1
|
Mikami M, Tanabe K, Imanishi T, Ikeda M, Hirasawa T, Yasaka M, Machida H, Yoshida H, Hasegawa M, Shimada M, Kato T, Kitamura S, Kato H, Fujii T, Kobayashi Y, Suzuki N, Tanaka K, Murakami I, Katahira T, Hayashi C, Matsuo K. Comprehensive serum glycopeptide spectra analysis to identify early-stage epithelial ovarian cancer. Sci Rep 2024; 14:20000. [PMID: 39198565 PMCID: PMC11358426 DOI: 10.1038/s41598-024-70228-6] [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: 05/24/2024] [Accepted: 08/14/2024] [Indexed: 09/01/2024] Open
Abstract
Epithelial ovarian cancer (EOC) is widely recognized as the most lethal gynecological malignancy; however, its early-stage detection remains a considerable clinical challenge. To address this, we have introduced a new method, named Comprehensive Serum Glycopeptide Spectral Analysis (CSGSA), which detects early-stage cancer by combining glycan alterations in serum glycoproteins with tumor markers. We detected 1712 glycopeptides using liquid chromatography-mass spectrometry from the sera obtained from 564 patients with EOC and 1149 controls across 13 institutions. Furthermore, we used a convolutional neural network to analyze the expression patterns of the glycopeptides and tumor markers. Using this approach, we successfully differentiated early-stage EOC (Stage I) from non-EOC, with an area under the curve (AUC) of 0.924 in receiver operating characteristic (ROC) analysis. This method markedly outperforms conventional tumor markers, including cancer antigen 125 (CA125, 0.842) and human epididymis protein 4 (HE4, 0.717). Notably, our method exhibited remarkable efficacy in differentiating early-stage ovarian clear cell carcinoma from endometrioma, achieving a ROC-AUC of 0.808, outperforming CA125 (0.538) and HE4 (0.557). Our study presents a promising breakthrough in the early detection of EOC through the innovative CSGSA method. The integration of glycan alterations with cancer-related tumor markers has demonstrated exceptional diagnostic potential.
Collapse
Affiliation(s)
- Mikio Mikami
- Department of Obstetrics and Gynecology, Tokai University School of Medicine, Isehara, Kanagawa, Japan.
| | - Kazuhiro Tanabe
- Medical Solution Promotion Department, Medical Solution Segment, LSI Medience Corporation, Itabashi-ku, Tokyo, Japan.
| | - Tadashi Imanishi
- Genome Diversity Research Center, Graduate School of Medicine, Tokai University, Isehara, Kanagawa, Japan
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
- Institute of Medical Sciences, Tokai University, Isehara, Kanagawa, Japan
| | - Masae Ikeda
- Department of Obstetrics and Gynecology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Takeshi Hirasawa
- Department of Obstetrics and Gynecology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Miwa Yasaka
- Department of Obstetrics and Gynecology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Hiroko Machida
- Department of Obstetrics and Gynecology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Hiroshi Yoshida
- Department of Obstetrics and Gynecology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Masanori Hasegawa
- Department of Urology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Muneaki Shimada
- Department of Obstetrics and Gynecology, Tohoku University School of Medicine, Sendai, Miyagi, Japan
| | - Tomoyasu Kato
- Department of Gynecology, National Cancer Center Hospital, Chuo-ku, Tokyo, Japan
| | - Shoichi Kitamura
- Department of Gynecology, National Cancer Center Hospital, Chuo-ku, Tokyo, Japan
| | - Hisamori Kato
- Department of Gynecologic Oncology, Kanagawa Cancer Center, Yokohama, Kanagawa, Japan
| | - Takuma Fujii
- Department of Obstetrics and Gynecology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Yoichi Kobayashi
- Department of Obstetrics and Gynecology, Faculty of Medicine, Kyorin University, Mitaka, Tokyo, Japan
| | - Nao Suzuki
- Department of Obstetrics and Gynecology, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Kyoko Tanaka
- Department of Obstetrics and Gynecology, Toho University Ohashi Medical Center, Meguro-ku, Tokyo, Japan
| | - Isao Murakami
- Department of Obstetrics and Gynecology, Toho University Ohashi Medical Center, Meguro-ku, Tokyo, Japan
| | - Tomoko Katahira
- Medical Solution Promotion Department, Medical Solution Segment, LSI Medience Corporation, Itabashi-ku, Tokyo, Japan
| | - Chihiro Hayashi
- Medical Solution Promotion Department, Medical Solution Segment, LSI Medience Corporation, Itabashi-ku, Tokyo, Japan
| | - Koji Matsuo
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| |
Collapse
|
2
|
