. [DOI: 10.1021/acs.jmedchem.8b01106] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Elena De Vita
- Cancer Drug Development Group, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
- Biosciences Faculty, University of Heidelberg, Heidelberg 69120, Germany
| | - Peter Schüler
- Cancer Drug Development Group, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Scott Lovell
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, U.K
| | - Jasmin Lohbeck
- Cancer Drug Development Group, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Sven Kullmann
- Cancer Drug Development Group, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Eitan Rabinovich
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Amiram Sananes
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Bernd Heßling
- Center for Molecular Biology, University of Heidelberg, Heidelberg 69120, Germany
| | - Veronique Hamon
- European Screening Centre, Biocity Scotland, University of Dundee, Newhouse ML1 5UH, U.K
| | - Niv Papo
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Jochen Hess
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, Heidelberg 69120, Germany
- Research Group Molecular Mechanisms of Head and Neck Tumors, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Edward W. Tate
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, U.K
| | - Nikolas Gunkel
- Cancer Drug Development Group, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
| | - Aubry K. Miller
- Cancer Drug Development Group, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
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Diagnostic and Prognostic Biomarkers in ovarian cancer and the potential roles of cancer stem cells – An updated review. Exp Cell Res 2018; 362:1-10. [DOI: 10.1016/j.yexcr.2017.10.018] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 10/20/2017] [Indexed: 01/06/2023]
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LI RN, WANG YN, PENG MH, WANG XY, GUO GS. Preparation and Application of Porous Layer Open Tubular Capillary Columns with Narrow Bore in Liquid Chromatography. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2017. [DOI: 10.1016/s1872-2040(17)61057-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Silva LM, Clements JA. Mass spectrometry based proteomics analyses in kallikrein-related peptidase research: implications for cancer research and therapy. Expert Rev Proteomics 2017; 14:1119-1130. [PMID: 29025353 DOI: 10.1080/14789450.2017.1389637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Kallikrein-related peptidases (KLKs) are a family of serine peptidases that are deregulated in numerous pathological conditions, with a multitude of KLK-mediated functional roles implicated in the progression of cancer. Advances in multidimensional mass spectrometry (MS)-based proteomics have facilitated the quantitative measurement of deregulated KLK expression in cancer, identifying certain KLKs, as well as their substrates, as potential cancer biomarkers. Areas covered: In this review, we discuss how these approaches have been utilized for KLK biomarker discovery and unbiased substrate determination in complex protein pools that mimic the in vivo extracellular microenvironment. Expert commentary: Although a limited number of studies have been performed, the quantity of information generated has greatly improved our understanding of the functional roles of KLKs in cancer progression. In addition, these data suggest additional means through which deregulated KLK expression may be targeted in cancer treatment, highlighting the potential therapeutic value of these state-of-the-art MS-based studies.
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Affiliation(s)
- Lakmali Munasinghage Silva
- a Proteases and Tissue Remodeling Section, Oral and Pharyngeal Cancer Branch , National Institute of Dental and Craniofacial Research, National Institutes of Health , Bethesda , MD , USA
| | - Judith Ann Clements
- b School of Biomedical Sciences , Institute of Health and Biomedical Innovation (IHBI), Queensland University of Technology (QUT), Translational Research Institute , Woolloongabba , Australia
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Korbakis D, Soosaipillai A, Diamandis EP. Study of kallikrein-related peptidase 6 (KLK6) and its complex with α1-antitrypsin in biological fluids. Clin Chem Lab Med 2017; 55:1385-1396. [PMID: 28672746 DOI: 10.1515/cclm-2017-0017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 04/27/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND Human kallikrein-related peptidase 6 (KLK6) is a member of the kallikrein family of serine proteases. KLK6 is synthesized as a preproenzyme, mainly in tissues of the central nervous system (CNS), and secreted as an inactive precursor. Serum KLK6 is a biomarker of unfavorable prognosis for ovarian cancer, but its sensitivity for early detection is relatively low. Differential glycosylation of KLK6 has been identified in ascites fluid obtained from ovarian cancer patients, suggesting the presence of unique KLK6 isoforms in biological samples. METHODS In the present study, we applied a two-step enrichment approach for KLK6 in ovarian cancer ascites, followed by mice immunization and production of monoclonal antibodies. Immunoaffinity techniques coupled to mass spectrometric methods were employed for hybridoma screening and target antigen identification. RESULTS We found that the main target of the newly-generated monoclonal antibodies target was the serine protease inhibitor α1-antitrypsin (A1AT). Additional experiments confirmed that A1AT is the main inhibitor of KLK6 in biological fluids. One new antibody (24ED138) was chosen to build a hybrid assay for the accurate quantification of the A1AT-KLK6 complex in biological samples. The aforementioned assay was evaluated with serum samples collected from patients with ovarian cancer (n=24) and normal donors (n=16) and showed slight improvement in sensitivity (~12%) compared to the standard in-house KLK6 assay. CONCLUSIONS We conclude that KLK6 is present in biological fluids either as free form, or bound to A1AT, and the bound form performs better than total KLK6 as a biomarker of ovarian carcinoma.
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12
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Yoon H, Scarisbrick IA. Kallikrein-related peptidase 6 exacerbates disease in an autoimmune model of multiple sclerosis. Biol Chem 2017; 397:1277-1286. [PMID: 27533119 DOI: 10.1515/hsz-2016-0239] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 08/10/2016] [Indexed: 12/22/2022]
Abstract
Kallikrein-related peptidase 6 (Klk6) is elevated in the serum of multiple sclerosis (MS) patients and is hypothesized to participate in inflammatory and neuropathogenic aspects of the disease. To test this hypothesis, we investigated the impact of systemic administration of recombinant Klk6 on the development and progression of MOG35-55-induced experimental autoimmune encephalomyelitis (EAE). First, we determined that Klk6 expression is elevated in the spinal cord of mice with EAE at the peak of clinical disease and in immune cells upon priming with the disease-initiating peptide in vitro. Systemic administration of recombinant Klk6 to mice during the priming phase of disease resulted in an exacerbation of clinical symptoms, including earlier onset of disease and higher levels of spinal cord inflammation and pathology. Treatment of MOG35-55-primed immune cells with Klk6 in culture enhanced expression of pro-inflammatory cytokines, interferon-γ, tumor necrosis factor, and interleukin-17, while reducing anti-inflammatory cytokines interleukin-4 and interleukin-5. Together these findings provide evidence that elevations in systemic Klk6 can bias the immune system towards pro-inflammatory responses capable of exacerbating the development of neuroinflammation and paralytic neurological deficits. We suggest that Klk6 represents an important target for conditions in which pro-inflammatory responses play a critical role in disease development, including MS.
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Ahmed N, Dorn J, Napieralski R, Drecoll E, Kotzsch M, Goettig P, Zein E, Avril S, Kiechle M, Diamandis EP, Schmitt M, Magdolen V. Clinical relevance of kallikrein-related peptidase 6 (KLK6) and 8 (KLK8) mRNA expression in advanced serous ovarian cancer. Biol Chem 2017; 397:1265-1276. [PMID: 27483364 DOI: 10.1515/hsz-2016-0177] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 07/29/2016] [Indexed: 02/06/2023]
Abstract
Most members of the kallikrein-related peptidase family have been demonstrated to be dysregulated in ovarian cancer and modulate tumor growth, migration, invasion, and resistance to chemotherapy. In the present study, we assessed the mRNA expression levels of KLK6 and KLK8 by quantitative PCR in 100 patients with advanced serous ovarian cancer FIGO stage III/IV. A pronounced correlation between KLK6 and KLK8 mRNA expression (rs = 0.636, p < 0.001) was observed, indicating coordinate expression of both peptidases. No significant associations of clinical parameters with KLK6, KLK8, and a combined score KLK6+KLK8 were found. In univariate Cox regression analysis, elevated mRNA levels of KLK6 were significantly linked with shortened overall survival (OS) (hazard ratio [HR] = 2.07, p = 0.007). While KLK8 values were not associated with patients' outcome, high KLK6+KLK8 values were significantly associated with shorter progression-free survival (HR = 1.82, p = 0.047) and showed a trend towards significance in the case of OS (HR = 1.82, p = 0.053). Strikingly, in multivariable analysis, elevated KLK6 mRNA values, apart from residual tumor mass, remained an independent predictive marker for poor OS (HR = 2.33, p = 0.005). As KLK6 mRNA and protein levels correlate, KLK6 may represent an attractive therapeutic target for potent and specific inhibitors of its enzymatic activity.
