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Li H, Peralta AG, Schoffelen S, Hansen AH, Arnsdorf J, Schinn SM, Skidmore J, Choudhury B, Paulchakrabarti M, Voldborg BG, Chiang AW, Lewis NE. LeGenD: determining N-glycoprofiles using an explainable AI-leveraged model with lectin profiling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.587044. [PMID: 38585977 PMCID: PMC10996628 DOI: 10.1101/2024.03.27.587044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Glycosylation affects many vital functions of organisms. Therefore, its surveillance is critical from basic science to biotechnology, including biopharmaceutical development and clinical diagnostics. However, conventional glycan structure analysis faces challenges with throughput and cost. Lectins offer an alternative approach for analyzing glycans, but they only provide glycan epitopes and not full glycan structure information. To overcome these limitations, we developed LeGenD, a lectin and AI-based approach to predict N-glycan structures and determine their relative abundance in purified proteins based on lectin-binding patterns. We trained the LeGenD model using 309 glycoprofiles from 10 recombinant proteins, produced in 30 glycoengineered CHO cell lines. Our approach accurately reconstructed experimentally-measured N-glycoprofiles of bovine Fetuin B and IgG from human sera. Explanatory AI analysis with SHapley Additive exPlanations (SHAP) helped identify the critical lectins for glycoprofile predictions. Our LeGenD approach thus presents an alternative approach for N-glycan analysis.
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Affiliation(s)
- Haining Li
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Angelo G. Peralta
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sanne Schoffelen
- National Biologics Facility Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby Denmark
| | - Anders Holmgaard Hansen
- National Biologics Facility Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby Denmark
| | - Johnny Arnsdorf
- National Biologics Facility Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby Denmark
| | - Song-Min Schinn
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jonathan Skidmore
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Biswa Choudhury
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mousumi Paulchakrabarti
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bjorn G. Voldborg
- National Biologics Facility Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby Denmark
| | - Austin W.T. Chiang
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nathan E. Lewis
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
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Yue Z, Yu Y, Gao B, Wang D, Sun H, Feng Y, Ma Z, Xie X. Advances in protein glycosylation and its role in tissue repair and regeneration. Glycoconj J 2023; 40:355-373. [PMID: 37097318 DOI: 10.1007/s10719-023-10117-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 04/10/2023] [Accepted: 04/16/2023] [Indexed: 04/26/2023]
Abstract
After tissue damage, a series of molecular and cellular events are initiated to promote tissue repair and regeneration to restore its original structure and function. These events include inter-cell communication, cell proliferation, cell migration, extracellular matrix differentiation, and other critical biological processes. Glycosylation is the crucial conservative and universal post-translational modification in all eukaryotic cells [1], with influential roles in intercellular recognition, regulation, signaling, immune response, cellular transformation, and disease development. Studies have shown that abnormally glycosylation of proteins is a well-recognized feature of cancer cells, and specific glycan structures are considered markers of tumor development. There are many studies on gene expression and regulation during tissue repair and regeneration. Still, there needs to be more knowledge of complex carbohydrates' effects on tissue repair and regeneration, such as glycosylation. Here, we present a review of studies investigating protein glycosylation in the tissue repair and regeneration process.
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Affiliation(s)
- Zhongyu Yue
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, China
| | - Yajie Yu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, China
| | - Boyuan Gao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, China
| | - Du Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, China
| | - Hongxiao Sun
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, China
| | - Yue Feng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, China
| | - Zihan Ma
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, China
| | - Xin Xie
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, China.
- GeWu Medical Research Institute (GMRI), Xi'an, China.
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Meng X, Song M, Vilaj M, Štambuk J, Dolikun M, Zhang J, Liu D, Wang H, Zhang X, Zhang J, Cao W, Momčilović A, Trbojević-Akmačić I, Li X, Zheng D, Wu L, Guo X, Wang Y, Lauc G, Wang W. Glycosylation of IgG Associates with Hypertension and Type 2 Diabetes Mellitus Comorbidity in the Chinese Muslim Ethnic Minorities and the Han Chinese. J Pers Med 2021; 11:jpm11070614. [PMID: 34209622 PMCID: PMC8307283 DOI: 10.3390/jpm11070614] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 01/07/2023] Open
Abstract
Objectives: Hypertension and type 2 diabetes mellitus comorbidity (HDC) is common, which confers a higher risk of cardiovascular disease than the presence of either condition alone. Describing the underlying glycomic changes of immunoglobulin G (IgG) that predispose individuals to HDC may help develop novel protective immune-targeted and anti-inflammatory therapies. Therefore, we investigated glycosylation changes of IgG associated with HDC. Methods: The IgG N-glycan profiles of 883 plasma samples from the three northwestern Chinese Muslim ethnic minorities and the Han Chinese were analyzed by ultra-performance liquid chromatography instrument. Results: We found that 12 and six IgG N-glycan traits showed significant associations with HDC in the Chinese Muslim ethnic minorities and the Han Chinese, respectively, after adjustment for potential confounders and false discovery rate. Adding the IgG N-glycan traits to the baseline models, the area under the receiver operating characteristic curves (AUCs) of the combined models differentiating HDC from hypertension (HTN), type 2 diabetes mellitus (T2DM), and healthy individuals were 0.717, 0.747, and 0.786 in the pooled samples of Chinese Muslim ethnic minorities, and 0.828, 0.689, and 0.901 in the Han Chinese, respectively, showing improved discriminating performance than both the baseline models and the glycan-based models. Conclusion: Altered IgG N-glycan profiles were shown to associate with HDC, suggesting the involvement of inflammatory processes of IgG glycosylation. The alterations of IgG N-glycome, illustrated here for the first time in HDC, demonstrate a biomarker potential, which may shed light on future studies investigating their potential for monitoring or preventing the progression from HTN or T2DM towards HDC.
