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Pradita T, Chen YJ, Su TH, Chang KH, Chen PJ, Chen YJ. Data Independent Acquisition Mass Spectrometry Enhanced Personalized Glycosylation Profiling of Haptoglobin in Hepatocellular Carcinoma. J Proteome Res 2024; 23:3571-3584. [PMID: 38994555 PMCID: PMC11301664 DOI: 10.1021/acs.jproteome.4c00227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/13/2024]
Abstract
Aberrant glycosylation has gained significant interest for biomarker discovery. However, low detectability, complex glycan structures, and heterogeneity present challenges in glycoprotein assay development. Using haptoglobin (Hp) as a model, we developed an integrated platform combining functionalized magnetic nanoparticles and zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC) for highly specific glycopeptide enrichment, followed by a data-independent acquisition (DIA) strategy to establish a deep cancer-specific Hp-glycosylation profile in hepatitis B virus (HBV, n = 5) and hepatocellular carcinoma (HCC, n = 5) patients. The DIA strategy established one of the deepest Hp-glycosylation landscapes (1029 glycopeptides, 130 glycans) across serum samples, including 54 glycopeptides exclusively detected in HCC patients. Additionally, single-shot DIA searches against a DIA-based spectral library outperformed the DDA approach by 2-3-fold glycopeptide coverage across patients. Among the four N-glycan sites on Hp (N-184, N-207, N-211, N-241), the total glycan type distribution revealed significantly enhanced detection of combined fucosylated-sialylated glycans, which were the most dominant glycoforms identified in HCC patients. Quantitation analysis revealed 48 glycopeptides significantly enriched in HCC (p < 0.05), including a hybrid monosialylated triantennary glycopeptide on the N-184 site with nearly none-to-all elevation to differentiate HCC from the HBV group (HCC/HBV ratio: 2462 ± 766, p < 0.05). In summary, DIA-MS presents an unbiased and comprehensive alternative for targeted glycoproteomics to guide discovery and validation of glyco-biomarkers.
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Affiliation(s)
- Tiara Pradita
- Institute
of Chemistry, Academia Sinica, Taipei 115, Taiwan
- Sustainable
Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan
- Department
of Applied Chemistry, National Yang Ming
Chiao Tung University, Hsinchu 300, Taiwan
| | - Yi-Ju Chen
- Institute
of Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Tung-Hung Su
- Division
of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei 100, Taiwan
- Hepatitis
Research Center, National Taiwan University
Hospital, Taipei 100, Taiwan
| | - Kun-Hao Chang
- Institute
of Chemistry, Academia Sinica, Taipei 115, Taiwan
- Molecular
Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan
- Department
of Chemistry, National Tsing-Hua University, Hsinchu 300, Taiwan
| | - Pei-Jer Chen
- Division
of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei 100, Taiwan
- Hepatitis
Research Center, National Taiwan University
Hospital, Taipei 100, Taiwan
- Graduate
Institute of Clinical Medicine, National
Taiwan University College of Medicine, Taipei 100, Taiwan
- Department
of Medical Research, National Taiwan University
Hospital, Taipei 100, Taiwan
| | - Yu-Ju Chen
- Institute
of Chemistry, Academia Sinica, Taipei 115, Taiwan
- Sustainable
Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan
- Department
of Chemistry, National Taiwan University, Taipei 106, Taiwan
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Elhassan EA, Kmochová T, Benson KA, Fennelly NK, Barešová V, Kidd K, Doyle B, Dorman A, Morrin MM, Kyne NC, Vyleťal P, Hartmannová H, Hodaňová K, Sovová J, Mušálková D, Vrbacká A, Přistoupilová A, Živný J, Svojšová K, Radina M, Stránecký V, Loginov D, Pompach P, Novák P, Vaníčková Z, Hansíková H, Rajnochová-Bloudíčková S, Viklický O, Hůlková H, Cavalleri GL, Hnízda A, Bleyer AJ, Kmoch S, Conlon PJ, Živná M. A Novel Monoallelic ALG5 Variant Causing Late-Onset ADPKD and Tubulointerstitial Fibrosis. Kidney Int Rep 2024; 9:2209-2226. [PMID: 39081747 PMCID: PMC11284371 DOI: 10.1016/j.ekir.2024.04.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/02/2024] [Accepted: 04/08/2024] [Indexed: 08/02/2024] Open
Abstract
Introduction Monoallelic variants in the ALG5 gene encoding asparagine-linked glycosylation protein 5 homolog (ALG5) have been recently shown to disrupt polycystin-1 (PC1) maturation and trafficking via underglycosylation, causing an autosomal dominant polycystic kidney disease-like (ADPKD-like) phenotype and interstitial fibrosis. In this report, we present clinical, genetic, histopathologic, and protein structure and functional correlates of a new ALG5 variant, p.R79W, that we identified in 2 distant genetically related Irish families displaying an atypical late-onset ADPKD phenotype combined with tubulointerstitial damage. Methods Whole exome and targeted sequencing were used for segregation analysis of available relatives. This was followed by immunohistochemistry examinations of kidney biopsies, and targeted (UMOD, MUC1) and untargeted plasma proteome and N-glycomic studies. Results We identified a monoallelic ALG5 variant [GRCh37 (NM_013338.5): g.37569565G>A, c.235C>T; p.R79W] that cosegregates in 23 individuals, of whom 18 were clinically affected. We detected abnormal localization of ALG5 in the Golgi apparatus of renal tubular cells in patients' kidney specimens. Further, we detected the pathological accumulation of uromodulin, an N-glycosylated glycosylphosphatidylinositol (GPI)-anchored protein, in the endoplasmic reticulum (ER), but not mucin-1, an O- and N-glycosylated protein. Biochemical investigation revealed decreased plasma and urinary uromodulin levels in clinically affected individuals. Proteomic and glycoproteomic profiling revealed the dysregulation of chronic kidney disease (CKD)-associated proteins. Conclusion ALG5 dysfunction adversely affects maturation and trafficking of N-glycosylated and GPI anchored protein uromodulin, leading to structural and functional changes in the kidney. Our findings confirm ALG5 as a cause of late-onset ADPKD and provide additional insight into the molecular mechanisms of ADPKD-ALG5.