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Effects of Glycosylation on the Enzymatic Activity and Mechanisms of Proteases. Int J Mol Sci 2016; 17:ijms17121969. [PMID: 27898009 PMCID: PMC5187769 DOI: 10.3390/ijms17121969] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 11/07/2016] [Accepted: 11/10/2016] [Indexed: 02/06/2023] Open
Abstract
Posttranslational modifications are an important feature of most proteases in higher organisms, such as the conversion of inactive zymogens into active proteases. To date, little information is available on the role of glycosylation and functional implications for secreted proteases. Besides a stabilizing effect and protection against proteolysis, several proteases show a significant influence of glycosylation on the catalytic activity. Glycans can alter the substrate recognition, the specificity and binding affinity, as well as the turnover rates. However, there is currently no known general pattern, since glycosylation can have both stimulating and inhibiting effects on activity. Thus, a comparative analysis of individual cases with sufficient enzyme kinetic and structural data is a first approach to describe mechanistic principles that govern the effects of glycosylation on the function of proteases. The understanding of glycan functions becomes highly significant in proteomic and glycomic studies, which demonstrated that cancer-associated proteases, such as kallikrein-related peptidase 3, exhibit strongly altered glycosylation patterns in pathological cases. Such findings can contribute to a variety of future biomedical applications.
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A case for protein-level and site-level specificity in glycoproteomic studies of disease. Glycoconj J 2016; 33:377-85. [PMID: 27007620 DOI: 10.1007/s10719-016-9663-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 02/16/2016] [Accepted: 03/09/2016] [Indexed: 12/12/2022]
Abstract
Abnormal glycosylation of proteins is known to be either resultant or causative of a variety of diseases. This makes glycoproteins appealing targets as potential biomarkers and focal points of molecular studies on the development and progression of human ailment. To date, a majority of efforts in disease glycoproteomics have tended to center on either determining the concentration of a given glycoprotein, or on profiling the total population of glycans released from a mixture of glycoproteins. While these approaches have demonstrated some diagnostic potential, they are inherently insensitive to the fine molecular detail which distinguishes unique and possibly disease relevant glycoforms of specific proteins. As a consequence, such analyses can be of limited sensitivity, specificity, and accuracy because they do not comprehensively consider the glycosylation status of any particular glycoprotein, or of any particular glycosylation site. Therefore, significant opportunities exist to improve glycoproteomic inquiry into disease by engaging in these studies at the level of individual glycoproteins and their exact loci of glycosylation. In this concise review, the rationale for glycoprotein and glycosylation site specificity is developed in the context of human disease glycoproteomics with an emphasis on N-glycosylation. Recent examples highlighting disease-related perturbations in glycosylation will be presented, including those involving alterations in the overall glycosylation of a specific protein, alterations in the occupancy of a given glycosylation site, and alterations in the compositional heterogeneity of glycans occurring at a given glycosylation site. Each will be discussed with particular emphasis on how protein-specific and site-specific approaches can contribute to improved discrimination between glycoproteomes and glycoproteins associated with healthy and unhealthy states.
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Guo S, Skala W, Magdolen V, Briza P, Biniossek ML, Schilling O, Kellermann J, Brandstetter H, Goettig P. A Single Glycan at the 99-Loop of Human Kallikrein-related Peptidase 2 Regulates Activation and Enzymatic Activity. J Biol Chem 2015; 291:593-604. [PMID: 26582203 PMCID: PMC4705380 DOI: 10.1074/jbc.m115.691097] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Indexed: 01/20/2023] Open
Abstract
Human kallikrein-related peptidase 2 (KLK2) is a key serine protease in semen liquefaction and prostate cancer together with KLK3/prostate-specific antigen. In order to decipher the function of its potential N-glycosylation site, we produced pro-KLK2 in Leishmania tarentolae cells and compared it with its non-glycosylated counterpart from Escherichia coli expression. Mass spectrometry revealed that Asn-95 carries a core glycan, consisting of two GlcNAc and three hexoses. Autocatalytic activation was retarded in glyco-pro-KLK2, whereas the activated glyco-form exhibited an increased proteolytic resistance. The specificity patterns obtained by the PICS (proteomic identification of protease cleavage sites) method are similar for both KLK2 variants, with a major preference for P1-Arg. However, glycosylation changes the enzymatic activity of KLK2 in a drastically substrate-dependent manner. Although glyco-KLK2 has a considerably lower catalytic efficiency than glycan-free KLK2 toward peptidic substrates with P2-Phe, the situation was reverted toward protein substrates, such as glyco-pro-KLK2 itself. These findings can be rationalized by the glycan-carrying 99-loop that prefers to cover the active site like a lid. By contrast, the non-glycosylated 99-loop seems to favor a wide open conformation, which mostly increases the apparent affinity for the substrates (i.e. by a reduction of Km). Also, the cleavage pattern and kinetics in autolytic inactivation of both KLK2 variants can be explained by a shift of the target sites due to the presence of the glycan. These striking effects of glycosylation pave the way to a deeper understanding of kallikrein-related peptidase biology and pathology.
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Affiliation(s)
- Shihui Guo
- From the Department of Molecular Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Wolfgang Skala
- From the Department of Molecular Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Viktor Magdolen
- the Klinische Forschergruppe der Frauenklinik, Klinikum Rechts der Isar der TU München, 81675 Munich, Germany
| | - Peter Briza
- From the Department of Molecular Biology, University of Salzburg, 5020 Salzburg, Austria
| | | | - Oliver Schilling
- the Institute of Molecular Medicine and Cell Research and BIOSS Centre for Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany, the German Cancer Consortium (DKTK), 69120 Heidelberg, Germany, the German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany, and
| | - Josef Kellermann
- the Max-Planck-Institute for Biochemistry, 82152 Martinsried, Germany
| | - Hans Brandstetter
- From the Department of Molecular Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Peter Goettig
- From the Department of Molecular Biology, University of Salzburg, 5020 Salzburg, Austria,
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Kallikreins - The melting pot of activity and function. Biochimie 2015; 122:270-82. [PMID: 26408415 DOI: 10.1016/j.biochi.2015.09.023] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 09/21/2015] [Indexed: 12/20/2022]
Abstract
The human tissue kallikrein and kallikrein-related peptidases (KLKs), encoded by the largest contiguous cluster of protease genes in the human genome, are secreted serine proteases with diverse expression patterns and physiological roles. Because of the broad spectrum of processes that are modulated by kallikreins, these proteases are the subject of extensive investigations. This review brings together basic information about the biochemical properties affecting enzymatic activity, with highlights on post-translational modifications, especially glycosylation. Additionally, we present the current state of knowledge regarding the physiological functions of KLKs in major human organs and outline recent discoveries pertinent to the involvement of kallikreins in cell signaling and in viral infections. Despite the current depth of knowledge of these enzymes, many questions regarding the roles of kallikreins in health and disease remain unanswered.