Vučković F, Novokmet M, Šoić D, Štambuk J, Kolčić I, Polašek O, Lauc G, Gornik O, Keser T. Variability of human Alpha-1-acid glycoprotein N-glycome in a Caucasian population. Glycobiology 2024; 34:cwae031. [PMID: 38591797 DOI: 10.1093/glycob/cwae031] [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: 08/21/2023] [Revised: 04/04/2024] [Accepted: 04/04/2024] [Indexed: 04/10/2024] Open
Abstract
AIM Alpha-1-acid glycoprotein (AGP) is a highly glycosylated protein in human plasma and one of the most abundant acute phase proteins in humans. Glycosylation plays a crucial role in its biological functions, and alterations in AGP N-glycome have been associated with various diseases and inflammatory conditions. However, large-scale studies of AGP N-glycosylation in the general population are lacking. METHODS Using recently developed high-throughput glycoproteomic workflow for site-specific AGP N-glycosylation analysis, 803 individuals from the Croatian island of Korcula were analyzed and their AGP N-glycome data associated with biochemical and physiological traits, as well as different environmental factors. RESULTS After regression analysis, we found that AGP N-glycosylation is strongly associated with sex, somewhat less with age, along with multiple biochemical and physiological traits (e.g. BMI, triglycerides, uric acid, glucose, smoking status, fibrinogen). CONCLUSION For the first time we have extensively explored the inter-individual variability of AGP N-glycome in a general human population, demonstrating its changes with sex, age, biochemical, and physiological status of individuals, providing the baseline for future population and clinical studies.
Collapse
Affiliation(s)
- Frano Vučković
- Genos Glycoscience Research Laboratory, Borongajska cesta 83h, 10000 Zagreb, Croatia
| | - Mislav Novokmet
- Genos Glycoscience Research Laboratory, Borongajska cesta 83h, 10000 Zagreb, Croatia
| | - Dinko Šoić
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Ante Kovačića 1, 10000 Zagreb, Croatia
| | - Jerko Štambuk
- Genos Glycoscience Research Laboratory, Borongajska cesta 83h, 10000 Zagreb, Croatia
| | - Ivana Kolčić
- Department of Public Health, University of Split School of Medicine, Šoltanska ulica 2A, 21000 Split, Croatia
| | - Ozren Polašek
- Department of Public Health, University of Split School of Medicine, Šoltanska ulica 2A, 21000 Split, Croatia
- Algebra University College, Gradišćanska ulica 24, 10000 Zagreb, Croatia
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Borongajska cesta 83h, 10000 Zagreb, Croatia
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Ante Kovačića 1, 10000 Zagreb, Croatia
| | - Olga Gornik
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Ante Kovačića 1, 10000 Zagreb, Croatia
| | - Toma Keser
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Ante Kovačića 1, 10000 Zagreb, Croatia
| |
Collapse
|
3
|
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.
Collapse
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
| | | | | |
Collapse
|
4
|
Wei X, Wang L, Yang B, Ma Y, Yuan W, Ma J. Orosomucoid 2 upregulation mediates liver injury-induced colorectal cancer liver metastasis by promoting EMT and cell migration. Cancer Sci 2024. [PMID: 38475962 DOI: 10.1111/cas.16131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 02/06/2024] [Accepted: 02/17/2024] [Indexed: 03/14/2024] Open
Abstract
The relationship between drug-induced liver injury and liver metastasis of colorectal cancer and the underlying mechanisms are not well understood. In this study, we used carbon tetrachloride to construct a classic mouse liver injury model and injected CT26 colorectal cancer cells into the mouse spleen to simulate the natural route of colorectal cancer liver metastasis. Liver injury significantly increased the number of colorectal cancer liver metastases. Transcriptome sequencing and data-independent acquisition protein quantification identified proteins that were significantly differentially expressed in injured livers, and orosomucoid (ORM) 2 was identified as a target protein for tumor liver metastasis. In vitro experiments showed that exogenous ORM2 protein increased the expression of EMT markers such as Twist, Zeb1, Vim, Snail1 and Snail2 and chemokine ligands to promote CT26 cell migration. In addition, liver-specific overexpression of the ORM2 protein in the mouse model significantly promoted tumor cell liver metastasis without inducing liver injury. Our results indicate that drug-induced liver injury can promote colorectal cancer liver metastasis and that ORM2 can promote cell migration by inducing EMT in tumor cells.