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Affiliation(s)
- Elhussein A.E. Elhassan
- Department of Nephrology and Transplantation, Beaumont Hospital, Dublin, Ireland
- Department of Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Tereza Kmochová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Katherine A. Benson
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons, Dublin, Ireland
| | | | - Veronika Barešová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Kendrah Kidd
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Brendan Doyle
- Department of Pathology, Beaumont Hospital, Dublin, Ireland
| | - Anthony Dorman
- Department of Pathology, Beaumont Hospital, Dublin, Ireland
| | - Martina M. Morrin
- Department of Radiology, Beaumont Hospital and Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Niamh C. Kyne
- Department of Nephrology and Transplantation, Beaumont Hospital, Dublin, Ireland
| | - Petr Vyleťal
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Hana Hartmannová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Kateřina Hodaňová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Jana Sovová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Dita Mušálková
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Alena Vrbacká
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Anna Přistoupilová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Jan Živný
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Klára Svojšová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Martin Radina
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Viktor Stránecký
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Dmitry Loginov
- Institute of Microbiology, The Czech Academy of Sciences, Vestec, Czech Republic
| | - Petr Pompach
- Institute of Microbiology, The Czech Academy of Sciences, Vestec, Czech Republic
| | - Petr Novák
- Institute of Microbiology, The Czech Academy of Sciences, Vestec, Czech Republic
| | - Zdislava Vaníčková
- Institute of Medical Biochemistry and Laboratory Diagnostics of the General University Hospital and of The First Faculty of medicine of Charles University in Prague, Prague, Czech Republic
| | - Hana Hansíková
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Silvie Rajnochová-Bloudíčková
- Department of Nephrology, Transplant Center, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Ondřej Viklický
- Department of Nephrology, Transplant Center, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Helena Hůlková
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Gianpiero L. Cavalleri
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons, Dublin, Ireland
| | - Aleš Hnízda
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Anthony J. Bleyer
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Stanislav Kmoch
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Peter J. Conlon
- Department of Nephrology and Transplantation, Beaumont Hospital, Dublin, Ireland
- Department of Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Martina Živná
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
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Soares J, Eiras M, Ferreira D, Santos DAR, Relvas-Santos M, Santos B, Gonçalves M, Ferreira E, Vieira R, Afonso LP, Santos LL, Dinis-Ribeiro M, Lima L, Ferreira JA. Stool Glycoproteomics Signatures of Pre-Cancerous Lesions and Colorectal Cancer. Int J Mol Sci 2024; 25:3722. [PMID: 38612533 PMCID: PMC11012158 DOI: 10.3390/ijms25073722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024] Open
Abstract
Colorectal cancer (CRC) screening relies primarily on stool analysis to identify occult blood. However, its sensitivity for detecting precancerous lesions is limited, requiring the development of new tools to improve CRC screening. Carcinogenesis involves significant alterations in mucosal epithelium glycocalyx that decisively contribute to disease progression. Building on this knowledge, we examined patient series comprehending premalignant lesions, colorectal tumors, and healthy controls for the T-antigen-a short-chain O-glycosylation of proteins considered a surrogate marker of malignancy in multiple solid cancers. We found the T-antigen in the secretions of dysplastic lesions as well as in cancer. In CRC, T-antigen expression was associated with the presence of distant metastases. In parallel, we analyzed a broad number of stools from individuals who underwent colonoscopy, which showed high T expressions in high-grade dysplasia and carcinomas. Employing mass spectrometry-based lectin-affinity enrichment, we identified a total of 262 proteins, 67% of which potentially exhibited altered glycosylation patterns associated with cancer and advanced pre-cancerous lesions. Also, we found that the stool (glyco)proteome of pre-cancerous lesions is enriched for protein species involved in key biological processes linked to humoral and innate immune responses. This study offers a thorough analysis of the stool glycoproteome, laying the groundwork for harnessing glycosylation alterations to improve non-invasive cancer detection.
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Affiliation(s)
- Janine Soares
- Experimental Pathology and Therapeutics Group, Research Center of IPO Porto (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; (J.S.); (M.E.); (D.F.); (D.A.R.S.); (M.R.-S.); (B.S.); (M.G.); (E.F.); (L.P.A.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- REQUIMTE-LAQV, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Mariana Eiras
- Experimental Pathology and Therapeutics Group, Research Center of IPO Porto (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; (J.S.); (M.E.); (D.F.); (D.A.R.S.); (M.R.-S.); (B.S.); (M.G.); (E.F.); (L.P.A.); (L.L.S.)
| | - Dylan Ferreira
- Experimental Pathology and Therapeutics Group, Research Center of IPO Porto (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; (J.S.); (M.E.); (D.F.); (D.A.R.S.); (M.R.-S.); (B.S.); (M.G.); (E.F.); (L.P.A.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- Center for Applied Medical Research, University of Navarra, 31008 Pamplona, Spain
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- INEB-Instituto Nacional de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
| | - Daniela A. R. Santos
- Experimental Pathology and Therapeutics Group, Research Center of IPO Porto (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; (J.S.); (M.E.); (D.F.); (D.A.R.S.); (M.R.-S.); (B.S.); (M.G.); (E.F.); (L.P.A.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- Faculty of Medicine (FMUP), University of Porto, 4200-072 Porto, Portugal;
| | - Marta Relvas-Santos
- Experimental Pathology and Therapeutics Group, Research Center of IPO Porto (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; (J.S.); (M.E.); (D.F.); (D.A.R.S.); (M.R.-S.); (B.S.); (M.G.); (E.F.); (L.P.A.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- INEB-Instituto Nacional de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
- REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Beatriz Santos
- Experimental Pathology and Therapeutics Group, Research Center of IPO Porto (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; (J.S.); (M.E.); (D.F.); (D.A.R.S.); (M.R.-S.); (B.S.); (M.G.); (E.F.); (L.P.A.); (L.L.S.)
| | - Martina Gonçalves
- Experimental Pathology and Therapeutics Group, Research Center of IPO Porto (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; (J.S.); (M.E.); (D.F.); (D.A.R.S.); (M.R.-S.); (B.S.); (M.G.); (E.F.); (L.P.A.); (L.L.S.)
| | - Eduardo Ferreira
- Experimental Pathology and Therapeutics Group, Research Center of IPO Porto (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; (J.S.); (M.E.); (D.F.); (D.A.R.S.); (M.R.-S.); (B.S.); (M.G.); (E.F.); (L.P.A.); (L.L.S.)
| | - Renata Vieira
- Department of Pathology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal;
| | - Luís Pedro Afonso
- Experimental Pathology and Therapeutics Group, Research Center of IPO Porto (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; (J.S.); (M.E.); (D.F.); (D.A.R.S.); (M.R.-S.); (B.S.); (M.G.); (E.F.); (L.P.A.); (L.L.S.)
- Department of Pathology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal;
| | - Lúcio Lara Santos
- Experimental Pathology and Therapeutics Group, Research Center of IPO Porto (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; (J.S.); (M.E.); (D.F.); (D.A.R.S.); (M.R.-S.); (B.S.); (M.G.); (E.F.); (L.P.A.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- FF-I3ID, University Fernando Pessoa, 4249-004 Porto, Portugal
- GlycoMatters Biotech, 4500-162 Espinho, Portugal
- Department of Surgical Oncology, Portuguese Oncology Institute of Porto (IPO-Porto), 4200-072 Porto, Portugal
| | - Mário Dinis-Ribeiro
- Faculty of Medicine (FMUP), University of Porto, 4200-072 Porto, Portugal;
- Precancerous Lesions and Early Cancer Management Group, Research Center of IPO Porto (CI-IPOP), Rise@CI-IPOP (Health Research Group), Portuguese Institute of Oncology of Porto (IPO Porto), Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal
- Department of Gastroenterology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal
| | - Luís Lima
- Experimental Pathology and Therapeutics Group, Research Center of IPO Porto (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; (J.S.); (M.E.); (D.F.); (D.A.R.S.); (M.R.-S.); (B.S.); (M.G.); (E.F.); (L.P.A.); (L.L.S.)