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Affiliation(s)
- Xiaoni Meng
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China; (X.M.); (J.Z.); (D.L.); (X.Z.); (J.Z.); (W.C.); (D.Z.); (L.W.); (X.G.); (Y.W.); (W.W.)
| | - Manshu Song
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China; (X.M.); (J.Z.); (D.L.); (X.Z.); (J.Z.); (W.C.); (D.Z.); (L.W.); (X.G.); (Y.W.); (W.W.)
- School of Medical and Health Sciences, Edith Cowan University, Perth, WA 6027, Australia;
- Correspondence:
| | - Marija Vilaj
- Genos Glycoscience Research Laboratory, 10000 Zagreb, Croatia; (M.V.); (J.Š.); (A.M.); (I.T.-A.); (G.L.)
| | - Jerko Štambuk
- Genos Glycoscience Research Laboratory, 10000 Zagreb, Croatia; (M.V.); (J.Š.); (A.M.); (I.T.-A.); (G.L.)
| | - Mamatyusupu Dolikun
- College of the Life Sciences and Technology, Xinjiang University, Urumqi 830046, China;
| | - Jie Zhang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China; (X.M.); (J.Z.); (D.L.); (X.Z.); (J.Z.); (W.C.); (D.Z.); (L.W.); (X.G.); (Y.W.); (W.W.)
| | - Di Liu
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China; (X.M.); (J.Z.); (D.L.); (X.Z.); (J.Z.); (W.C.); (D.Z.); (L.W.); (X.G.); (Y.W.); (W.W.)
| | - Hao Wang
- Department of Clinical Epidemiology and Evidence-Based Medicine, National Clinical Research Center for Digestive Disease, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China;
| | - Xiaoyu Zhang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China; (X.M.); (J.Z.); (D.L.); (X.Z.); (J.Z.); (W.C.); (D.Z.); (L.W.); (X.G.); (Y.W.); (W.W.)
| | - Jinxia Zhang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China; (X.M.); (J.Z.); (D.L.); (X.Z.); (J.Z.); (W.C.); (D.Z.); (L.W.); (X.G.); (Y.W.); (W.W.)
| | - Weijie Cao
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China; (X.M.); (J.Z.); (D.L.); (X.Z.); (J.Z.); (W.C.); (D.Z.); (L.W.); (X.G.); (Y.W.); (W.W.)
| | - Ana Momčilović
- Genos Glycoscience Research Laboratory, 10000 Zagreb, Croatia; (M.V.); (J.Š.); (A.M.); (I.T.-A.); (G.L.)
| | - Irena Trbojević-Akmačić
- Genos Glycoscience Research Laboratory, 10000 Zagreb, Croatia; (M.V.); (J.Š.); (A.M.); (I.T.-A.); (G.L.)
| | - Xingang Li
- School of Medical and Health Sciences, Edith Cowan University, Perth, WA 6027, Australia;
- Centre for Precision Health, Edith Cowan University, Perth, WA 6027, Australia
| | - Deqiang Zheng
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China; (X.M.); (J.Z.); (D.L.); (X.Z.); (J.Z.); (W.C.); (D.Z.); (L.W.); (X.G.); (Y.W.); (W.W.)
| | - Lijuan Wu
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China; (X.M.); (J.Z.); (D.L.); (X.Z.); (J.Z.); (W.C.); (D.Z.); (L.W.); (X.G.); (Y.W.); (W.W.)
| | - Xiuhua Guo
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China; (X.M.); (J.Z.); (D.L.); (X.Z.); (J.Z.); (W.C.); (D.Z.); (L.W.); (X.G.); (Y.W.); (W.W.)
| | - Youxin Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China; (X.M.); (J.Z.); (D.L.); (X.Z.); (J.Z.); (W.C.); (D.Z.); (L.W.); (X.G.); (Y.W.); (W.W.)
- School of Medical and Health Sciences, Edith Cowan University, Perth, WA 6027, Australia;
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, 10000 Zagreb, Croatia; (M.V.); (J.Š.); (A.M.); (I.T.-A.); (G.L.)
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia
| | - Wei Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China; (X.M.); (J.Z.); (D.L.); (X.Z.); (J.Z.); (W.C.); (D.Z.); (L.W.); (X.G.); (Y.W.); (W.W.)
