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Colombino E, Gariglio M, Biasato I, Ferrocino I, Pozzo S, Fragola E, Battisti E, Zanet S, Ferroglio E, Capucchio MT, Schiavone A. Insect live larvae as a new nutritional model in duck: effects on gut health. Anim Microbiome 2024; 6:31. [PMID: 38812012 PMCID: PMC11137933 DOI: 10.1186/s42523-024-00316-5] [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: 12/06/2023] [Accepted: 05/13/2024] [Indexed: 05/31/2024] Open
Abstract
BACKGROUND This study aimed to evaluate the effects of Hermetia illucens (Black soldier fly-BSF) and Tenebrio molitor (Yellow mealworm-YMW) live larvae as a new nutritional model on duck's gut health, considering gut histomorphometry, mucin composition, cytokines transcription levels, and microbiota. A total of 126, 3-days-old, females Muscovy ducks were randomly allotted to three dietary treatments (6 replicates/treatment, 7 birds/pen): (i) C: basal diet; (ii) BSF: C + BSF live larvae; (iii) YMW: C + YMW live larvae. BSF and YMW live larvae were administered on top of the basal diet, based on the 5% of the expected daily feed intake. The live weight, average daily gain, average daily feed intake and feed conversion ratio were evaluated for the whole experimental period. On day 52, 12 ducks/treatment (2 birds/replicate) were slaughtered and samples of duodenum, jejunum, ileum, spleen, liver, thymus and bursa of Fabricius were collected for histomorphometry. Mucin composition was evaluated in the small intestine through histochemical staining while jejunal MUC-2 and cytokines transcription levels were evaluated by rt-qPCR. Cecal microbiota was also analyzed by means of 16 S rRNA gene sequencing. RESULTS Birds' growth performance and histomorphometry were not influenced by diet, with a proximo-distal decreasing gradient from duodenum to ileum (p < 0.001), respecting the physiological gut development. Mucin staining intensity and MUC-2 gene expression did not vary among dietary treatments, even though mucin intensity increased from duodenum to ileum, according to normal gut mucus physiology (p < 0.001). Regarding local immune response, IL-6 was higher in YMW group when compared to the other groups (p = 0.009). Insect live larvae did not affect cecal microbiota diversity, but BSF and YMW groups showed a higher presence of Helicobacter, Elusimicrobium, and Succinatimonas and a lower abundance of Coriobacteriaceae and Phascolarctobacterium compared to C birds (p < 0.05). CONCLUSIONS The use of BSF and YMW live larvae as new nutritional model did not impair gut development and mucin composition of Muscovy ducks, but slightly improved the intestinal immune status and the microbiota composition by enhancing regulatory cytokine IL-6 and by increasing minor Operational Taxonomic Units (OTUs) involved in short-chain fatty acids production.
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Affiliation(s)
- Elena Colombino
- Department of Veterinary Sciences, University of Turin, Grugliasco, 10095, TO, Italy
| | - Marta Gariglio
- Department of Veterinary Sciences, University of Turin, Grugliasco, 10095, TO, Italy.
| | - Ilaria Biasato
- Department of Agricultural, Forestry and Food Sciences, University of Turin, Grugliasco, 10095, TO, Italy
| | - Ilario Ferrocino
- Department of Agricultural, Forestry and Food Sciences, University of Turin, Grugliasco, 10095, TO, Italy
| | - Sara Pozzo
- National Research Council, Institute of Agricultural Biology and Biotechnology (CNR-IBBA), Milano, 20133, MI, Italy
| | - Emma Fragola
- Department of Veterinary Sciences, University of Turin, Grugliasco, 10095, TO, Italy
| | - Elena Battisti
- Department of Veterinary Sciences, University of Turin, Grugliasco, 10095, TO, Italy
| | - Stefania Zanet
- Department of Veterinary Sciences, University of Turin, Grugliasco, 10095, TO, Italy
| | - Ezio Ferroglio
- Department of Veterinary Sciences, University of Turin, Grugliasco, 10095, TO, Italy
| | - Maria Teresa Capucchio
- Department of Veterinary Sciences, University of Turin, Grugliasco, 10095, TO, Italy
- National Research Council, Institute of Science of Food Production, Grugliasco, 10095, TO, Italy
| | - Achille Schiavone
- Department of Veterinary Sciences, University of Turin, Grugliasco, 10095, TO, Italy
- National Research Council, Institute of Science of Food Production, Grugliasco, 10095, TO, Italy
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2