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Lee DY, Chang GD. Simultaneous immunoblotting analysis with activity gel electrophoresis and 2-D gel electrophoresis. Methods Mol Biol 2015; 1312:61-72. [PMID: 26043990 DOI: 10.1007/978-1-4939-2694-7_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Diffusion blotting method can couple immunoblotting analysis with another biochemical technique in a single polyacrylamide gel, however, with lower transfer efficiency as compared to the conventional electroblotting method. Thus, with diffusion blotting, protein blots can be obtained from an SDS polyacrylamide gel for zymography assay, from a native polyacrylamide gel for electrophoretic mobility shift assay (EMSA) or from a 2-D polyacrylamide gel for large-scale screening and identification of a protein marker. Thereafter, a particular signal in zymography, electrophoretic mobility shift assay, and 2-dimensional gel can be confirmed or identified by simultaneous immunoblotting analysis with a corresponding antiserum. These advantages make diffusion blotting desirable when partial loss of transfer efficiency can be tolerated or be compensated by a more sensitive immunodetection reaction using enhanced chemiluminescence detection.
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Affiliation(s)
- Der-Yen Lee
- Graduate Institute of Biochemical Sciences, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei, 106, Taiwan
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19
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Bults P, van de Merbel NC, Bischoff R. Quantification of biopharmaceuticals and biomarkers in complex biological matrices: a comparison of liquid chromatography coupled to tandem mass spectrometry and ligand binding assays. Expert Rev Proteomics 2015; 12:355-74. [DOI: 10.1586/14789450.2015.1050384] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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20
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Goyallon A, Cholet S, Chapelle M, Junot C, Fenaille F. Evaluation of a combined glycomics and glycoproteomics approach for studying the major glycoproteins present in biofluids: Application to cerebrospinal fluid. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:461-473. [PMID: 26160412 DOI: 10.1002/rcm.7125] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 12/08/2014] [Accepted: 12/14/2014] [Indexed: 06/04/2023]
Abstract
RATIONALE Glycosylation is one of the most complex types of post-translational modifications of proteins. The alteration of glycans bound to proteins from cerebrospinal fluid (CSF) in relation to disorders of the central nervous system is a highly relevant subject, but only few studies have focused on the glycosylation of CSF proteins. METHODS Reproducible profiles of CSF N-glycans were first obtained by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry after permethylation. Tryptic glycopeptides from CSF proteins were also enriched by hydrophilic interaction, and the resulting extracts divided into two equal aliquots. A first aliquot was enzymatically deglycosylated and analyzed by nano-liquid chromatography/tandem mass spectrometry while the second one, containing intact enriched glycopeptides, was directly analyzed. Site-specific data were obtained by combining the data from these three experiments. RESULTS We describe the development of a versatile approach for obtaining site-specific information on the N-glycosylation of CSF glycoproteins. Under these conditions, 124 N-glycopeptides representing 55 N-glycosites from 36 glycoproteins were tentatively identified. Special emphasis was placed on the analysis of glycoproteins/glycopeptides bearing 'brain-type' N-glycans, representing potential biologically relevant structures in the field of neurodegenerative disorders. Using our workflow, only a few proteins were shown to carry such particular glycan motifs. CONCLUSIONS We developed an approach combining N-glycomics and N-glycoproteomics and underline its usefulness to study the site-specific glycosylation of major human CSF proteins. The final rather long-term objective is to combine these data with those from other omics approaches to delve deeper into the understanding of particular neurological disorders.
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Affiliation(s)
- Arnaud Goyallon
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, 91191, Gif-sur-Yvette, France
| | - Sophie Cholet
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, 91191, Gif-sur-Yvette, France
| | | | - Christophe Junot
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, 91191, Gif-sur-Yvette, France
| | - François Fenaille
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, 91191, Gif-sur-Yvette, France
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Korbakis D, Brinc D, Schiza C, Soosaipillai A, Jarvi K, Drabovich AP, Diamandis EP. Immunocapture-Selected Reaction Monitoring Screening Facilitates the Development of ELISA for the Measurement of Native TEX101 in Biological Fluids. Mol Cell Proteomics 2015; 14:1517-26. [PMID: 25813379 DOI: 10.1074/mcp.m114.047571] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Indexed: 11/06/2022] Open
Abstract
Monoclonal antibodies that bind the native conformation of proteins are indispensable reagents for the development of immunoassays, production of therapeutic antibodies and delineating protein interaction networks by affinity purification-mass spectrometry. Antibodies generated against short peptides, protein fragments, or even full length recombinant proteins may not bind the native protein form in biological fluids, thus limiting their utility. Here, we report the application of immunocapture coupled with selected reaction monitoring measurements (immunocapture-SRM), in the rapid screening of hybridoma culture supernatants for monoclonal antibodies that bind the native protein conformation. We produced mouse monoclonal antibodies, which detect in human serum or seminal plasma the native form of the human testis-expressed sequence 101 (TEX101) protein-a recently proposed biomarker of male infertility. Pairing of two monoclonal antibodies against unique TEX101 epitopes led to the development of an ELISA for the measurement of TEX101 in seminal plasma (limit of detection: 20 pg/ml) and serum (limit of detection: 40 pg/ml). Measurements of matched seminal plasma samples, obtained from men pre- and post-vasectomy, confirmed the absolute diagnostic specificity and sensitivity of TEX101 for noninvasive identification of physical obstructions in the male reproductive tract. Measurement of male and female serum samples revealed undetectable levels of TEX101 in the systemic circulation of healthy individuals. Immunocapture-SRM screening may facilitate development of monoclonal antibodies and immunoassays against native forms of challenging protein targets.
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Affiliation(s)
- Dimitrios Korbakis
- From the ‡Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; §Department of Clinical Biochemistry, University Health Network, Toronto, Canada
| | - Davor Brinc
- ¶Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
| | - Christina Schiza
- From the ‡Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; ¶Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
| | | | - Keith Jarvi
- ‖Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada; **Department of Surgery, Division of Urology, Mount Sinai Hospital, University of Toronto, Canada
| | - Andrei P Drabovich
- From the ‡Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; §Department of Clinical Biochemistry, University Health Network, Toronto, Canada;
| | - Eleftherios P Diamandis
- From the ‡Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; §Department of Clinical Biochemistry, University Health Network, Toronto, Canada; ¶Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada; ‖Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada;
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Sialic acids: biomarkers in endocrinal cancers. Glycoconj J 2015; 32:79-85. [PMID: 25777812 DOI: 10.1007/s10719-015-9577-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 02/11/2015] [Accepted: 02/18/2015] [Indexed: 12/20/2022]
Abstract
Sialylations are post translational modification of proteins and lipids that play important role in recognition, signaling, immunological response and cell-cell interaction. Improper sialylations due to altered sialyl transferases, sialidases, gene structure and expression, sialic acid metabolism however lead to diseases and thus sialic acids form an important biomarker in disease. In the endocrinal biology such improper sialylations including altered expression of sialylated moieties have been shown to be associated with disorders. Cancer still remains to be the major cause of global death and the cancer of the endocrine organs suffer from the dearth of appropriate markers for disease prediction at the early stage and monitoring. This review is aimed at evaluating the role of sialic acids as markers in endocrinal disorders with special reference to cancer of the endocrine organs. The current study is summarized under the following headings of altered sialylations in endocrinal cancer of the (i) ovary (ii) pancreas (iii) thyroid (iv) adrenal and (v) pituitary gland. Studies in expression of sialic acid in testis cancer are limited. The future scope of this review remains in the targeting of endocrinal cancer by targeting altered sialylation which is a common expression associated with endocrinal cancer.