Collapse
Affiliation(s)
- Xundong Wei
- Center of Biotherapy, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
| | - Lei Wang
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Medical Laboratory Center, Chifeng Municipal Hospital/Chifeng Clinical College, Inner Mongolia Medical University, Chifeng, China
| | - Bing Yang
- Center of Biotherapy, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Yuanyuan Ma
- Center of Biotherapy, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Wei Yuan
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Ma
- Center of Biotherapy, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
| |
Collapse
|
5
|
van der Burgt Y, Wuhrer M. The role of clinical glyco(proteo)mics in precision medicine. Mol Cell Proteomics 2023:100565. [PMID: 37169080 DOI: 10.1016/j.mcpro.2023.100565] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/12/2023] [Accepted: 05/02/2023] [Indexed: 05/13/2023] Open
Abstract
Glycoproteomics reveals site-specific O- and N-glycosylation that may influence protein properties including binding, activity and half-life. The increasingly mature toolbox with glycomic- and glycoproteomic strategies is applied for the development of biopharmaceuticals and discovery and clinical evaluation of glycobiomarkers in various disease fields. Notwithstanding the contributions of glycoscience in identifying new drug targets, the current report is focused on the biomarker modality that is of interest for diagnostic and monitoring purposes. To this end it is noted that the identification of biomarkers has received more attention than corresponding quantification. Most analytical methods are very efficient in detecting large numbers of analytes but developments to accurately quantify these have so far been limited. In this perspective a parallel is made with earlier proposed tiers for protein quantification using mass spectrometry. Moreover, the foreseen reporting of multimarker readouts is discussed to describe an individual's health or disease state and their role in clinical decision-making. The potential of longitudinal sampling and monitoring of glycomic features for diagnosis and treatment monitoring is emphasized. Finally, different strategies that address quantification of a multimarker panel will be discussed.
Collapse
Affiliation(s)
- Yuri van der Burgt
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands.
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| |
Collapse
|
6
|
Grzesik K, Janik M, Hoja-Łukowicz D. The hidden potential of glycomarkers: Glycosylation studies in the service of cancer diagnosis and treatment. Biochim Biophys Acta Rev Cancer 2023; 1878:188889. [PMID: 37001617 DOI: 10.1016/j.bbcan.2023.188889] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023]
Abstract
Changes in the glycosylation process appear early in carcinogenesis and evolve with the growth and spread of cancer. The correlation of the characteristic glycosylation signature with the tumor stage and the appropriate therapy choice is an important issue in translational medicine. Oncologists also pay attention to extracellular vesicles as reservoirs of new cancer glycomarkers that can be potent for cancer diagnosis/prognosis. In this review, we recall glycomarkers used in oncology and show their new glycoforms of improved clinical relevance. We summarize current knowledge on the biological functions of glycoepitopes in cancer-derived extracellular vesicles and their potential use in clinical practice. Is glycomics a future of cancer diagnosis? It may be, but in combination with other omics analyses than alone.
Collapse
|
7
|
Visconti A, Rossi N, Deriš H, Lee KA, Hanić M, Trbojević-Akmačić I, Thomas AM, Bolte LA, Björk JR, Hooiveld-Noeken JS, Board R, Harland M, Newton-Bishop J, Harries M, Sacco JJ, Lorigan P, Shaw HM, de Vries EGE, Fehrmann RSN, Weersma RK, Spector TD, Nathan P, Hospers GAP, Sasieni P, Bataille V, Lauc G, Falchi M. Total serum N-glycans associate with response to immune checkpoint inhibition therapy and survival in patients with advanced melanoma. BMC Cancer 2023; 23:166. [PMID: 36805683 PMCID: PMC9938582 DOI: 10.1186/s12885-023-10511-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 01/04/2023] [Indexed: 02/20/2023] Open
Abstract
BACKGROUND Immune checkpoint inhibitors (ICIs) have revolutionized the treatment of melanoma and other cancers. However, no reliable biomarker of survival or response has entered the clinic to identify those patients with melanoma who are most likely to benefit from ICIs. Glycosylation affects proteins and lipids' structure and functions. Tumours are characterized by aberrant glycosylation which may contribute to their progression and hinder an effective antitumour immune response. METHODS We aim at identifying novel glyco-markers of response and survival by leveraging the N-glycome of total serum proteins collected in 88 ICI-naive patients with advanced melanoma from two European countries. Samples were collected before and during ICI treatment. RESULTS We observe that responders to ICIs present with a pre-treatment N-glycome profile significantly shifted towards higher abundancy of low-branched structures containing lower abundances of antennary fucose, and that this profile is positively associated with survival and a better predictor of response than clinical variables alone. CONCLUSION While changes in serum protein glycosylation have been previously implicated in a pro-metastatic melanoma behaviour, we show here that they are also associated with response to ICI, opening new avenues for the stratification of patients and the design of adjunct therapies aiming at improving immune response.