| | - José Alexandre Ferreira
- Experimental Pathology and Therapeutics Group, Research Center of IPO Porto (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; (J.S.); (M.E.); (D.F.); (D.A.R.S.); (M.R.-S.); (B.S.); (M.G.); (E.F.); (L.P.A.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- GlycoMatters Biotech, 4500-162 Espinho, Portugal
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He K, Baniasad M, Kwon H, Caval T, Xu G, Lebrilla C, Hommes DW, Bertozzi C. Decoding the glycoproteome: a new frontier for biomarker discovery in cancer. J Hematol Oncol 2024; 17:12. [PMID: 38515194 PMCID: PMC10958865 DOI: 10.1186/s13045-024-01532-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 03/04/2024] [Indexed: 03/23/2024] Open
Abstract
Cancer early detection and treatment response prediction continue to pose significant challenges. Cancer liquid biopsies focusing on detecting circulating tumor cells (CTCs) and DNA (ctDNA) have shown enormous potential due to their non-invasive nature and the implications in precision cancer management. Recently, liquid biopsy has been further expanded to profile glycoproteins, which are the products of post-translational modifications of proteins and play key roles in both normal and pathological processes, including cancers. The advancements in chemical and mass spectrometry-based technologies and artificial intelligence-based platforms have enabled extensive studies of cancer and organ-specific changes in glycans and glycoproteins through glycomics and glycoproteomics. Glycoproteomic analysis has emerged as a promising tool for biomarker discovery and development in early detection of cancers and prediction of treatment efficacy including response to immunotherapies. These biomarkers could play a crucial role in aiding in early intervention and personalized therapy decisions. In this review, we summarize the significant advance in cancer glycoproteomic biomarker studies and the promise and challenges in integration into clinical practice to improve cancer patient care.
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Affiliation(s)
- Kai He
- James Comprehensive Cancer Center, The Ohio State University, Columbus, USA.
| | | | - Hyunwoo Kwon
- James Comprehensive Cancer Center, The Ohio State University, Columbus, USA
| | | | - Gege Xu
- InterVenn Biosciences, South San Francisco, USA
| | - Carlito Lebrilla
- Department of Biochemistry and Molecular Medicine, UC Davis Health, Sacramento, USA
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Zhu Y. Plasma/Serum Proteomics based on Mass Spectrometry. Protein Pept Lett 2024; 31:192-208. [PMID: 38869039 PMCID: PMC11165715 DOI: 10.2174/0109298665286952240212053723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/22/2024] [Accepted: 01/31/2024] [Indexed: 06/14/2024]
Abstract
Human blood is a window of physiology and disease. Examination of biomarkers in blood is a common clinical procedure, which can be informative in diagnosis and prognosis of diseases, and in evaluating treatment effectiveness. There is still a huge demand on new blood biomarkers and assays for precision medicine nowadays, therefore plasma/serum proteomics has attracted increasing attention in recent years. How to effectively proceed with the biomarker discovery and clinical diagnostic assay development is a question raised to researchers who are interested in this area. In this review, we comprehensively introduce the background and advancement of technologies for blood proteomics, with a focus on mass spectrometry (MS). Analyzing existing blood biomarkers and newly-built diagnostic assays based on MS can shed light on developing new biomarkers and analytical methods. We summarize various protein analytes in plasma/serum which include total proteome, protein post-translational modifications, and extracellular vesicles, focusing on their corresponding sample preparation methods for MS analysis. We propose screening multiple protein analytes in the same set of blood samples in order to increase success rate for biomarker discovery. We also review the trends of MS techniques for blood tests including sample preparation automation, and further provide our perspectives on their future directions.
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Affiliation(s)
- Yiying Zhu
- Department of Chemistry, Tsinghua University, Beijing, China
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6
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Zheng Y, Gao K, Gao Q, Zhang S. Glycoproteomic contributions to hepatocellular carcinoma research: a 2023 update. Expert Rev Proteomics 2023; 20:211-220. [PMID: 37882248 DOI: 10.1080/14789450.2023.2265064] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 09/12/2023] [Indexed: 10/27/2023]
Abstract
INTRODUCTION Hepatocellular carcinoma (HCC) represents a significant burden globally, which ranks sixth among the most frequently diagnosed cancers and stands as the third leading cause of cancer-related mortality. Glycoproteomics, as an important branch of proteomics, has already made significant achievements in the field of HCC research. Aberrant protein glycosylation has shown to promote the malignant transformation of hepatocytes by modulating a wide range of tumor-promoting signaling pathways. The glycoproteome provides valuable information for understanding cancer progression, tumor immunity, and clinical outcome, which could serve as potential diagnostic, prognostic, and therapeutic tools in HCC. AREAS COVERED In this review, recent advances of glycoproteomics contribute to clinical applications (diagnosis and prognosis) and molecular mechanisms (hepatocarcinogenesis, progression, stemness and recurrence, and drug resistance) of HCC are summarized. EXPERT OPINION Glycoproteomics shows promise in HCC, enhancing early detection, risk stratification, and personalized treatments. Challenges include sample heterogeneity, diverse glycans structures, sensitivity issues, complex workflows, limited databases, and incomplete understanding of immune cell glycosylation. Addressing these limitations requires collaborative efforts, technological advancements, standardization, and validation studies. Future research should focus on targeting abnormal protein glycosylation therapeutically. Advancements in glycobiomarkers and glycosylation-targeted therapies will greatly impact HCC diagnosis, prognosis, and treatment.
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Affiliation(s)
- Yingqi Zheng
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Ke Gao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Qiang Gao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Shu Zhang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
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7
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Pan Y, Wang Z, Xu S, Zhang L, Zhang W. Selective profiling of liver-related specific proteins based on sofosbuvir-modified magnetic separation material. ANAL SCI 2023; 39:313-323. [PMID: 36572835 DOI: 10.1007/s44211-022-00238-9] [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: 08/31/2022] [Accepted: 12/09/2022] [Indexed: 12/27/2022]
Abstract
It has great significance in profiling specific proteins throughout for better understanding of complex pathological processes and in-depth pharmacological studies. In this work, an efficient protein profiling strategy was developed based on the specific protein-drug interaction. Sofosbuvir (SOF), as a first-line drug for the treatment of hepatitis C, was modified onto the surface of nanoparticles through stable chemical bonds to fabricate a novel magnetic separation material denoted as Fe3O4@SiO2@PAA@SOF. With sequence coverage as the screening parameter, nine proteins were profiled from fetal bovine serum (FBS) of which eight were liver related. Similarly, the strategy was applied to hepatocellular carcinoma (HCC) patient serum. Eight proteins were profiled and all of them were liver related, demonstrating the superb specificity and selectivity of this strategy for profiling liver-related proteins by virtue of protein-SOF interaction. When serum proteins from HCC patients were compared to those from healthy people, one unique differential protein (D3DQX7) was profiled, which was liver related and was a potential target for ameliorating liver diseases. For further research, this material design concept and protein profiling strategy can be extended to employ other drugs for corresponding studies. Sofosbuvir, as a therapeutic drug for liver diseases, was modified onto the surface of magnetic nanoparticles to fabricate the specific selective separation material (Fe3O4@SiO2@PAA@SOF). Based on protein-SOF interaction, the material was applied to adsorb specific proteins from different serum samples. After MS analysis, specific proteins, most of which were liver related, were successfully profiled from FBS and HCC patient serum, fully demonstrating the superb specificity and selectivity of this protein profiling strategy.