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23
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Michaelidou K, Kladi-Skandali A, Scorilas A. Kallikreins as Biomarkers in Human Malignancies. BIOMARKERS IN CANCER 2015. [DOI: 10.1007/978-94-007-7681-4_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Zhou L, Qian Y, Zhang X, Ruan Y, Ren S, Gu J. Elucidation of differences in N-glycosylation between different molecular weight forms of recombinant CLEC-2 by LC MALDI tandem MS. Carbohydr Res 2015; 402:180-8. [DOI: 10.1016/j.carres.2014.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/17/2014] [Accepted: 07/07/2014] [Indexed: 10/25/2022]
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25
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Qi YJ, Ward DG, Pang C, Wang QM, Wei W, Ma J, Zhang J, Lou Q, Shimwell NJ, Martin A, Wong N, Chao WX, Wang M, Ma YF, Johnson PJ. Proteomic profiling of N-linked glycoproteins identifies ConA-binding procathepsin D as a novel serum biomarker for hepatocellular carcinoma. Proteomics 2014; 14:186-95. [PMID: 24259486 DOI: 10.1002/pmic.201300226] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 10/02/2013] [Accepted: 11/07/2013] [Indexed: 01/13/2023]
Abstract
The aim of this study was to identify novel biomarkers for the diagnosis of, and potential therapeutic targets for, hepatocellular carcinoma (HCC). Multilectin affinity chromatography was used to enrich N-linked glycoproteins from nontumorous liver and HCC tissues followed by 2DE and protein identification by MS. Twenty-eight differentially expressed proteins were identified. Western blotting validated consistently lower concentrations of human liver carboxylesterase 1 and haptoglobin, and higher concentration of procathepsin D (pCD) in HCC tissues. Knockdown of cathepsin D (CD) expression mediated by siRNA significantly inhibited the in vitro invasion of two HCC cell lines, SNU449 and SNU473, which normally secrete high-levels of CD. Prefractionation using individual lectins demonstrated an elevation in ConA-binding glycoforms of proCD and CD in HCC tissues. In the serum of HCC patients, "ConA-binding proCD" (ConA-pCD) is significantly increased in concentration and this increase is comprised of several distinct upregulated acidic isoforms (pI 4.5-5.5). Receiver operating characteristic analysis showed that the sensitivity and specificity of serum ConA-pCD for HCC diagnosis were 85% and 80%, respectively. This is the first report that serum ConA-pCD is increased significantly in HCC and is potentially useful as a serological biomarker for diagnosis of HCC.
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Affiliation(s)
- Yi-Jun Qi
- Key Laboratory of Cellular and Molecular Immunology, College of Medicine, Henan University, Kaifeng, P. R. China
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Drabovich AP, Martínez-Morillo E, Diamandis EP. Toward an integrated pipeline for protein biomarker development. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:677-86. [PMID: 25218201 DOI: 10.1016/j.bbapap.2014.09.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 08/08/2014] [Accepted: 09/04/2014] [Indexed: 01/06/2023]
Abstract
Protein biomarker development is a multidisciplinary task involving basic, translational and clinical research. Integration of multidisciplinary efforts in a single pipeline is challenging, but crucial to facilitate rational discovery of protein biomarkers and alleviate existing disappointments in the field. In this review, we discuss in detail individual phases of biomarker development pipeline, such as biomarker candidate identification, verification and validation. We focus on mass spectrometry as a principal technique for protein identification and quantification, and discuss complementary -omics approaches for selection of biomarker candidates. Proteomic samples, protein-based clinical laboratory tests and limitations of biomarker development are reviewed in detail, and critical assessment of all phases of biomarker development pipeline is provided. This article is part of a Special Issue entitled: Medical Proteomics.
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Affiliation(s)
- Andrei P Drabovich
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
| | | | - Eleftherios P Diamandis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada; Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
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Fuhrman-Luck RA, Silva ML, Dong Y, Irving-Rodgers H, Stoll T, Hastie ML, Loessner D, Gorman JJ, Clements JA. Proteomic and other analyses to determine the functional consequences of deregulated kallikrein-related peptidase (KLK) expression in prostate and ovarian cancer. Proteomics Clin Appl 2014; 8:403-15. [PMID: 24535680 DOI: 10.1002/prca.201300098] [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: 09/30/2013] [Revised: 11/23/2013] [Accepted: 11/30/2013] [Indexed: 02/06/2023]
Abstract
Rapidly developing proteomic tools are improving detection of deregulated kallikrein-related peptidase (KLK) expression, at the protein level, in prostate and ovarian cancer, as well as facilitating the determination of functional consequences downstream. MS-driven proteomics uniquely allows for the detection, identification, and quantification of thousands of proteins in a complex protein pool, and this has served to identify certain KLKs as biomarkers for these diseases. In this review, we describe applications of this technology in KLK biomarker discovery and elucidate MS-based techniques that have been used for unbiased, global screening of KLK substrates within complex protein pools. Although MS-based KLK degradomic studies are limited to date, they helped to discover an array of novel KLK substrates. Substrates identified by MS-based degradomics are reported with improved confidence over those determined by incubating a purified or recombinant substrate and protease of interest, in vitro. We propose that these novel proteomic approaches represent the way forward for KLK research, in order to correlate proteolysis of biological substrates with tissue-related consequences, toward clinical targeting of KLK expression and function for cancer diagnosis, prognosis, and therapies.
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Affiliation(s)
- Ruth Anna Fuhrman-Luck
- Institute of Health and Biomedical Innovation, Translational Research Institute, Queensland University of Technology, Brisbane, Australia; Australian Prostate Cancer Research Centre - Queensland, Translational Research Institute, Queensland University of Technology, Brisbane, Australia
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Freire-de-Lima L. Sweet and sour: the impact of differential glycosylation in cancer cells undergoing epithelial-mesenchymal transition. Front Oncol 2014; 4:59. [PMID: 24724053 PMCID: PMC3971198 DOI: 10.3389/fonc.2014.00059] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 03/11/2014] [Indexed: 01/11/2023] Open
Abstract
Glycosylation changes are a feature of disease states. One clear example is cancer cells, which commonly express glycans at atypical levels or with different structural attributes than those found in normal cells. Epithelial–mesenchymal transition (EMT) was initially recognized as an important step for morphogenesis during embryonic development, and is now shown to be one of the key steps promoting tumor metastasis. Cancer cells undergoing EMT are characterized by significant changes in glycosylation of the extracellular matrix (ECM) components and cell-surface glycoconjugates. Current scientific methodology enables all hallmarks of EMT to be monitored in vitro and this experimental model has been extensively used in oncology research during the last 10 years. Several studies have shown that cell-surface carbohydrates attached to proteins through the amino acids, serine, or threonine (O-glycans), are involved in tumor progression and metastasis, however, the impact of O-glycans on EMT is poorly understood. Recent studies have demonstrated that transforming growth factor-beta (TGF-β), a known EMT inducer, has the ability to promote the up-regulation of a site-specific O-glycosylation in the IIICS domain of human oncofetal fibronectin, a major ECM component expressed by cancer cells and embryonic tissues. Armed with the knowledge that cell-surface glycoconjugates play a major role in the maintenance of cell homeostasis and that EMT is closely associated with glycosylation changes, we may benefit from understanding how unusual glycans can govern the molecular pathways associated with cancer progression. This review initially focuses on some well-known changes found in O-glycans expressed by cancer cells, and then discusses how these alterations may modulate the EMT process.