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Le MT, Holden DT, Manheim JM, Dziekonski ET, Iyer K, Graham Cooks R. Two-Dimensional Tandem Mass Spectrometry for Biopolymer Structural Analysis. Angew Chem Int Ed Engl 2024; 63:e202315904. [PMID: 38117612 DOI: 10.1002/anie.202315904] [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: 11/10/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 12/22/2023]
Abstract
Biopolymer analysis, including proteomics and glycomics, relies heavily on the use of mass spectrometry for structural elucidation, including sequence determination. Novel methods to improve sample workup, instrument performance, and data analysis continue to be developed to address shortcomings associated with sample preparation, analysis time, data quality, and data interpretation. Here, we present a new method that couples in-source collision-induced dissociation (IS-CID) with two-dimensional tandem mass spectrometry (2D MS/MS) as a way to simplify proteomics and glycomics workflows while also providing additional insight into analyte structures over traditional MS/MS experiments. Specifically, IS-CID is employed as a gas-phase digestion method, i.e., to break down intact full-length polysaccharide or peptide ions prior to mass analysis. The resulting mixtures of oligomeric ions are analyzed by 2D-MS/MS, a technique that allows association of product ions with their precursor ions without isolation of the latter. A novel data analysis strategy is introduced to leverage the second dimension of 2D MS/MS spectra, in which stairstep patterns, representing outputs of a molecule's MSn scans, are extracted for structural interconnectivity information on the oligomer. The results demonstrate the potential applicability of 2D MS/MS strategies to the modern omics workflow and structural analysis of various classes of biopolymers.
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Affiliation(s)
- MyPhuong T Le
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA
| | - Dylan T Holden
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA
| | - Jeremy M Manheim
- Merck & Co., Inc., Analytical Research and Development, Rahway, NJ 07065, USA
| | - Eric T Dziekonski
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA
| | - Kiran Iyer
- Merck & Co., Inc., Analytical Research and Development, Rahway, NJ 07065, USA
| | - R Graham Cooks
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA
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3
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Gallego P, Garcia-Bonete MJ, Trillo-Muyo S, Recktenwald CV, Johansson MEV, Hansson GC. The intestinal MUC2 mucin C-terminus is stabilized by an extra disulfide bond in comparison to von Willebrand factor and other gel-forming mucins. Nat Commun 2023; 14:1969. [PMID: 37031240 PMCID: PMC10082768 DOI: 10.1038/s41467-023-37666-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 03/20/2023] [Indexed: 04/10/2023] Open
Abstract
The MUC2 mucin polymer is the main building unit of the intestinal mucus layers separating intestinal microbiota from the host epithelium. The MUC2 mucin is a large glycoprotein with a C-terminal domain similar to the MUC5AC and MUC5B mucins and the von Willebrand factor (VWF). A structural model of the C-terminal part of MUC2, MUC2-C, was generated by combining Cryo-electron microscopy, AlphaFold prediction, information of its glycosylation, and small angle X-ray scattering information. The globular VWD4 assembly in the N-terminal of MUC2-C is followed by 3.5 linear VWC domains that form an extended flexible structure before the C-terminal cystine-knot. All gel-forming mucins and VWF form tail-tail disulfide-bonded dimers in their C-terminal cystine-knot domain, but interestingly the MUC2 mucin has an extra stabilizing disulfide bond on the N-terminal side of the VWD4 domain, likely essential for a stable intestinal mucus barrier.
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Affiliation(s)
- Pablo Gallego
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, SE-405 30, Gothenburg, Sweden
| | - Maria-Jose Garcia-Bonete
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, SE-405 30, Gothenburg, Sweden
| | - Sergio Trillo-Muyo
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, SE-405 30, Gothenburg, Sweden
| | - Christian V Recktenwald
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, SE-405 30, Gothenburg, Sweden
| | - Malin E V Johansson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, SE-405 30, Gothenburg, Sweden
| | - Gunnar C Hansson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, SE-405 30, Gothenburg, Sweden.