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Affiliation(s)
- Yini Pan
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Zhenxin Wang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Sen Xu
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Lingyi Zhang
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, People's Republic of China.
| | - Weibing Zhang
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, People's Republic of China.
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8
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Yin H, Zhu J. Methods for quantification of glycopeptides by liquid separation and mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:887-917. [PMID: 35099083 PMCID: PMC9339036 DOI: 10.1002/mas.21771] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 11/14/2021] [Accepted: 01/13/2022] [Indexed: 05/05/2023]
Abstract
Recent advances in analytical techniques provide the opportunity to quantify even low-abundance glycopeptides derived from complex biological mixtures, allowing for the identification of glycosylation differences between healthy samples and those derived from disease states. Herein, we discuss the sample preparation procedures and the mass spectrometry (MS) strategies that have facilitated glycopeptide quantification, as well as the standards used for glycopeptide quantification. For sample preparation, various glycopeptide enrichment methods are summarized including the columns used for glycopeptide separation in liquid chromatography separation. For MS analysis strategies, MS1 level-based quantification and MS2 level-based quantification are described, either with or without labeling, where we have covered isotope labeling, TMT/iTRAQ labeling, data dependent acquisition, data independent acquisition, multiple reaction monitoring, and parallel reaction monitoring. The strengths and weaknesses of these methods are compared, particularly those associated with the figures of merit that are important for clinical biomarker studies and the pathological and functional studies of glycoproteins in various diseases. Possible future developments for glycopeptide quantification are discussed.
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Affiliation(s)
- Haidi Yin
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China
- Correspondence to: Haidi Yin, Shenzhen Bay Laboratory, A1201, Shenzhen, Guangdong, 518132, China. Phone: 0755-26849276. , Jianhui Zhu, Department of Surgery, University of Michigan, 1150 West Medical Center Drive, Building MSRB1, Rm A500, Ann Arbor, MI 48109-0656, USA. Tel: 734-615-2567. Fax: 734-615-2088.
| | - Jianhui Zhu
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA
- Correspondence to: Haidi Yin, Shenzhen Bay Laboratory, A1201, Shenzhen, Guangdong, 518132, China. Phone: 0755-26849276. , Jianhui Zhu, Department of Surgery, University of Michigan, 1150 West Medical Center Drive, Building MSRB1, Rm A500, Ann Arbor, MI 48109-0656, USA. Tel: 734-615-2567. Fax: 734-615-2088.
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9
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A multiplexed microflow LC-MS/MS-PRM assay for serologic quantification of IgG N- and HPX O- glycoforms in liver fibrosis. Sci Rep 2023; 13:606. [PMID: 36635317 PMCID: PMC9837073 DOI: 10.1038/s41598-023-27382-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/02/2023] [Indexed: 01/14/2023] Open
Abstract
Targeted quantification of glycoproteins has not reached its full potential because of limitations of the existing analytical workflows. In this study, we introduce a targeted microflow LC-MS/MS-PRM method for the quantification of multiple glycopeptides in unfractionated serum samples. The entire preparation of 16 samples in a batch is completed within 3 h, and the LC-MS quantification of all the glycoforms in a sample is completed in 15 min in triplicate, including online capture and desalting. We demonstrate applicability of the workflow on a multiplexed quantification of eight N-glycoforms of immunoglobulin G (IgG) together with two O-glycoforms of hemopexin (HPX). We applied the assay to a serologic study of fibrotic liver disease in patients of HCV etiology. The results document that specific IgG- and HPX-glycoforms detect efficiently fibrotic disease of different degree, and suggest that the LC-MS/MS-PRM assays may provide rapid and reproducible biomarker assay targeting simultaneously the N- and O-glycoforms of the peptides. We propose that such high throughput multiplexed methods may advance the clinical use of the LC-MS/MS assays.
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10
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Liu QW, Ruan HJ, Chao WX, Li MX, Jiao YL, Ward DG, Gao SG, Qi YJ. N-linked glycoproteomic profiling in esophageal squamous cell carcinoma. World J Gastroenterol 2022; 28:3869-3885. [PMID: 36157541 PMCID: PMC9367225 DOI: 10.3748/wjg.v28.i29.3869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/26/2022] [Accepted: 07/06/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Mass spectrometry-based proteomics and glycomics reveal post-translational modifications providing significant biological insights beyond the scope of genomic sequencing.
AIM To characterize the N-linked glycoproteomic profile in esophageal squamous cell carcinoma (ESCC) via two complementary approaches.
METHODS Using tandem multilectin affinity chromatography for enrichment of N-linked glycoproteins, we performed N-linked glycoproteomic profiling in ESCC tissues by two-dimensional gel electrophoresis (2-DE)-based and isobaric tags for relative and absolute quantification (iTRAQ) labeling-based mass spectrometry quantitation in parallel, followed by validation of candidate glycoprotein biomarkers by Western blot.
RESULTS 2-DE-based and iTRAQ labeling-based quantitation identified 24 and 402 differentially expressed N-linked glycoproteins, respectively, with 15 in common, demonstrating the outperformance of iTRAQ labeling-based quantitation over 2-DE and complementarity of these two approaches. Proteomaps showed the distinct compositions of functional categories between proteins and glycoproteins with differential expression associated with ESCC. Western blot analysis validated the up-regulation of total procathepsin D and high-mannose procathepsin D, and the down-regulation of total haptoglobin, high-mannose clusterin, and GlcNAc/sialic acid-containing fraction of 14-3-3ζ in ESCC tissues. The serum levels of glycosylated fractions of clusterin, proline-arginine-rich end leucine-rich repeat protein, and haptoglobin in patients with ESCC were remarkably higher than those in healthy controls.
CONCLUSION Our study provides insights into the aberrant N-linked glycoproteome associated with ESCC, which will be a valuable resource for future investigations.