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Affiliation(s)
- Leonardo Freire-de-Lima
- Laboratório de Glicobiologia, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro , Rio de Janeiro , RJ, Brazil
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Yang G, Cui T, Wang Y, Sun S, Ma T, Wang T, Chen Q, Li Z. Selective isolation and analysis of glycoprotein fractions and their glycomes from hepatocellular carcinoma sera. Proteomics 2013; 13:1481-98. [PMID: 23436760 DOI: 10.1002/pmic.201200259] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 01/29/2013] [Accepted: 02/12/2013] [Indexed: 01/20/2023]
Abstract
As one of the most important post-translational modifications, the discovery, isolation, and identification of glycoproteins are becoming increasingly important. In this study, a Con A-magnetic particle conjugate-based method was utilized to selectively isolate the glycoproteins and their glycomes from the healthy donor and hepatocellular carcinoma (HCC) case sera. The isolated glycoproteins and their N-linked glycans were identified by LC-ESI-MS/MS and MALDI-TOF/TOF-MS, respectively. A total of 93 glycoproteins from the healthy donors and 85 glycoproteins from the HCC cases were identified. There were 34 different glycoproteins shown between the healthy donors (21/34) and the HCC cases (13/34). Twenty-eight glycans from the healthy donors and 30 glycans from the HCC cases were detected and there were 22 different glycans shown between the healthy donors (10/22) and HCC cases (12/22). Among these glycoproteins, 50 were known to be N-linked glycoproteins and three novel glycopeptides from two predicted potential glycoproteins were discovered. Moreover, lectin blotting, Western blotting and lectin/glyco-antibody microarrays were applied to definitely elucidate the change of selective protein expressions and their glycosylation levels, the results indicated that the differences of the identified glycoproteins between the healthy donors and HCC cases were caused by the change of both protein expression and their glycosylation levels.
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Affiliation(s)
- Ganglong Yang
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, PR China
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31
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Parker BL, Thaysen-Andersen M, Solis N, Scott NE, Larsen MR, Graham ME, Packer NH, Cordwell SJ. Site-Specific Glycan-Peptide Analysis for Determination of N-Glycoproteome Heterogeneity. J Proteome Res 2013; 12:5791-800. [DOI: 10.1021/pr400783j] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Benjamin L. Parker
- Discipline
of Pathology, School of Medical Sciences, The University of Sydney, Sydney 2006, Australia
| | - Morten Thaysen-Andersen
- Department
of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde 2106, Australia
| | - Nestor Solis
- School
of Molecular Bioscience, The University of Sydney, Sydney 2006, Australia
| | - Nichollas E. Scott
- School
of Molecular Bioscience, The University of Sydney, Sydney 2006, Australia
| | - Martin R. Larsen
- Department of Biochemistry
and Molecular Biology, The University of Southern Denmark, DK-5230, Denmark
| | - Mark E. Graham
- Cell Signalling Unit, Children’s Medical Research Institute, Westmead 2145, Australia
| | - Nicolle H. Packer
- Department
of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde 2106, Australia
| | - Stuart J. Cordwell
- Discipline
of Pathology, School of Medical Sciences, The University of Sydney, Sydney 2006, Australia
- School
of Molecular Bioscience, The University of Sydney, Sydney 2006, Australia
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Hua S, Williams CC, Dimapasoc LM, Ro GS, Ozcan S, Miyamoto S, Lebrilla CB, An HJ, Leiserowitz GS. Isomer-specific chromatographic profiling yields highly sensitive and specific potential N-glycan biomarkers for epithelial ovarian cancer. J Chromatogr A 2013; 1279:58-67. [PMID: 23380366 PMCID: PMC5628020 DOI: 10.1016/j.chroma.2012.12.079] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2012] [Revised: 12/17/2012] [Accepted: 12/26/2012] [Indexed: 12/13/2022]
Abstract
Aberrant glycosylation has been observed for decades in essentially all types of cancer, and is now well established as an indicator of carcinogenesis. Mining the glycome for biomarkers, however, requires analytical methods that can rapidly separate, identify, and quantify isomeric glycans. We have developed a rapid-throughput method for chromatographic glycan profiling using microfluidic chip-based nanoflow liquid chromatography (nano-LC)/mass spectrometry. To demonstrate the utility of this method, we analyzed and compared serum samples from epithelial ovarian cancer cases (n=46) and healthy control individuals (n=48). Over 250 N-linked glycan compound peaks with over 100 distinct N-linked glycan compositions were identified. Statistical testing identified 26 potential glycan biomarkers based on both compositional and structure-specific analyses. Using these results, an optimized model was created incorporating the combined abundances of seven potential glycan biomarkers. The receiver operating characteristic (ROC) curve of this optimized model had an area under the curve (AUC) of 0.96, indicating robust discrimination between cancer cases and healthy controls. Rapid-throughput chromatographic glycan profiling was found to be an effective platform for structure-specific biomarker discovery.
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Affiliation(s)
- Serenus Hua
- Department of Chemistry, University of California, Davis, CA, USA
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33
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Abstract
Glycopeptide-based analysis is used to inform researchers about the glycans on one or more proteins. The method's key attractive feature is its ability to link glycosylation information to exact locations (glycosylation sites) on proteins. Numerous applications for glycopeptide analysis are known, and several examples are described herein. The techniques used to characterize glycopeptides are still emerging, and recently, research focused on facilitating aspects of glycopeptide analysis has advanced significantly in the areas of sample preparation, MS fragmentation, and automation of data analysis. These recent developments, described herein, provide the foundation for the growth of glycopeptide analysis as a blossoming field.
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Affiliation(s)
- Heather Desaire
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA.
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34
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Drake P, Schilling B, Gibson B, Fisher S. Elucidation of N-glycosites within human plasma glycoproteins for cancer biomarker discovery. Methods Mol Biol 2013; 951:307-322. [PMID: 23296540 DOI: 10.1007/978-1-62703-146-2_21] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Glycans are an important class of post-translational modifications that decorate a wide array of protein substrates. These cell-type specific molecules, which are modulated during developmental and disease processes, are attractive biomarker candidates as biology regarding altered glycosylation can be used to guide the experimental design. The mass spectrometry (MS)-based workflow described here incorporates chromatography on affinity matrices formed from lectins, proteins that bind specific glycan motifs. The goal was to design a relatively simple method for the rapid analysis of small plasma volumes (e.g., clinical specimens). As increases in sialylation and fucosylation are prominent among cancer-associated modifications, we focused on Sambucus nigra agglutinin and AAL, which bind sialic acid- and fucose-containing structures, respectively. Positive controls (fucosylated and sialylated human lactoferrin glycopeptides), and negative controls (high-mannose glycopeptides from Saccharomyces cerevisiae invertase) were used to monitor the specificity of lectin capture and optimize the workflow. Multiple Affinity Removal System 14-depleted, trypsin-digested human plasma from healthy donors served as the target analyte. Samples were loaded onto the lectin columns and separated by high performance liquid chromatography (HPLC) into flow through and bound fractions, which were treated with PNGase F, an amidase that removes N-linked glycans and marks the underlying asparagine glycosite by a +1 Da mass shift. The deglycosylated peptide fractions were interrogated by HPLC ESI-MS/MS on a quadrupole time-of-flight mass spectrometer. The method allowed identification of 122 human plasma glycoproteins containing 247 unique glycosites. Notably, glycoproteins that circulate at ng/mL levels (e.g., cadherin-5 at 0.3-4.9 ng/mL, and neutrophil gelatinase-associated lipocalin which is present at ∼2.5 ng/mL) were routinely observed, suggesting that this method enables the detection of low-abundance cancer-specific glycoproteins.