Collapse
Affiliation(s)
- Alessia Visconti
- Department of Twins Research & Genetics Epidemiology, King's College London, London, UK
| | - Niccolò Rossi
- Department of Twins Research & Genetics Epidemiology, King's College London, London, UK
| | - Helena Deriš
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Karla A Lee
- Department of Twins Research & Genetics Epidemiology, King's College London, London, UK
| | - Maja Hanić
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | | | | | - Laura A Bolte
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center, Groningen, The Netherlands
| | - Johannes R Björk
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center, Groningen, The Netherlands
| | | | - Ruth Board
- Department of Oncology, Lancashire Teaching Hospitals NHS Trust, Chorley, UK
| | - Mark Harland
- Division of Haematology and Immunology, Institute of Medical Research at St. James', University of Leeds, Leeds, UK
| | - Julia Newton-Bishop
- Division of Haematology and Immunology, Institute of Medical Research at St. James', University of Leeds, Leeds, UK
| | - Mark Harries
- Department of Medical Oncology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Joseph J Sacco
- Liverpool Clatterbridge Cancer Centre, Liverpool, UK
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Paul Lorigan
- The Christie NHS Foundation Trust, Manchester, UK
| | - Heather M Shaw
- Department of Medical Oncology, Mount Vernon Cancer Centre, Northwood, UK
| | - Elisabeth G E de Vries
- Department of Medical Oncology, University Medical Center Groningen, Groningen, The Netherlands
| | - Rudolf S N Fehrmann
- Department of Medical Oncology, University Medical Center Groningen, Groningen, The Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center, Groningen, The Netherlands
| | - Tim D Spector
- Department of Twins Research & Genetics Epidemiology, King's College London, London, UK
| | - Paul Nathan
- Department of Medical Oncology, Mount Vernon Cancer Centre, Northwood, UK
| | - Geke A P Hospers
- Department of Medical Oncology, University Medical Center Groningen, Groningen, The Netherlands
| | - Peter Sasieni
- School of Cancer and Pharmaceutical Sciences, King's College London, London, UK
| | - Veronique Bataille
- Department of Twins Research & Genetics Epidemiology, King's College London, London, UK.
- Department of Dermatology, Mount Vernon Cancer Centre, Northwood, UK.
- Department of Dermatology, West Herts NHS Trust, Herts, UK.
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Mario Falchi
- Department of Twins Research & Genetics Epidemiology, King's College London, London, UK.
| |
Collapse
|
8
|
Georgescu SR, Mitran CI, Mitran MI, Matei C, Constantin C, Neagu M, Tampa M. Apprising Diagnostic and Prognostic Biomarkers in Cutaneous Melanoma—Persistent Updating. J Pers Med 2022; 12:jpm12091506. [PMID: 36143291 PMCID: PMC9505119 DOI: 10.3390/jpm12091506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/11/2022] [Accepted: 09/11/2022] [Indexed: 12/11/2022] Open
Abstract
The incidence of melanoma, a very aggressive skin cancer, has increased over the past few decades. Although there are well-established clinical, dermoscopic and histopathological criteria, the diagnosis is often performed late, which has important implications on the patient’s clinical outcome. Unfortunately, melanoma is one of the most challenging tumors to diagnose because it is a heterogeneous neoplasm at the clinical, histopathological, and molecular level. The use of reliable biomarkers for the diagnosis and monitoring of disease progression is becoming a standard of care in modern medicine. In this review, we discuss the latest studies, which highlight findings from the genomics, epitranscriptomics, proteomics and metabolomics areas, pointing out different genes, molecules and cells as potential diagnostic and prognostic biomarkers in cutaneous melanoma.