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Affiliation(s)
- Qi-Wei Liu
- Henan Key Laboratory of Microbiome and Esophageal Cancer Prevention and Treatment; Henan Key Laboratory of Cancer Epigenetics; Cancer Hospital, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang 471003, Henan Province, China
| | - Hao-Jie Ruan
- Henan Key Laboratory of Microbiome and Esophageal Cancer Prevention and Treatment; Henan Key Laboratory of Cancer Epigenetics; Cancer Hospital, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang 471003, Henan Province, China
| | - Wei-Xia Chao
- Henan Key Laboratory of Microbiome and Esophageal Cancer Prevention and Treatment; Henan Key Laboratory of Cancer Epigenetics; Cancer Hospital, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang 471003, Henan Province, China
| | - Meng-Xiang Li
- Henan Key Laboratory of Microbiome and Esophageal Cancer Prevention and Treatment; Henan Key Laboratory of Cancer Epigenetics; Cancer Hospital, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang 471003, Henan Province, China
| | - Ye-Lin Jiao
- Department of Pathology, The First People’s Hospital of Luo Yang, Luoyang 471000, Henan Province, China
| | - Douglas G Ward
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - She-Gan Gao
- Henan Key Laboratory of Microbiome and Esophageal Cancer Prevention and Treatment; Henan Key Laboratory of Cancer Epigenetics; Cancer Hospital, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang 471003, Henan Province, China
| | - Yi-Jun Qi
- Henan Key Laboratory of Microbiome and Esophageal Cancer Prevention and Treatment; Henan Key Laboratory of Cancer Epigenetics; Cancer Hospital, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang 471003, Henan Province, China
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11
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Campos D, Girgis M, Sanda M. Site-specific glycosylation of SARS-CoV-2: Big challenges in mass spectrometry analysis. Proteomics 2022; 22:e2100322. [PMID: 35700310 PMCID: PMC9349404 DOI: 10.1002/pmic.202100322] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/03/2022] [Accepted: 06/13/2022] [Indexed: 12/24/2022]
Abstract
Glycosylation of viral proteins is required for the progeny formation and infectivity of virtually all viruses. It is increasingly clear that distinct glycans also play pivotal roles in the virus's ability to shield and evade the host's immune system. Recently, there has been a great advancement in structural identification and quantitation of viral glycosylation, especially spike proteins. Given the ongoing pandemic and the high demand for structure analysis of SARS-CoV-2 densely glycosylated spike protein, mass spectrometry methodologies have been employed to accurately determine glycosylation patterns. There are still many challenges in the determination of site-specific glycosylation of SARS-CoV-2 viral spike protein. This is compounded by some conflicting results regarding glycan site occupancy and glycan structural characterization. These are probably due to differences in the expression systems, form of expressed spike glycoprotein, MS methodologies, and analysis software. In this review, we recap the glycosylation of spike protein and compare among various studies. Also, we describe the most recent advancements in glycosylation analysis in greater detail and we explain some misinterpretation of previously observed data in recent publications. Our study provides a comprehensive view of the spike protein glycosylation and highlights the importance of consistent glycosylation determination.
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Affiliation(s)
- Diana Campos
- Max‐Planck‐Institut fuer Herz‐ und LungenforschungBad NauheimGermany
| | - Michael Girgis
- Department of BioengineeringVolgenau School of Engineering and ComputingGeorge Mason UniversityFairfaxVirginiaUSA
| | - Miloslav Sanda
- Max‐Planck‐Institut fuer Herz‐ und LungenforschungBad NauheimGermany
- Clinical and Translational Glycoscience Research CenterGeorgetown UniversityWashingtonDCUSA
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12
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Molnarova K, Cokrtova K, Tomnikova A, Krizek T, Kozlik P. Liquid chromatography and capillary electrophoresis in glycomic and glycoproteomic analysis. MONATSHEFTE FUR CHEMIE 2022; 153:659-686. [PMID: 35754790 PMCID: PMC9212196 DOI: 10.1007/s00706-022-02938-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/29/2022] [Indexed: 11/28/2022]
Abstract
Glycosylation is one of the most significant and abundant post-translational modifications in cells. Glycomic and glycoproteomic analyses involve the characterization of oligosaccharides (glycans) conjugated to proteins. Glycomic and glycoproteomic analysis is highly challenging because of the large diversity of structures, low abundance, site-specific heterogeneity, and poor ionization efficiency of glycans and glycopeptides in mass spectrometry (MS). MS is a key tool for characterization of glycans and glycopeptides. However, MS alone does not always provide full structural and quantitative information for many reasons, and thus MS is combined with some separation technique. This review focuses on the role of separation techniques used in glycomic and glycoproteomic analyses, liquid chromatography and capillary electrophoresis. The most important separation conditions and results are presented and discussed. Graphical abstract
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Affiliation(s)
- Katarina Molnarova
- Department of Analytical Chemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Katerina Cokrtova
- Department of Analytical Chemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Alice Tomnikova
- Department of Analytical Chemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Tomas Krizek
- Department of Analytical Chemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Petr Kozlik
- Department of Analytical Chemistry, Faculty of Science, Charles University, Prague, Czech Republic
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13
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Ramachandran P, Xu G, Huang HH, Rice R, Zhou B, Lindpaintner K, Serie D. Serum Glycoprotein Markers in Nonalcoholic Steatohepatitis and Hepatocellular Carcinoma. J Proteome Res 2022; 21:1083-1094. [PMID: 35286803 PMCID: PMC8981307 DOI: 10.1021/acs.jproteome.1c00965] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Fatty liver disease progresses through stages of fat accumulation and inflammation to nonalcoholic steatohepatitis (NASH), fibrosis and cirrhosis, and eventually hepatocellular carcinoma (HCC). Currently available diagnostic tools for HCC lack sensitivity and specificity. In this study, we investigated the use of circulating serum glycoproteins to identify a panel of potential prognostic markers that may be indicative of progression from the healthy state to NASH and further to HCC. Serum samples were processed and analyzed using a novel high-throughput glycoproteomics platform. Our initial dataset contained healthy, NASH, and HCC serum samples. We analyzed 413 glycopeptides, representing 57 abundant serum proteins, and compared among the three phenotypes. We studied the normalized abundance of common glycoforms and found 40 glycopeptides with statistically significant differences in abundances in NASH and HCC compared to controls. Summary level relative abundances of core-fucosylated, sialylated, and branched glycans containing glycopeptides were higher in NASH and HCC as compared to controls. We replicated some of our findings in an independent set of samples of individuals with benign liver conditions and HCC. Our results may be of value in the management of liver diseases. Data generated in this work can be downloaded from MassIVE (https://massive.ucsd.edu) with identifier MSV000088809.
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Affiliation(s)
| | - Gege Xu
- InterVenn Biosciences, South San Francisco, California 94080, United States
| | - Hector H Huang
- InterVenn Biosciences, South San Francisco, California 94080, United States
| | - Rachel Rice
- InterVenn Biosciences, South San Francisco, California 94080, United States
| | - Bo Zhou
- InterVenn Biosciences, South San Francisco, California 94080, United States
| | - Klaus Lindpaintner
- InterVenn Biosciences, South San Francisco, California 94080, United States
| | - Daniel Serie
- InterVenn Biosciences, South San Francisco, California 94080, United States
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14
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Goto K, Osaki M, Izutsu R, Tanaka H, Sasaki R, Tanio A, Satofuka H, Kazuki Y, Yamamoto M, Kugoh H, Ito H, Oshimura M, Fujiwara Y, Okada F. Establishment of an antibody specific for AMIGO2 improves immunohistochemical evaluation of liver metastases and clinical outcomes in patients with colorectal cancer. Diagn Pathol 2022; 17:16. [PMID: 35094710 PMCID: PMC8802484 DOI: 10.1186/s13000-021-01176-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/26/2021] [Indexed: 12/11/2022] Open
Abstract
Abstract
Instruction
The human amphoterin-induced gene and open reading frame (AMIGO) was identified as a novel cell adhesion molecule of type I transmembrane protein. AMIGO2 is one of three members of the AMIGO family (AMIGO1, 2, and 3), and the similarity between them is approximately 40% at the amino acid level. We have previously shown that AMIGO2 functions as a driver of liver metastasis. Immunohistochemical analysis of AMIGO2 expression in colorectal cancer (CRC) using a commercially available anti-AMIGO2 mouse monoclonal antibody clone sc-373699 (sc mAb) correlated with liver metastasis and poor prognosis. However, the sc mAb was found to be cross-reactive with all three molecules in the AMIGO family.