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Affiliation(s)
- Penelope Drake
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, CA, USA
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35
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Palmisano G, Larsen MR, Packer NH, Thaysen-Andersen M. Structural analysis of glycoprotein sialylation – part II: LC-MS based detection. RSC Adv 2013. [DOI: 10.1039/c3ra42969e] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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36
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Early detection biomarkers for ovarian cancer. JOURNAL OF ONCOLOGY 2012; 2012:709049. [PMID: 23319948 PMCID: PMC3540796 DOI: 10.1155/2012/709049] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 11/19/2012] [Indexed: 12/12/2022]
Abstract
Despite the widespread use of conventional and contemporary methods to detect ovarian cancer development, ovarian cancer remains a common and commonly fatal gynecological malignancy. The identification and validation of early detection biomarkers highly specific to ovarian cancer, which would permit development of minimally invasive screening methods for detecting early onset of the disease, are urgently needed. Current practices for early detection of ovarian cancer include transvaginal ultrasonography, biomarker analysis, or a combination of both. In this paper we review recent research on novel and robust biomarkers for early detection of ovarian cancer and provide specific details on their contributions to tumorigenesis. Promising biomarkers for early detection of ovarian cancer include KLK6/7, GSTT1, PRSS8, FOLR1, ALDH1, and miRNAs.
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37
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Shukla HD, Vaitiekunas P, Cotter RJ. Advances in membrane proteomics and cancer biomarker discovery: current status and future perspective. Proteomics 2012; 12:3085-104. [PMID: 22890602 DOI: 10.1002/pmic.201100519] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 07/05/2012] [Accepted: 07/27/2012] [Indexed: 02/06/2023]
Abstract
Membrane proteomic analysis has been proven to be a promising tool for identifying new and specific biomarkers that can be used for prognosis and monitoring of various cancers. Membrane proteins are of great interest particularly those with functional domains exposed to the extracellular environment. Integral membrane proteins represent about one-third of the proteins encoded by the human genome and assume a variety of key biological functions, such as cell-to-cell communication, receptor-mediated signal transduction, selective transport, and pharmacological actions. More than two-thirds of membrane proteins are drug targets, highlighting their immensely important pharmaceutical significance. Most plasma membrane proteins and proteins from other cellular membranes have several PTMs; for example, glycosylation, phosphorylation, and nitrosylation, and moreover, PTMs of proteins are known to play a key role in tumor biology. These modifications often cause change in stoichiometry and microheterogeneity in a protein molecule, which is apparent during electrophoretic separation. Furthermore, the analysis of glyco- and phosphoproteome of cell membrane presents a number of challenges mainly due to their low abundance, their large dynamic range, and the inherent hydrophobicity of membrane proteins. Under pathological conditions, PTMs, such as phosphorylation and glycosylation are frequently altered and have been recognized as a potential source for disease biomarkers. Thus, their accurate differential expression analysis, along with differential PTM analysis is of paramount importance. Here we summarize the current status of membrane-based biomarkers in various cancers, and future perspective of membrane biomarker research.
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Affiliation(s)
- Hem D Shukla
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.
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38
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Kuzmanov U, Smith CR, Batruch I, Soosaipillai A, Diamandis A, Diamandis EP. Separation of kallikrein 6 glycoprotein subpopulations in biological fluids by anion-exchange chromatography coupled to ELISA and identification by mass spectrometry. Proteomics 2012; 12:799-809. [PMID: 22539431 DOI: 10.1002/pmic.201100371] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Kallikrein 6 (KLK6) has been shown to be aberrantly glycosylated in ovarian cancer. Here, we report a novel HPLC anion exchange method, coupled to a KLK6-specific ELISA, capable of differentiating KLK6 glycoform subgroups in biological fluids. Biological fluids were fractionated using anion exchange and resulting fractions were analyzed for KLK6 content by ELISA producing a four-peak elution profile. Using this assay, the KLK6 elution profile and distribution across peaks of a set (n = 7) of ovarian cancer patient matched serum and ascites fluid samples was found to be different than the profile of serum and cerebrospinal fluid (CSF) of normal individuals (n = 7). Glycosylation patterns of recombinant KLK6 (rKLK6) were characterized using tandem mass spectrometry (MS/MS), and found to consist of a highly heterogeneous KLK6 population. This protein was found to contain all of the four diagnostic KLK6 peaks present in the previously assayed biological fluids. The rKLK6 glycoform composition of each peak was assessed by lectin affinity and MS/MS based glycopeptide quantification by product ion monitoring. The combined results showed an increase in terminal alpha 2-6 linked sialic acid in the N-glycans found on KLK6 from ovarian cancer serum and ascites, as opposed to CSF and serum of normal individuals.
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Affiliation(s)
- Uros Kuzmanov
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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39
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Mai J, Sommer GJ, Hatch AV. Microfluidic digital isoelectric fractionation for rapid multidimensional glycoprotein analysis. Anal Chem 2012; 84:3538-45. [PMID: 22409593 DOI: 10.1021/ac203076p] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Here we present an integrated microfluidic device for rapid and automated isolation and quantification of glycoprotein biomarkers directly from biological samples on a multidimensional analysis platform. In the first dimension, digital isoelectric fractionation (dIEF) uses discrete pH-specific membranes to separate proteins and their isoforms into precise bins in a highly flexible spatial arrangement on-chip. dIEF provides high sample preconcentration factors followed by immediate high-fidelity transfer of fractions for downstream analysis. We successfully fractionate isoforms of two potential glycoprotein cancer markers, fetuin and prostate-specific antigen (PSA), with 10 min run time, and results are compared qualitatively and quantitatively to conventional slab gel IEF. In the second dimension, functionalized monolithic columns are used to capture and detect targeted analytes from each fraction. We demonstrate rapid two-dimensional fractionation, immunocapture, and detection of C-reactive protein (CRP) spiked in human serum. This rapid, flexible, and automated approach is well-suited for glycoprotein biomarker research and verification studies and represents a practical avenue for glycoprotein isoform-based diagnostic testing.
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Affiliation(s)
- Junyu Mai
- Department of Biotechnology and Bioengineering, Sandia National Laboratories, Livermore, California 94551, United States
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40
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Hiss D. Optimizing molecular-targeted therapies in ovarian cancer: the renewed surge of interest in ovarian cancer biomarkers and cell signaling pathways. JOURNAL OF ONCOLOGY 2012; 2012:737981. [PMID: 22481932 PMCID: PMC3306947 DOI: 10.1155/2012/737981] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 11/24/2011] [Indexed: 12/18/2022]
Abstract
The hallmarks of ovarian cancer encompass the development of resistance, disease recurrence and poor prognosis. Ovarian cancer cells express gene signatures which pose significant challenges for cancer drug development, therapeutics, prevention and management. Despite enhancements in contemporary tumor debulking surgery, tentative combination regimens and abdominal radiation which can achieve beneficial response rates, the majority of ovarian cancer patients not only experience adverse effects, but also eventually relapse. Therefore, additional therapeutic possibilities need to be explored to minimize adverse events and prolong progression-free and overall response rates in ovarian cancer patients. Currently, a revival in cancer drug discovery is devoted to identifying diagnostic and prognostic ovarian cancer biomarkers. However, the sensitivity and reliability of such biomarkers may be complicated by mutations in the BRCA1 or BRCA2 genes, diverse genetic risk factors, unidentified initiation and progression elements, molecular tumor heterogeneity and disease staging. There is thus a dire need to expand existing ovarian cancer therapies with broad-spectrum and individualized molecular targeted approaches. The aim of this review is to profile recent developments in our understanding of the interrelationships among selected ovarian tumor biomarkers, heterogeneous expression signatures and related molecular signal transduction pathways, and their translation into more efficacious targeted treatment rationales.