Collapse
Affiliation(s)
- Simona Roxana Georgescu
- Department of Dermatology, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Department of Dermatology, “Victor Babes” Clinical Hospital for Infectious Diseases, 030303 Bucharest, Romania
| | - Cristina Iulia Mitran
- Department of Microbiology, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Correspondence: (C.I.M.); (M.I.M.)
| | - Madalina Irina Mitran
- “Cantacuzino” National Medico-Military Institute for Research and Development, 011233 Bucharest, Romania
- Correspondence: (C.I.M.); (M.I.M.)
| | - Clara Matei
- Department of Dermatology, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Carolina Constantin
- Immunology Department, “Victor Babes” National Institute of Pathology, 050096 Bucharest, Romania
- Colentina Clinical Hospital, 020125 Bucharest, Romania
| | - Monica Neagu
- Immunology Department, “Victor Babes” National Institute of Pathology, 050096 Bucharest, Romania
- Colentina Clinical Hospital, 020125 Bucharest, Romania
- Faculty of Biology, University of Bucharest, 030018 Bucharest, Romania
| | - Mircea Tampa
- Department of Dermatology, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Department of Dermatology, “Victor Babes” Clinical Hospital for Infectious Diseases, 030303 Bucharest, Romania
| |
Collapse
|
9
|
Zeng W, Zheng S, Su T, Cheng J, Mao Y, Zhong Y, Liu Y, Chen J, Zhao W, Lin T, Liu F, Li G, Yang H, Zhang Y. Comparative N-Glycoproteomics Analysis of Clinical Samples Via Different Mass Spectrometry Dissociation Methods. Front Chem 2022; 10:839470. [PMID: 35281567 PMCID: PMC8907888 DOI: 10.3389/fchem.2022.839470] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 01/20/2022] [Indexed: 11/13/2022] Open
Abstract
Site-specific N-glycosylation characterization requires intact N-glycopeptide analysis based on suitable tandem mass spectrometry (MS/MS) method. Electron-transfer/higher-energy collisional dissociation (EThcD), stepped collision energy/higher-energy collisional dissociation (sceHCD), higher-energy collisional dissociation-product-dependent electron-transfer dissociation (HCD-pd-ETD), and a hybrid mass spectrometry fragmentation method EThcD-sceHCD have emerged as valuable approaches for glycoprotein analysis. However, each of them incurs some compromise, necessitating the systematic performance comparisons when applied to the analysis of complex clinical samples (e.g., plasma, urine, cells, and tissues). Herein, we compared the performance of EThcD-sceHCD with those previous approaches (EThcD, sceHCD, HCD-pd-ETD, and sceHCD-pd-ETD) in the intact N-glycopeptide analysis, and determined its applicability for clinical N-glycoproteomic study. The intact N-glycopeptides of distinct samples, namely, plasma from prostate cancer (PCa) patients, urine from immunoglobulin A nephropathy (IgAN) patients, human hepatocarcinoma cell line (HepG2), and thyroid tissues from thyroid cancer (TC) patients were analyzed by these methods. We found that EThcD-sceHCD outperformed other methods in the balance of depth and accuracy of intact N-glycopeptide identification, and sceHCD and EThcD-sceHCD have good complementarity. EThcD-sceHCD holds great potential for biomarker discovery from clinical samples.
Collapse
Affiliation(s)
- Wenjuan Zeng
- Institutes for Systems Genetics, National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Shanshan Zheng
- Institutes for Systems Genetics, National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Tao Su
- Institutes for Systems Genetics, National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Jiahan Cheng
- Department of Thoracic Surgery, Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Yonghong Mao
- Department of Thoracic Surgery, Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Yi Zhong
- Institutes for Systems Genetics, National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Yueqiu Liu
- Institutes for Systems Genetics, National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Jianhai Chen
- Institutes for Systems Genetics, National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Wanjun Zhao
- Department of Thyroid Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Tianhai Lin
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Fang Liu
- Division of Nephrology, West China Hospital, Sichuan University, Chengdu, China
| | - Guisen Li
- Renal Department and Institute of Nephrology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Sichuan Clinical Research Center for Kidney Diseases, Chengdu, China
| | - Hao Yang
- Institutes for Systems Genetics, National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Hao Yang, ; Yong Zhang,
| | - Yong Zhang
- Institutes for Systems Genetics, National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Hao Yang, ; Yong Zhang,
| |
Collapse
|