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4
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Gao H, Gao CC, Wang TT, Gao L, Li GW, Jin LY, He CW, Wang BY, Zhang L, Guo YX, Hua RX, Shang HW, Xu JD. An Unexpected Alteration Colonic Mucus Appearance in the Constipation Model via an Intestinal Microenvironment. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:1-14. [PMID: 35644608 DOI: 10.1017/s1431927622000836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Due to the lack of research between the inner layers in the structure of colonic mucous and the metabolism of fatty acid in the constipation model, we aim to determine the changes in the mucous phenotype of the colonic glycocalyx and the microbial community structure following treatment with Rhubarb extract in our research. The constipation and treatment models are generated using adult male C57BL/6N mice. We perform light microscopy and transmission electron microscopy (TEM) to detect a Muc2-rich inner mucus layer attached to mice colon under different conditions. In addition, 16S rDNA sequencing is performed to examine the intestinal flora. According to TEM images, we demonstrate that Rhubarb can promote mucin secretion and find direct evidence of dendritic structure-linked mucus structures with its assembly into a lamellar network in a pore size distribution in the isolated colon section. Moreover, the diversity of intestinal flora has noticeable changes in constipated mice. The present study characterizes a dendritic structure and persistent cross-links have significant changes accompanied by the alteration of intestinal flora in feces in models of constipation and pretreatment with Rhubarb extract.
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Affiliation(s)
- Han Gao
- Department of Physiology and Pathophysiology, Basic Medical College, Capital Medical University, Beijing 100069, China
| | - Chen-Chen Gao
- Department of Physiology and Pathophysiology, Basic Medical College, Capital Medical University, Beijing 100069, China
| | - Tian-Tian Wang
- Department of Physiology and Pathophysiology, Basic Medical College, Capital Medical University, Beijing 100069, China
| | - Lei Gao
- Department of Biomedical Informatics, School of Biomedical Engineering, Capital Medical University, Beijing 100069, China
| | - Guang-Wen Li
- Department of Physiology and Pathophysiology, Basic Medical College, Capital Medical University, Beijing 100069, China
| | - Liang-Yun Jin
- Experimental Center for Morphological Research Platform, Capital Medical University, Beijing 100069, China
| | - Cheng-Wei He
- Department of Physiology and Pathophysiology, Basic Medical College, Capital Medical University, Beijing 100069, China
| | - Bo-Ya Wang
- Undergraduate Student of 2018 Eight Program of Clinical Medicine, Peking University Health Science Center, Beijing 100069, China
| | - Lucia Zhang
- Class of 2025, Loomis Chaffee School, 4 Batchelder Road, Windsor, CT 06095, USA
| | - Yue-Xin Guo
- Oral Medicine "5+3" process, Basic Medical College, Capital Medical University, Beijing 100069, China
| | - Rong-Xuan Hua
- Department of Clinical Medicine, Basic Medical College, Capital Medical University, Beijing 100069, China
| | - Hong-Wei Shang
- Experimental Center for Morphological Research Platform, Capital Medical University, Beijing 100069, China
| | - Jing-Dong Xu
- Department of Physiology and Pathophysiology, Basic Medical College, Capital Medical University, Beijing 100069, China
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5
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Gong Y, Qin S, Dai L, Tian Z. The glycosylation in SARS-CoV-2 and its receptor ACE2. Signal Transduct Target Ther 2021; 6:396. [PMID: 34782609 PMCID: PMC8591162 DOI: 10.1038/s41392-021-00809-8] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/10/2021] [Accepted: 10/24/2021] [Indexed: 02/05/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), a highly infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected more than 235 million individuals and led to more than 4.8 million deaths worldwide as of October 5 2021. Cryo-electron microscopy and topology show that the SARS-CoV-2 genome encodes lots of highly glycosylated proteins, such as spike (S), envelope (E), membrane (M), and ORF3a proteins, which are responsible for host recognition, penetration, binding, recycling and pathogenesis. Here we reviewed the detections, substrates, biological functions of the glycosylation in SARS-CoV-2 proteins as well as the human receptor ACE2, and also summarized the approved and undergoing SARS-CoV-2 therapeutics associated with glycosylation. This review may not only broad the understanding of viral glycobiology, but also provide key clues for the development of new preventive and therapeutic methodologies against SARS-CoV-2 and its variants.
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Affiliation(s)
- Yanqiu Gong
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, 610041, Chengdu, China
| | - Suideng Qin
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, 200092, Shanghai, China
| | - Lunzhi Dai
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, 610041, Chengdu, China.
| | - Zhixin Tian
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, 200092, Shanghai, China.