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Affiliation(s)
- Donavon Hiss
- Molecular Oncology Research Laboratory, Department of Medical BioSciences, University of the Western Cape, Bellville 7535, South Africa
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41
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Hart-Smith G, Raftery MJ. Detection and characterization of low abundance glycopeptides via higher-energy C-trap dissociation and orbitrap mass analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:124-140. [PMID: 22083589 DOI: 10.1007/s13361-011-0273-y] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 10/05/2011] [Accepted: 10/06/2011] [Indexed: 05/31/2023]
Abstract
Broad-scale mass spectrometric analyses of glycopeptides are constrained by the considerable complexity inherent to glycoproteomics, and techniques are still being actively developed to address the associated analytical difficulties. Here we apply Orbitrap mass analysis and higher-energy C-trap dissociation (HCD) to facilitate detailed insights into the compositions and heterogeneity of complex mixtures of low abundance glycopeptides. By generating diagnostic oxonium product ions at mass measurement errors of <5 ppm, highly selective glycopeptide precursor ion detections are made at sub-fmol limits of detection: analyses of proteolytic digests of a hen egg glycoprotein mixture detect 88 previously uncharacterized glycopeptides from 666 precursor ions selected for MS/MS, with only one false positive due to co-fragmentation of a non-glycosylated peptide with a glycopeptide. We also demonstrate that by (1) identifying multiple series of glycoforms using high mass accuracy single stage MS spectra, and (2) performing product ion scans at optimized HCD collision energies, the identification of peptide + N-acetylhexosamine (HexNAc) ions (Y1 ions) can be readily achieved at <5 ppm mass measurement errors. These data allow base peptide sequences and glycan compositional information to be attained with high confidence, even for glycopeptides that produce weak precursor ion signals and/or low quality MS/MS spectra. The glycopeptides characterized from low fmol abundances using these methods allow two previously unreported glycosylation sites on the Gallus gallus protein ovoglycoprotein (amino acids 82 and 90) to be confirmed; considerable glycan heterogeneities at amino acid 90 of ovoglycoprotein, and amino acids 34 and 77 of Gallus gallus ovomucoid are also revealed.
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Affiliation(s)
- Gene Hart-Smith
- NSW Systems Biology Initiative, University of New South Wales, Sydney, New South Wales 2052, Australia.
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42
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Bayani J, Diamandis EP. The physiology and pathobiology of human kallikrein-related peptidase 6 (KLK6). Clin Chem Lab Med 2011; 50:211-33. [PMID: 22047144 DOI: 10.1515/cclm.2011.750] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 09/21/2011] [Indexed: 12/11/2022]
Abstract
The human kallikrein-related peptidase 6 (KLK6) gene belongs to the 15-member kallikrein (KLK) gene family mapping to chromosome 19q13.3-13.4. Encoding for an enzyme with trypsin-like properties, KLK6 can degrade components of the extracellular matrix. The successful utilisation of another KLK member (KLK3/PSA) for prostate cancer diagnosis has led many to evaluate KLK6 as a potential biomarker for other cancer and diseased states. The observed dysregulated expression in cancers, neurodegenerative diseases and skin conditions has led to the discovery that KLK6 participates in other cellular pathways including inflammation, receptor activation and regulation of apoptosis. Moreover, the improvements in high-throughput genomics have not only enabled the identification of sequence polymorphisms, but of transcript variants, whose functional significances have yet to be realised. This comprehensive review will summarise the current findings of KLK6 pathophysiology and discuss its potential as a viable biomarker.
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Affiliation(s)
- Jane Bayani
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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43
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Zhu P, Bowden P, Zhang D, Marshall JG. Mass spectrometry of peptides and proteins from human blood. MASS SPECTROMETRY REVIEWS 2011; 30:685-732. [PMID: 24737629 DOI: 10.1002/mas.20291] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 12/09/2009] [Accepted: 01/19/2010] [Indexed: 06/03/2023]
Abstract
It is difficult to convey the accelerating rate and growing importance of mass spectrometry applications to human blood proteins and peptides. Mass spectrometry can rapidly detect and identify the ionizable peptides from the proteins in a simple mixture and reveal many of their post-translational modifications. However, blood is a complex mixture that may contain many proteins first expressed in cells and tissues. The complete analysis of blood proteins is a daunting task that will rely on a wide range of disciplines from physics, chemistry, biochemistry, genetics, electromagnetic instrumentation, mathematics and computation. Therefore the comprehensive discovery and analysis of blood proteins will rank among the great technical challenges and require the cumulative sum of many of mankind's scientific achievements together. A variety of methods have been used to fractionate, analyze and identify proteins from blood, each yielding a small piece of the whole and throwing the great size of the task into sharp relief. The approaches attempted to date clearly indicate that enumerating the proteins and peptides of blood can be accomplished. There is no doubt that the mass spectrometry of blood will be crucial to the discovery and analysis of proteins, enzyme activities, and post-translational processes that underlay the mechanisms of disease. At present both discovery and quantification of proteins from blood are commonly reaching sensitivities of ∼1 ng/mL.
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Affiliation(s)
- Peihong Zhu
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, Ontario, Canada M5B 2K3
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44
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Wang D, Hincapie M, Rejtar T, Karger BL. Ultrasensitive characterization of site-specific glycosylation of affinity-purified haptoglobin from lung cancer patient plasma using 10 μm i.d. porous layer open tubular liquid chromatography-linear ion trap collision-induced dissociation/electron transfer dissociation mass spectrometry. Anal Chem 2011; 83:2029-37. [PMID: 21338062 PMCID: PMC3073582 DOI: 10.1021/ac102825g] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Site-specific analysis of protein glycosylation is important for biochemical and clinical research efforts. Glycopeptide analysis using liquid chromatography-collision-induced dissociation/electron transfer dissociation mass spectrometry (LC-CID/ETD-MS) allows simultaneous characterization of the glycan structure and attached peptide site. However, due to the low ionization efficiency of glycopeptides during electrospray ionization, 200-500 fmol of sample per injection is needed for a single LC-MS run, which makes it challenging for the analysis of limited amounts of glycoprotein purified from biological matrixes. To improve the sensitivity of LC-MS analysis for glycopeptides, an ultranarrow porous layer open tubular (PLOT) LC column (2.5 m × 10 μm i.d.) was coupled to a linear ion trap (LTQ) collision-induced dissociation/electron transfer dissociation mass spectrometer to provide sensitive analysis of N-linked protein glycosylation heterogeneity. The potential of the developed method is demonstrated by the characterization of site-specific glycosylation using haptoglobin (Hpt) as a model protein. To limit the amount of haptoglobin to low picomole amounts of protein, we affinity purified it from 1 μL of pooled lung cancer patient plasma. A total of 26 glycoforms/glycan compositions on three Hpt tryptic glycopeptides were identified and quantified from 10 LC-MS runs with a consumption of 100 fmol of Hpt digest (13 ng of protein, 10 fmol per injection). Included in this analysis was the determination of the glycan occupancy level. At this sample consumption level, the high sensitivity of the PLOT LC-LTQ-CID/ETD-MS system allowed glycopeptide identification and structure determination, along with relative quantitation of glycans presented on the same peptide backbone, even for low abundant glycopeptides at the ∼100 amol level. The PLOT LC-MS system is shown to have sufficient sensitivity to allow characterization of site-specific protein glycosylation from trace levels of glycosylated proteins.