Methods
We generated a rat monoclonal antibody clone rTNK1A0012 (rTNK mAb) for human AMIGO2. The rTNK mAb was used to re-evaluate the association between AMIGO2 expression and liver metastases/clinical outcomes using the same CRC tissue samples previously reported with sc mAb.
Results
Western blot analysis revealed that a rTNK mAb was identified as being specific for AMIGO2 protein and did not cross-react with AMIGO1 and AMIGO3. The rTNK mAb and sc mAb showed higher AMIGO2 expression, which correlates with a high frequency of liver metastases (65.3% and 47.5%, respectively), while multivariate analysis showed that AMIGO2 expression was an independent prognostic factor for liver metastases (p = 7.930E-10 and p = 1.707E-5). The Kaplan-Meier analyses showed that the rTNK mAb (p = 0.004), but not sc mAb (p = 0.107), predicted worse overall survival in patients with high AMIGO2 expression. The relationship between AMIGO2 expression and poor disease-specific survival showed a higher level of significance for rTNK mAb (p = 0.00004) compared to sc mAb (p = 0.001).
Conclusions
These results indicate that the developed rTNK1A0012 mAb is an antibody that specifically recognizes AMIGO2 by immunohistochemistry and can be a more reliable and applicable method for the diagnostic detection of liver metastases and worse prognosis in patients with high AMIGO2-expressing CRC.
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15
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Hackett WE, Zaia J. Calculating Glycoprotein Similarities From Mass Spectrometric Data. Mol Cell Proteomics 2021; 20:100028. [PMID: 32883803 PMCID: PMC8724611 DOI: 10.1074/mcp.r120.002223] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/24/2020] [Accepted: 09/03/2020] [Indexed: 12/23/2022] Open
Abstract
Complex protein glycosylation occurs through biosynthetic steps in the secretory pathway that create macro- and microheterogeneity of structure and function. Required for all life forms, glycosylation diversifies and adapts protein interactions with binding partners that underpin interactions at cell surfaces and pericellular and extracellular environments. Because these biological effects arise from heterogeneity of structure and function, it is necessary to measure their changes as part of the quest to understand nature. Quite often, however, the assumption behind proteomics that posttranslational modifications are discrete additions that can be modeled using the genome as a template does not apply to protein glycosylation. Rather, it is necessary to quantify the glycosylation distribution at each glycosite and to aggregate this information into a population of mature glycoproteins that exist in a given biological system. To date, mass spectrometric methods for assigning singly glycosylated peptides are well-established. But it is necessary to quantify glycosylation heterogeneity accurately in order to gauge the alterations that occur during biological processes. The task is to quantify the glycosylated peptide forms as accurately as possible and then apply appropriate bioinformatics algorithms to the calculation of micro- and macro-similarities. In this review, we summarize current approaches for protein quantification as they apply to this glycoprotein similarity problem.
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Affiliation(s)
- William E Hackett
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
| | - Joseph Zaia
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA; Department of Biochemistry, Boston University, Boston, Massachusetts, USA.
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16
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Molnarova K, Kozlík P. Comparison of Different HILIC Stationary Phases in the Separation of Hemopexin and Immunoglobulin G Glycopeptides and Their Isomers. Molecules 2020; 25:E4655. [PMID: 33065988 PMCID: PMC7594091 DOI: 10.3390/molecules25204655] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/05/2020] [Accepted: 10/10/2020] [Indexed: 01/16/2023] Open
Abstract
Protein glycosylation analysis is challenging due to the structural variety of complex conjugates. However, chromatographically separating glycans attached to tryptic peptides enables their site-specific characterization. For this purpose, we have shown the importance of selecting a suitable hydrophilic interaction liquid chromatography (HILIC) stationary phase in the separation of glycopeptides and their isomers. Three different HILIC stationary phases, i.e., HALO® penta-HILIC, Glycan ethylene bridged hybrid (BEH) Amide, and ZIC-HILIC, were compared in the separation of complex N-glycopeptides of hemopexin and Immunoglobulin G glycoproteins. The retention time increased with the polarity of the glycans attached to the same peptide backbone in all HILIC columns tested in this study, except for the ZIC-HILIC column when adding sialic acid to the glycan moiety, which caused electrostatic repulsion with the negatively charged sulfobetaine functional group, thereby decreasing retention. The HALO® penta-HILIC column provided the best separation results, and the ZIC-HILIC column the worst. Moreover, we showed the potential of these HILIC columns for the isomeric separation of fucosylated and sialylated glycoforms. Therefore, HILIC is a useful tool for the comprehensive characterization of glycoproteins and their isomers.
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Affiliation(s)
| | - Petr Kozlík
- Department of Analytical Chemistry, Faculty of Science, Charles University, Hlavova 8, 128-43 Prague, Czech Republic;
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17
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Park GW, Lee JW, Lee HK, Shin JH, Kim JY, Yoo JS. Classification of Mucin-Type O-Glycopeptides Using Higher-Energy Collisional Dissociation in Mass Spectrometry. Anal Chem 2020; 92:9772-9781. [PMID: 32584546 DOI: 10.1021/acs.analchem.0c01218] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Changes in mucin-type O-glycosylation of human proteins affect protein function, immune response, and cancer progression. Since O-glycoproteins are characterized by the microheterogeneity of diverse O-glycans with no conserved sequence and the macroheterogeneity of multiple glycosylation sites on serine and/or threonine in human proteins, the assessment of different mucin types, such as Tn-antigen, core 1, and core 2, and their extended core types in O-glycopeptides, is extremely challenging. Here, we present an O-GlycoProteome Analyzer (O-GPA) that automatically classifies mucin-type O-glycosylation using higher-energy collisional dissociation (HCD) in mass spectrometry. First, we estimated the number of GlcNAc residues using the intensity ratio of GlcNAc-specific fragment ions (HexNAc-CH6O3 and HexNAc-2H2O) over GalNAc-specific fragment ions (HexNAc-C2H6O3 and HexNAc-C2H4O2) in the HCD spectrum. Furthermore, we classified the different mucin types of O-glycopeptides from characteristic B2 (HexNAc2) or Y2α (PEP + HexNAc2), and Y2β (PEP + HexNAcHex) fragment ions, along with the number of GlcNAc. Furthermore, O-GPA automatically determined single or multiple O-glycosylation, regardless of the mucin types. The mucin type of O-glycopeptides from human urine and plasma was confirmed with an overall accuracy of 96%. We found 97 core 1, 56 core 2, 13 extended core 1, and 12 extended core 2 glycopeptides from urine; and 22 core 1, 13 core 2, 7 extended core 1, 1 extended core 2, and 1 Tn-antigen from plasma. Our strategy can be used to successfully characterize specific mucin types of O-glycoproteins in human biological samples.