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6
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Abstract
Mucin-domain glycoproteins comprise a class of proteins whose densely O-glycosylated mucin domains adopt a secondary structure with unique biophysical and biochemical properties. The canonical family of mucins is well-known to be involved in various diseases, especially cancer. Despite this, very little is known about the site-specific molecular structures and biological activities of mucins, in part because they are extremely challenging to study by mass spectrometry (MS). Here, we summarize recent advancements toward this goal, with a particular focus on mucin-domain glycoproteins as opposed to general O-glycoproteins. We summarize proteolytic digestion techniques, enrichment strategies, MS fragmentation, and intact analysis, as well as new bioinformatic platforms. In particular, we highlight mucin directed technologies such as mucin-selective proteases, tunable mucin platforms, and a mucinomics strategy to enrich mucin-domain glycoproteins from complex samples. Finally, we provide examples of targeted mucin-domain glycoproteomics that combine these techniques in comprehensive site-specific analyses of proteins. Overall, this Review summarizes the methods, challenges, and new opportunities associated with studying enigmatic mucin domains.
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Affiliation(s)
- Valentina Rangel-Angarita
- Department of Chemistry, Yale University, 275 Prospect Street, New Haven, Connecticut 06511, United States
| | - Stacy A. Malaker
- Department of Chemistry, Yale University, 275 Prospect Street, New Haven, Connecticut 06511, United States
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7
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Wang Y, Wen R, Liu D, Zhang C, Wang ZA, Du Y. Exploring Effects of Chitosan Oligosaccharides on the DSS-Induced Intestinal Barrier Impairment In Vitro and In Vivo. Molecules 2021; 26:2199. [PMID: 33920375 PMCID: PMC8070450 DOI: 10.3390/molecules26082199] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 12/12/2022] Open
Abstract
Intestinal barrier dysfunction is an essential pathological change in inflammatory bowel disease (IBD). The mucus layer and the intestinal epithelial tight junction act together to maintain barrier integrity. Studies showed that chitosan oligosaccharide (COS) had a positive effect on gut health, effectively protecting the intestinal barrier in IBD. However, these studies usually focused on its impact on the intestinal epithelial tight junction. The influence of COS on the intestinal mucus layer is still poorly understood. In this study, we explored the effect of COS on intestinal mucus in vitro using human colonic mucus-secreted HT-29 cells. COS relieved DSS (dextran sulfate sodium)-induced mucus defects. Additionally, the structural characteristics of COS greatly influenced this activity. Finally, we evaluated the protective effect of COS on intestinal barrier function in mice with DSS-induced colitis. The results indicated that COS could manipulate intestinal mucus production, which likely contributed to its intestinal protective effects.
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Affiliation(s)
- Yujie Wang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; (Y.W.); (R.W.); (D.L.)
- School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rong Wen
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; (Y.W.); (R.W.); (D.L.)
- College of Life Science, Sichuan Normal University, Chengdu 610101, China
| | - Dongdong Liu
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; (Y.W.); (R.W.); (D.L.)
| | - Chen Zhang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; (Y.W.); (R.W.); (D.L.)
| | - Zhuo A. Wang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; (Y.W.); (R.W.); (D.L.)
| | - Yuguang Du
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; (Y.W.); (R.W.); (D.L.)
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8
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Thomas DR, Scott NE. Glycoproteomics: growing up fast. Curr Opin Struct Biol 2020; 68:18-25. [PMID: 33278752 DOI: 10.1016/j.sbi.2020.10.028] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/20/2020] [Accepted: 10/25/2020] [Indexed: 02/06/2023]
Abstract
Glycoproteomics is a rapidly growing field which seeks to identify and characterise glycosylation events at a proteome scale. Over the last few years considerable effort has been made in developing new technologies, enrichment systems, and analysis strategies to enhance the quality of glycoproteomic studies. Within this review we discuss the recent developments in glycoproteomics and the current state of the art approaches for analysing glycosylated substrates. We highlight key improvements in mass spectrometry instrumentation coupled with the advancements in enrichment approaches for key classes of glycosylation including mucin-O-glycosylation, O-GlcNAc glycosylation and N-linked glycosylation which now allow the identification/quantification of hundreds to thousands of glycosylation sites within individual experiments. Finally, we summarise the emerging trends within glycoproteomics to illustrate how the field is moving away from studies simply focused on identifying glycosylated substrates to studying specific mechanisms and disease states.