- School of Medical and Health Sciences, Edith Cowan University, Perth, WA 6027, Australia;
- Centre for Precision Health, Edith Cowan University, Perth, WA 6027, Australia
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Wang M, Zhu J, Lubman DM, Gao C. Aberrant glycosylation and cancer biomarker discovery: a promising and thorny journey. Clin Chem Lab Med 2019; 57:407-416. [PMID: 30138110 PMCID: PMC6785348 DOI: 10.1515/cclm-2018-0379] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 07/15/2018] [Indexed: 12/12/2022]
Abstract
Glycosylation is among the most important post-translational modifications for proteins and is of intrinsic complex character compared with DNAs and naked proteins. Indeed, over 50%-70% of proteins in circulation are glycosylated, and the "sweet attachments" have versatile structural and functional implications. Both the configuration and composition of the attached glycans affect the biological activities of consensus proteins significantly. Glycosylation is generated by complex biosynthetic pathways comprising hundreds of glycosyltransferases, glycosidases, transcriptional factors, transporters and the protein backbone. In addition, lack of direct genetic templates and glyco-specific antibodies such as those commonly used in DNA amplification and protein capture makes research on glycans and glycoproteins even more difficult, thus resulting in sparse knowledge on the pathophysiological implications of glycosylation. Fortunately, cutting-edge technologies have afforded new opportunities and approaches for investigating cancer-related glycosylation. Thus, glycans as well as aberrantly glycosylated protein-based cancer biomarkers have been increasingly recognized. This mini-review highlights the most recent developments in glyco-biomarker studies in an effort to discover clinically relevant cancer biomarkers using advanced analytical methodologies such as mass spectrometry, high-performance liquid chromatographic/ultra-performance liquid chromatography, capillary electrophoresis, and lectin-based technologies. Recent clinical-centered glycobiological studies focused on determining the regulatory mechanisms and the relation with diagnostics, prognostics and even therapeutics are also summarized. These studies indicate that glycomics is a treasure waiting to be mined where the growth of cancer-related glycomics and glycoproteomics is the next great challenge after genomics and proteomics.
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Affiliation(s)
- Mengmeng Wang
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, P.R. China
| | - Jianhui Zhu
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA
| | - David M. Lubman
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Chunfang Gao
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai 200438, P.R. China
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Abstract
Ultrahigh performance liquid chromatography (UHPLC) uses small stationary-phase particle size (<2 μm) and high pressure in order to achieve rapid and efficient separations. The speed and high resolution of this method has made it a valuable tool for analyzing the complex glycosylation patterns found in post-translationally modified proteins. This article highlights the differences between UHPLC and HPLC and reviews recent UHPLC applications and developments for detecting glycosylated proteins (e.g., glycomics studies) and characterizing glycosylated pharmaceuticals (e.g., monoclonal antibodies).
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Largy E, Cantais F, Van Vyncht G, Beck A, Delobel A. Orthogonal liquid chromatography-mass spectrometry methods for the comprehensive characterization of therapeutic glycoproteins, from released glycans to intact protein level. J Chromatogr A 2017; 1498:128-146. [PMID: 28372839 DOI: 10.1016/j.chroma.2017.02.072] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 01/04/2017] [Accepted: 02/28/2017] [Indexed: 01/16/2023]
Abstract
Proteins are increasingly used as therapeutics. Their characterization is challenging due to their size and inherent heterogeneity notably caused by post-translational modifications, among which glycosylation is probably the most prominent. The glycosylation profile of therapeutic proteins must therefore be thoroughly analyzed. Here, we illustrate how the use of a combination of various cutting-edge LC or LC/MS(/MS) methods, and operating at different levels of analysis allows the comprehensive characterization of both the N- and O-glycosylations of therapeutic proteins without the need for other approaches (capillary electrophoresis, MALDI-TOF). This workflow does not call for the use of highly specialized/custom hardware and software nor an extensive knowledge of glycan analysis. Most notably, we present the point of view of a contract research organization, with the constraints associated to the work in a regulated environment (GxP). Two salient points of this work are i) the use of mixed-mode chromatography as a fast and straightforward mean of profiling N-glycans sialylation as well as an orthogonal method to separate N-glycans co-eluting in the HILIC mode; and ii) the use of widepore HILIC/MS to analyze challenging N/O-glycosylation profiles at both the peptide and subunit levels. A particular attention was given to the sample preparations in terms of duration, specificity, versatility, and robustness, as well as the ease of data processing.
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Affiliation(s)
- Eric Largy
- Quality Assistance sa, Technoparc de Thudinie 2, 6536, Donstiennes, Belgium
| | - Fabrice Cantais
- Quality Assistance sa, Technoparc de Thudinie 2, 6536, Donstiennes, Belgium
| | - Géry Van Vyncht
- Quality Assistance sa, Technoparc de Thudinie 2, 6536, Donstiennes, Belgium
| | - Alain Beck
- Centre d'Immunologie Pierre Fabre (CIPF), 5 Av. Napoléon III, BP 60497, 74164, Saint-Julien-en-Genevois, France
| | - Arnaud Delobel
- Quality Assistance sa, Technoparc de Thudinie 2, 6536, Donstiennes, Belgium.
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