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Affiliation(s)
- Gun Wook Park
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, Ochang-eup 28119, Republic of Korea
| | - Ji Won Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, Ochang-eup 28119, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Hyun Kyoung Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, Ochang-eup 28119, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Jong Hwan Shin
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, Ochang-eup 28119, Republic of Korea
| | - Jin Young Kim
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, Ochang-eup 28119, Republic of Korea
| | - Jong Shin Yoo
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, Ochang-eup 28119, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
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18
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Parikh ND, Mehta AS, Singal AG, Block T, Marrero JA, Lok AS. Biomarkers for the Early Detection of Hepatocellular Carcinoma. Cancer Epidemiol Biomarkers Prev 2020; 29:2495-2503. [PMID: 32238405 DOI: 10.1158/1055-9965.epi-20-0005] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 02/17/2020] [Accepted: 03/16/2020] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death worldwide, and the cancer with the fastest increase in mortality in the United States, with more than 39,000 cases and 29,000 deaths in 2018. As with many cancers, survival is significantly improved by early detection. The median survival of patients with early HCC is >60 months but <15 months when detected at an advanced stage. Surveillance of at-risk patients improves outcome, but fewer than 20% of those at risk for HCC receive surveillance, and current surveillance strategies have limited sensitivity and specificity. Ideally, blood-based biomarkers with adequate sensitivity or specificity would be available for early detection of HCC; however, the most commonly used biomarker for HCC, alpha-fetoprotein, has inadequate performance characteristics. There are several candidate serum proteomic, glycomic, and genetic markers that have gone through early stages of biomarker validation and have shown promise for the early detection of HCC, but these markers require validation in well-curated cohorts. Ongoing prospective cohort studies will permit retrospective longitudinal (phase III biomarker study) validation of biomarkers. In this review, we highlight promising candidate biomarkers and biomarker panels that have completed phase II evaluation but require further validation prior to clinical use.See all articles in this CEBP Focus section, "NCI Early Detection Research Network: Making Cancer Detection Possible."
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Affiliation(s)
- Neehar D Parikh
- Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, Michigan.
| | - Anand S Mehta
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina
| | - Amit G Singal
- Division of Digestive and Liver Diseases, UT Southwestern Medical Center, Dallas, Texas
| | - Timothy Block
- Baruch S. Blumberg Institute of The Hepatitis B Foundation, Doylestown, Pennsylvania
| | - Jorge A Marrero
- Division of Digestive and Liver Diseases, UT Southwestern Medical Center, Dallas, Texas
| | - Anna S Lok
- Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, Michigan
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Klein JA, Zaia J. A Perspective on the Confident Comparison of Glycoprotein Site-Specific Glycosylation in Sample Cohorts. Biochemistry 2019; 59:3089-3097. [PMID: 31833756 DOI: 10.1021/acs.biochem.9b00730] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein glycosylation, resulting from glycosyl transferase reactions under complex control in the secretory pathway, consists of a distribution of related glycoforms at each glycosylation site. Because the biosynthetic substrate concentration and transport rates depend on architecture and other aspects of cellular phenotypes, site-specific glycosylation cannot be predicted accurately from genomic, transcriptomic, or proteomic information. Rather, it is necessary to quantify glycosylation at each protein site and how this changes among a sample cohort to provide information about disease mechanisms. At present, mature mass spectrometry-based methods allow for qualitative assignment of the glycan composition and glycosylation site of singly glycosylated proteolytic peptides. To make such quantitative comparisons, it is necessary to sample the glycosylation distribution with sufficient coverage and accuracy for confident assessment of the glycosylation changes that occur in the biological cohort. In this Perspective, we discuss the unmet needs for mass spectrometry acquisition methods and bioinformatics for the confident comparison of protein site-specific glycosylation among sample cohorts.
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20
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Kim KH, Kim JY, Yoo JS. Mass spectrometry analysis of glycoprotein biomarkers in human blood of hepatocellular carcinoma. Expert Rev Proteomics 2019; 16:553-568. [DOI: 10.1080/14789450.2019.1626235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Kwang Hoe Kim
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - Jin Young Kim
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - Jong Shin Yoo
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, Republic of Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea
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21
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Gizaw ST, Gaunitz S, Novotny MV. Highly Sensitive O-Glycan Profiling for Human Serum Proteins Reveals Gender-Dependent Changes in Colorectal Cancer Patients. Anal Chem 2019; 91:6180-6189. [PMID: 30983323 PMCID: PMC6602050 DOI: 10.1021/acs.analchem.9b00822] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A newly developed microscale protocol for profiling serum O-glycans has been validated here with multiple serum samples obtained from different cohorts of colorectal cancer patients. The simultaneous cleavage and permethylation steps in this procedure preserve the integrity of released minor O-glycans, so that 39 O-linked oligosaccharides could be reliably recorded in a profile. This is far more detected components than shown in any previous studies. The analytical results were further subjected to a battery of statistical tests. Our O-glycan compositions compare favorably with the previous results obtained with solid tumors and cancer cell lines, suggesting that smaller circulatory mucins protruding into the blood circulation may be one source of O-glycans that we observe in the serum samples. While the control vs cancer statistical comparisons generally agree with the expected glycosylation trends, the comparisons of male vs female subjects have led to some surprising results for which we do not have a ready explanation due to lack of any literature describing hormonal control of O-glycosylation. Our results thus underscore the necessity of applying new analytical technologies to clinically interesting sample sets.
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Affiliation(s)
- Solomon T. Gizaw
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405
| | - Stefan Gaunitz
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405
| | - Milos V. Novotny
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405
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22
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Mato JM, Elortza F, Lu SC, Brun V, Paradela A, Corrales FJ. Liver cancer-associated changes to the proteome: what deserves clinical focus? Expert Rev Proteomics 2018; 15:749-756. [PMID: 30204005 DOI: 10.1080/14789450.2018.1521277] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
INTRODUCTION Hepatocellular carcinoma (HCC) is recognized as the fifth most common neoplasm and currently represents the second leading form of cancer-related death worldwide. Despite great progress has been done in the understanding of its pathogenesis, HCC represents a heavy societal and economic burden as most patients are still diagnosed at advanced stages and the 5-year survival rate remain below 20%. Early detection and revolutionary therapies that rely on the discovery of new molecular biomarkers and therapeutic targets are therefore urgently needed to develop precision medicine strategies for a more efficient management of patients. Areas covered: This review intends to comprehensively analyse the proteomics-based research conducted in the last few years to address some of the principal still open riddles in HCC biology, based on the identification of molecular drivers of tumor progression and metastasis. Expert commentary: The technical advances in mass spectrometry experienced in the last decade have significantly improved the analytical capacity of proteome wide studies. Large-scale protein and protein variant (post-translational modifications) identification and quantification have allowed detailed dissections of molecular mechanisms underlying HCC progression and are already paving the way for the identification of clinically relevant proteins and the development of their use on patient care.