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Affiliation(s)
- David R Thomas
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St, Melbourne 3000, Australia
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St, Melbourne 3000, Australia.
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9
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Kudelka MR, Stowell SR, Cummings RD, Neish AS. Intestinal epithelial glycosylation in homeostasis and gut microbiota interactions in IBD. Nat Rev Gastroenterol Hepatol 2020; 17:597-617. [PMID: 32710014 PMCID: PMC8211394 DOI: 10.1038/s41575-020-0331-7] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/05/2020] [Indexed: 02/08/2023]
Abstract
Inflammatory bowel disease (IBD) affects 6.8 million people globally. A variety of factors have been implicated in IBD pathogenesis, including host genetics, immune dysregulation and gut microbiota alterations. Emerging evidence implicates intestinal epithelial glycosylation as an underappreciated process that interfaces with these three factors. IBD is associated with increased expression of truncated O-glycans as well as altered expression of terminal glycan structures. IBD genes, glycosyltransferase mislocalization, altered glycosyltransferase and glycosidase expression and dysbiosis drive changes in the glycome. These glycan changes disrupt the mucus layer, glycan-lectin interactions, host-microorganism interactions and mucosal immunity, and ultimately contribute to IBD pathogenesis. Epithelial glycans are especially critical in regulating the gut microbiota through providing bacterial ligands and nutrients and ultimately determining the spatial organization of the gut microbiota. In this Review, we discuss the regulation of intestinal epithelial glycosylation, altered epithelial glycosylation in IBD and mechanisms for how these alterations contribute to disease pathobiology. We hope that this Review provides a foundation for future studies on IBD glycosylation and the emergence of glycan-inspired therapies for IBD.
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Affiliation(s)
- Matthew R Kudelka
- Medical Scientist Training Program, Emory University School of Medicine, Atlanta, GA, USA
- Department of Internal Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Sean R Stowell
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Richard D Cummings
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Andrew S Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA.
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10
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Choi YJ, Ohn JH, Kim N, Kim W, Park K, Won S, Sael L, Shin CM, Lee SM, Lee S, An HJ, Jang DM, Han BW, Lee HS, Kang SJ, Kim JS, Lee DH. Family-based exome sequencing combined with linkage analyses identifies rare susceptibility variants of MUC4 for gastric cancer. PLoS One 2020; 15:e0236197. [PMID: 32701958 PMCID: PMC7377420 DOI: 10.1371/journal.pone.0236197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 06/30/2020] [Indexed: 12/24/2022] Open
Abstract
Genome-wide association studies of gastric cancer (GC) cases have revealed common gastric cancer susceptibility loci with low effect size. We investigated rare variants with high effect size via whole-exome sequencing (WES) of subjects with familial clustering of gastric cancer. WES of DNAs from the blood of 19 gastric cancer patients and 36 unaffected family members from 14 families with two or more gastric cancer patients were tested. Linkage analysis combined with association tests were performed using Pedigree Variant Annotation, Analysis, and Search Tool (pVAAST) software. Based on the logarithm of odds (LOD) and permutation-based composite likelihood ratio test (CLRT) from pVAAST, MUC4 was identified as a predisposing gene (LOD P-value = 1.9×10-5; permutation-based P-value of CLRT ≤ 9.9×10-9). In a larger cohort consisting of 597 GC patients and 9,759 healthy controls genotyped with SNP array, we discovered common variants in MUC4 regions (rs148735556, rs11717039, and rs547775645) significantly associated with GC supporting the association of MUC4 with gastric cancer. And the MUC4 variants were found in higher frequency in The Cancer Genome Atlas Study (TCGA) germline samples of patients with multiple cancer types. Immunohistochemistry indicated that MUC4 was downregulated in the noncancerous gastric mucosa of subjects with MUC4 germline missense variants, suggesting that loss of the protective function of MUC4 predisposes an individual to gastric cancer. Rare variants in MUC4 can be novel gastric cancer susceptibility loci in Koreans possessing the familial clustering of gastric cancer.