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Affiliation(s)
- Dongdong Wang
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115
| | - Marina Hincapie
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115
| | - Tomas Rejtar
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115
| | - Barry L. Karger
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115
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45
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Avgeris M, Mavridis K, Scorilas A. Kallikrein-related peptidase genes as promising biomarkers for prognosis and monitoring of human malignancies. Biol Chem 2010; 391:505-11. [PMID: 20302518 DOI: 10.1515/bc.2010.056] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Tissue kallikrein (KLK1) and the kallikrein-related peptidase (KLK2-15) genes encode for a subgroup of 15 homologous secreted serine proteases possessing numerous physiological roles, such as the regulation of blood pressure, hormone processing and tissue remodeling. The expression of KLKs is detected in a broad spectrum of human tissues where it has been found to be regulated mainly by steroids hormones. The aberrant expression of KLKs, presented in many human malignancies, highlights the significance of this gene family for early diagnosis, prognosis and monitoring of cancer patients, as it is strongly emphasized by the routine use of PSA (KLK3) for prostate cancer management. Here, we review the presently known data regarding the role of KLKs as cancer biomarkers, giving emphasis on novel information about the subject.
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Affiliation(s)
- Margaritis Avgeris
- Department of Biochemistry and Molecular Biology, University of Athens, Greece
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46
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Mavridis K, Scorilas A. Prognostic value and biological role of the kallikrein-related peptidases in human malignancies. Future Oncol 2010; 6:269-85. [PMID: 20146586 DOI: 10.2217/fon.09.149] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Cancer is a substantial health problem for the populations of the Western world. The discovery of new molecular biomarkers for diagnosis, prognosis and monitoring patients' response to therapy can aid in combating this complicated disease. The human kallikrein-related peptidases (human tissue kallikreins [KLKs]) are encoded by a continuous multigene family, located on chromosomal region 19q13.3-4. KLK3 (prostate-specific antigen) is the most efficient cancer biomarker ever employed. KLK genes are expressed abnormally in various malignancies, where they affect cancer-cell growth and metastasis. Their deregulated expression pattern, often associated with various clinicopathological characteristics of cancer patients, can be exploited, solely or within multiparametric panels, as a prognostic biomarker. Recent data illustrate that discernible molecular modulations of KLKs, occurring as a result of cancer cells' treatment with antitumor agents, may serve as new potential biomarkers, possibly predicting patients' treatment response. It is believed that KLKs might be employed in future clinical practice as novel and effective tumor markers.
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Affiliation(s)
- Konstantinos Mavridis
- Department of Biochemistry & Molecular Biology, University of Athens, Athens, Greece.
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47
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Segu ZM, Mechref Y. Characterizing protein glycosylation sites through higher-energy C-trap dissociation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:1217-1225. [PMID: 20391591 DOI: 10.1002/rcm.4485] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Assigning glycosylation sites of glycoproteins and their microheterogeneity is still a very challenging analytical task despite the rapid advancements in mass spectrometry. It is shown here that glycopeptide ions can be fragmented efficiently using the higher-energy C-trap dissociation (HCD) feature of a linear ion trap orbitrap hybrid mass spectrometer (LTQ Orbitrap). An attractive aspect of this dissociation option is the generation of distinct Y1 ions (peptide+GlcNAc), thus allowing unequivocal assignment of N-glycosylation sites of glycoproteins. The combination of the very informative collision-induced dissociation spectra acquired in the linear ion trap with the distinct features of HCD offers very useful information aiding in the characterization of the glycosylation sites of glycoproteins. The HCD activation energy needed to obtain optimum Y1 ions was studied in terms of glycan structure and charge state, and size and structure of the peptide backbone. The latter appeared to be primarily dictating the needed HCD energy. The distinct Y1 ion formation in HCD facilitated an easy assignment of such an ion and its subsequent isolation and dissociation through multiple-stage tandem mass spectrometry. The resulting MS(3) spectrum of the Y1 ion facilitates database searching and de novo sequencing thus prompting the subsequent identification of the peptide backbone and associated glycosylation sites. Moreover, fragment ions formed by HCD are detected in the Orbitrap, thus overcoming the 1/3 cut-off limitation that is commonly associated with ion trap mass spectrometers. As a result, in addition to the Y1 ion, the common glycan oxonium ions are also detected. The high mass accuracy offered by the LTQ Orbitrap mass spectrometer is also an attractive feature that allows a confident assignment of protein glycosylation sites and the microheterogeneity of such sites.
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Affiliation(s)
- Zaneer M Segu
- METACyt Biochemical Analysis Center, Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
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48
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Drake PM, Cho W, Li B, Prakobphol A, Johansen E, Anderson NL, Regnier FE, Gibson BW, Fisher SJ. Sweetening the pot: adding glycosylation to the biomarker discovery equation. Clin Chem 2009; 56:223-36. [PMID: 19959616 DOI: 10.1373/clinchem.2009.136333] [Citation(s) in RCA: 235] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
BACKGROUND Cancer has profound effects on gene expression, including a cell's glycosylation machinery. Thus, tumors produce glycoproteins that carry oligosaccharides with structures that are markedly different from the same protein produced by a normal cell. A single protein can have many glycosylation sites that greatly amplify the signals they generate compared with their protein backbones. CONTENT In this article, we survey clinical tests that target carbohydrate modifications for diagnosing and treating cancer. We present the biological relevance of glycosylation to disease progression by highlighting the role these structures play in adhesion, signaling, and metastasis and then address current methodological approaches to biomarker discovery that capitalize on selectively capturing tumor-associated glycoforms to enrich and identify disease-related candidate analytes. Finally, we discuss emerging technologies--multiple reaction monitoring and lectin-antibody arrays--as potential tools for biomarker validation studies in pursuit of clinically useful tests. SUMMARY The future of carbohydrate-based biomarker studies has arrived. At all stages, from discovery through verification and deployment into clinics, glycosylation should be considered a primary readout or a way of increasing the sensitivity and specificity of protein-based analyses.
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49
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Darula Z, Medzihradszky KF. Affinity enrichment and characterization of mucin core-1 type glycopeptides from bovine serum. Mol Cell Proteomics 2009; 8:2515-26. [PMID: 19674964 DOI: 10.1074/mcp.m900211-mcp200] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The lack of consensus sequence, common core structure, and universal endoglycosidase for the release of O-linked oligosaccharides makes O-glycosylation more difficult to tackle than N-glycosylation. Structural elucidation by mass spectrometry is usually inconclusive as the CID spectra of most glycopeptides are dominated by carbohydrate-related fragments, preventing peptide identification. In addition, O-linked structures also undergo a gas-phase rearrangement reaction, which eliminates the sugar without leaving a telltale sign at its former attachment site. In the present study we report the enrichment and mass spectrometric analysis of proteins from bovine serum bearing Galbeta1-3GalNAcalpha (mucin core-1 type) structures and the analysis of O-linked glycopeptides utilizing electron transfer dissociation and high resolution, high mass accuracy precursor ion measurements. Electron transfer dissociation (ETD) analysis of intact glycopeptides provided sufficient information for the identification of several glycosylation sites. However, glycopeptides frequently feature precursor ions of low charge density (m/z > approximately 850) that will not undergo efficient ETD fragmentation. Exoglycosidase digestion was utilized to reduce the mass of the molecules while retaining their charge. ETD analysis of species modified by a single GalNAc at each site was significantly more successful in the characterization of multiply modified molecules. We report the unambiguous identification of 21 novel glycosylation sites. We also detail the limitations of the enrichment method as well as the ETD analysis.
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Affiliation(s)
- Zsuzsanna Darula
- Proteomics Research Group, Biological Research Center of the Hungarian Academy of Sciences, Szeged P. O. Box 521, Szeged H-6701, Hungary
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