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Affiliation(s)
- José M Mato
- a CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park , Derio , Spain.,b National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health , Madrid , Spain
| | - Félix Elortza
- a CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park , Derio , Spain.,b National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health , Madrid , Spain
| | - Shelly C Lu
- c Division of Digestive and Liver Diseases , Cedars-Sinai Medical Center , LA , CA , USA
| | - Virginie Brun
- d Université Grenoble-Alpes, CEA, BIG, Biologie à Grande Echelle, Inserm , Grenoble , France
| | - Alberto Paradela
- e Functional Proteomics Laboratory , Centro Nacional de Biotecnología-CSIC, Proteored-ISCIII, CIBERehd , Madrid , Spain
| | - Fernando J Corrales
- b National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health , Madrid , Spain.,e Functional Proteomics Laboratory , Centro Nacional de Biotecnología-CSIC, Proteored-ISCIII, CIBERehd , Madrid , Spain
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23
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Ruhaak LR, Xu G, Li Q, Goonatilleke E, Lebrilla CB. Mass Spectrometry Approaches to Glycomic and Glycoproteomic Analyses. Chem Rev 2018; 118:7886-7930. [PMID: 29553244 PMCID: PMC7757723 DOI: 10.1021/acs.chemrev.7b00732] [Citation(s) in RCA: 253] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Glycomic and glycoproteomic analyses involve the characterization of oligosaccharides (glycans) conjugated to proteins. Glycans are produced through a complicated nontemplate driven process involving the competition of enzymes that extend the nascent chain. The large diversity of structures, the variations in polarity of the individual saccharide residues, and the poor ionization efficiencies of glycans all conspire to make the analysis arguably much more difficult than any other biopolymer. Furthermore, the large number of glycoforms associated with a specific protein site makes it more difficult to characterize than any post-translational modification. Nonetheless, there have been significant progress, and advanced separation and mass spectrometry methods have been at its center and the main reason for the progress. While glycomic and glycoproteomic analyses are still typically available only through highly specialized laboratories, new software and workflow is making it more accessible. This review focuses on the role of mass spectrometry and separation methods in advancing glycomic and glycoproteomic analyses. It describes the current state of the field and progress toward making it more available to the larger scientific community.
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Affiliation(s)
- L. Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Gege Xu
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Qiongyu Li
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Elisha Goonatilleke
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Carlito B. Lebrilla
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California 95616, United States
- Foods for Health Institute, University of California, Davis, Davis, California 95616, United States
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24
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Yuan W, Benicky J, Wei R, Goldman R, Sanda M. Quantitative Analysis of Sex-Hormone-Binding Globulin Glycosylation in Liver Diseases by Liquid Chromatography-Mass Spectrometry Parallel Reaction Monitoring. J Proteome Res 2018; 17:2755-2766. [PMID: 29972295 DOI: 10.1021/acs.jproteome.8b00201] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Sex-hormone-binding globulin (SHBG) is a liver-secreted glycoprotein and a major regulator of steroid distribution. It has been reported that the serum concentration of SHBG changes in liver disease. To explore the involvement of SHBG in liver disease of different etiologies in greater detail, we developed a sensitive and selective liquid chromatography-mass spectrometry parallel reaction monitoring workflow to achieve quantitative analysis of SHBG glycosylation microheterogeneity. The method uses energy-optimized "soft" fragmentation to extract informative Y ions for maximal coverage of glycoforms and their quantitative comparisons. A total of 15 N-glycoforms of two N-glycosites and 3 O-glycoforms of 1 O-glycosite of this low-abundance serum protein were simultaneously analyzed in the complex samples. At the same time, we were able to partially resolve linkage isoforms of the fucosylated glycoforms and to identify and quantify SHBG N-glycoforms that were not previously reported. The results show that both core and outer-arm fucosylation of the N-glycoforms increases with liver cirrhosis but that a further increase of fucosylation is not observed with hepatocellular carcinoma (HCC). In contrast, the α-2-6 sialylated glycoform of the O-glycopeptide of SHBG increases in liver cirrhosis, and a significant 2-fold further increase is observed in HCC. In general, we do not find a significant contribution of different liver disease etiologies to the observed changes in glycosylation; however, elevation of the newly reported HexNAc(4)Hex(6) N-glycoform is associated with alcoholic liver disease.
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Gianazza E, Banfi C. Post-translational quantitation by SRM/MRM: applications in cardiology. Expert Rev Proteomics 2018; 15:477-502. [DOI: 10.1080/14789450.2018.1484283] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Erica Gianazza
- Unit of Proteomics, Centro Cardiologico Monzino IRCCS, Milan, Italy
| | - Cristina Banfi
- Unit of Proteomics, Centro Cardiologico Monzino IRCCS, Milan, Italy
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26
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Liu S, Cheng L, Fu Y, Liu BF, Liu X. Characterization of IgG N-glycome profile in colorectal cancer progression by MALDI-TOF-MS. J Proteomics 2018; 181:225-237. [DOI: 10.1016/j.jprot.2018.04.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/21/2018] [Accepted: 04/18/2018] [Indexed: 12/17/2022]
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27
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Liu Y, Wang C, Wang R, Wu Y, Zhang L, Liu BF, Cheng L, Liu X. Isomer-specific profiling of N-glycans derived from human serum for potential biomarker discovery in pancreatic cancer. J Proteomics 2018; 181:160-169. [DOI: 10.1016/j.jprot.2018.04.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 04/02/2018] [Accepted: 04/11/2018] [Indexed: 02/03/2023]
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28
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de Oliveira RM, Ornelas Ricart CA, Araujo Martins AM. Use of Mass Spectrometry to Screen Glycan Early Markers in Hepatocellular Carcinoma. Front Oncol 2018; 7:328. [PMID: 29379771 PMCID: PMC5775512 DOI: 10.3389/fonc.2017.00328] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 12/21/2017] [Indexed: 12/13/2022] Open
Abstract
Association between altered glycosylation patterns and poor prognosis in cancer points glycans as potential specific tumor markers. Most proteins are glycosylated and functionally arranged on cell surface and extracellular matrix, mediating interactions and cellular signaling. Thereby, aberrant glycans may be considered a pathological phenotype at least as important as changes in protein expression for cancer and other complex diseases. As most serum glycoproteins have hepatic origin, liver disease phenotypes, such as hepatocellular carcinoma (HCC), may present altered glycan profile and display important modifications. One of the prominent obstacles in HCC is the diagnostic in advanced stages when patients have several liver dysfunctions, limiting treatment options and life expectancy. The characterization of glycomic profiles in pathological conditions by means of mass spectrometry (MS) may lead to the discovery of early diagnostic markers using non-invasive approaches. MS is a powerful analytical technique capable of elucidating many glycobiological issues and overcome limitations of the serological markers currently applied in clinical practice. Therefore, MS-based glycomics of tumor biomarkers is a promising tool to increase early detection and monitoring of disease.
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Affiliation(s)
- Raphaela Menezes de Oliveira
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasilia, Brazil
| | - Carlos Andre Ornelas Ricart
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasilia, Brazil
| | - Aline Maria Araujo Martins
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasilia, Brazil.,University Hospital Walter Cantídeo, Surgery Department, Federal University of Ceara, Fortaleza, Brazil
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29
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Kailemia MJ, Xu G, Wong M, Li Q, Goonatilleke E, Leon F, Lebrilla CB. Recent Advances in the Mass Spectrometry Methods for Glycomics and Cancer. Anal Chem 2018; 90:208-224. [PMID: 29049885 PMCID: PMC6200424 DOI: 10.1021/acs.analchem.7b04202] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Muchena J. Kailemia
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
- These authors contributed equally to this work
| | - Gege Xu
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
- These authors contributed equally to this work
| | - Maurice Wong
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Qiongyu Li
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Elisha Goonatilleke
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Frank Leon
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Carlito B. Lebrilla
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
- Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
- Foods for Health Institute, University of California, Davis, CA 95616, USA
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