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Affiliation(s)
- Yoon Jin Choi
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Jung Hun Ohn
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Nayoung Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, South Korea
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, South Korea
- * E-mail:
| | - Wonji Kim
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Kyungtaek Park
- Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, South Korea
| | - Sungho Won
- Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, South Korea
- Department of Public Health Sciences, Seoul National University, Seoul, South Korea
- Institute of Health and Environment, Seoul National University, Seoul, South Korea
| | - Lee Sael
- Department of Artificial Intelligence and Data Science, Ajou University, Seoul, South Korea
| | - Cheol Min Shin
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Sun Min Lee
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Sejoon Lee
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Hyun Joo An
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, South Korea
| | - Dong Man Jang
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Byung Woo Han
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Hye Seung Lee
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Seung Joo Kang
- Department of Internal Medicine and Healthcare Research Institute, Healthcare System Gangnam Center, Seoul National University Hospital, Seoul, South Korea
| | - Joo Sung Kim
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, South Korea
- Department of Internal Medicine and Healthcare Research Institute, Healthcare System Gangnam Center, Seoul National University Hospital, Seoul, South Korea
| | - Dong Ho Lee
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, South Korea
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, South Korea
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11
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Chen Y, Doud E, Stone T, Xin L, Hong W, Li Y. Rapid global characterization of immunoglobulin G1 following oxidative stress. MAbs 2019; 11:1089-1100. [PMID: 31156028 PMCID: PMC6748588 DOI: 10.1080/19420862.2019.1625676] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Although peroxide and leachable metal-induced chemical modifications are among the most important quality attributes in bioprocess development, there is no mainstream characterization method covering all common modifications theoretically possible on therapeutic proteins that also gives consistent results quickly. Here, we describe a method for rapid and consistent global characterization of leachable metals- or peroxide-stressed immunoglobulin (Ig) G1 monoclonal antibodies (mAbs). Using two independent protease digestions, data-independent acquisition and data-dependent acquisition liquid chromatography high-resolution mass spectrometry, we monitored 55 potential chemical modifications on trastuzumab, a humanized IgG1 mAb. Processing templates including all observed peptides were developed on Skyline to consistently monitor all modifications throughout the stress conditions for both enzymatic digestions. The Global Characterization Data Processing Site, a universal automated data processing application, was created to batch process data, plot modification trends for peptides, generate sortable and downloadable modification tables, and produce Jmol code for three-dimensional structural models of the analyzed protein. In total, 53 sites on the mAb were found to be modified. Oxidation rates generally increased with the peroxide concentration, while leachable metals alone resulted in lower rates of modifications but more oxidative degradants. Multiple chemical modifications were found on IgG1 surfaces known to interact with FcɣRIII, complement protein C1q, and FcRn, potentially affecting activity. The combination of Skyline templates and the Global Characterization Data Processing Site results in a universally applicable assay allowing users to batch process numerous modifications. Applying this new method to stability studies will promote a broader and deeper understanding of stress modifications on therapeutic proteins.
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Affiliation(s)
- Yao Chen
- a Process Development, Catalent Pharma Solutions, Inc , Bloomington , IN , USA
| | - Emma Doud
- a Process Development, Catalent Pharma Solutions, Inc , Bloomington , IN , USA
| | - Todd Stone
- a Process Development, Catalent Pharma Solutions, Inc , Bloomington , IN , USA
| | - Lun Xin
- a Process Development, Catalent Pharma Solutions, Inc , Bloomington , IN , USA
| | - Wei Hong
- a Process Development, Catalent Pharma Solutions, Inc , Bloomington , IN , USA
| | - Yunsong Li
- a Process Development, Catalent Pharma Solutions, Inc , Bloomington , IN , USA
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12
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Yamashita MSDA, Melo EO. Mucin 2 (MUC2) promoter characterization: an overview. Cell Tissue Res 2018; 374:455-463. [PMID: 30218241 DOI: 10.1007/s00441-018-2916-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 08/13/2018] [Indexed: 12/24/2022]
Abstract
Transgenic livestock have been studied with a well-known interest in improving quantitative and qualitative traits. In order to direct heterologous gene expression, it is indispensable to identify and characterize a promoter suitable for directing the expression of the gene of interest (GOI) in a tissue-specific way. The gastrointestinal tract is a desirable target for gene expression in several mammalian models. Throughout the surface of the intestinal epithelium, there is an intricate polymer network, formed by gel-forming mucins (especially MUC2 and MUC5AC, of which MUC2 is the major one), which plays a protective role due to the formation of a physical, chemical and immunological barrier between the organism and the environment. The characterization of the gel-forming mucins is difficult because of their large size and repetitive DNA sequences and domains. The main mucin in the small and large intestine, mucin 2 (MUC2), is expressed specifically in goblet cells. MUC2 plays an important role in intestinal homeostasis and its disruption is associated with several diseases and carcinomas. This mucin is also an important marker for elucidating mechanisms that regulate differentiation of the secretory cell lineage. This review presents the state of the art of MUC2 promoter structure and functional characterization.
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Affiliation(s)
| | - Eduardo O Melo
- EMBRAPA Genetic Resources and Biotechnology, PqEB Av W5 Norte, Brasilia, DF, 70770-917, Brazil
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13
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Leclaire C, Lecointe K, Gunning PA, Tribolo S, Kavanaugh DW, Wittmann A, Latousakis D, MacKenzie DA, Kawasaki N, Juge N. Molecular basis for intestinal mucin recognition by galectin-3 and C-type lectins. FASEB J 2018; 32:3301-3320. [PMID: 29401627 PMCID: PMC5976236 DOI: 10.1096/fj.201700619r] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 01/16/2018] [Indexed: 01/05/2023]
Abstract
Intestinal mucins trigger immune responses upon recognition by dendritic cells via protein-carbohydrate interactions. We used a combination of structural, biochemical, biophysical, and cell-based approaches to decipher the specificity of the interaction between mucin glycans and mammalian lectins expressed in the gut, including galectin (Gal)-3 and C-type lectin receptors. Gal-3 differentially recognized intestinal mucins with different O-glycosylation profiles, as determined by mass spectrometry (MS). Modification of mucin glycosylation, via chemical treatment leading to a loss of terminal glycans, promoted the interaction of Gal-3 to poly- N-acetyllactosamine. Specific interactions were observed between mucins and mouse dendritic cell-associated lectin (mDectin)-2 or specific intercellular adhesion molecule-grabbing nonintegrin-related-1 (SIGN-R1), but not mDectin-1, using a cell-reporter assay, as also confirmed by atomic force spectroscopy. We characterized the N-glycosylation profile of mouse colonic mucin (Muc)-2 by MS and showed that the interaction with mDectin-2 was mediated by high-mannose N-glycans. Furthermore, we observed Gal-3 binding to the 3 C-type lectins by force spectroscopy. We showed that mDectin-1, mDectin-2, and SIGN-R1 are decorated by N-glycan structures that can be recognized by the carbohydrate recognition domain of Gal-3. These findings provide a structural basis for the role of mucins in mediating immune responses and new insights into the structure and function of major mammalian lectins.-Leclaire, C., Lecointe, K., Gunning, P. A., Tribolo, S., Kavanaugh, D. W., Wittmann, A., Latousakis, D., MacKenzie, D. A., Kawasaki, N., Juge, N. Molecular basis for intestinal mucin recognition by galectin-3 and C-type lectins.
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Affiliation(s)
- Charlotte Leclaire
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Karine Lecointe
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Patrick A. Gunning
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Sandra Tribolo
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Devon W. Kavanaugh
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Alexandra Wittmann
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | | | - Donald A. MacKenzie
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Norihito Kawasaki
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Nathalie Juge
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
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14
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Affiliation(s)
- Nicholas
M. Riley
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Genome
Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Joshua J. Coon
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Genome
Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department
of Biomolecular Chemistry, University of
Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Morgridge
Institute for Research, Madison, Wisconsin 53715, United States
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15
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Ramsey KA, Rushton ZL, Ehre C. Mucin Agarose Gel Electrophoresis: Western Blotting for High-molecular-weight Glycoproteins. J Vis Exp 2016. [PMID: 27341489 DOI: 10.3791/54153] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Mucins, the heavily-glycosylated proteins lining mucosal surfaces, have evolved as a key component of innate defense by protecting the epithelium against invading pathogens. The main role of these macromolecules is to facilitate particle trapping and clearance while promoting lubrication of the mucosa. During protein synthesis, mucins undergo intense O-glycosylation and multimerization, which dramatically increase the mass and size of these molecules. These post-translational modifications are critical for the viscoelastic properties of mucus. As a result of the complex biochemical and biophysical nature of these molecules, working with mucins provides many challenges that cannot be overcome by conventional protein analysis methods. For instance, their high-molecular-weight prevents electrophoretic migration via regular polyacrylamide gels and their sticky nature causes adhesion to experimental tubing. However, investigating the role of mucins in health (e.g., maintaining mucosal integrity) and disease (e.g., hyperconcentration, mucostasis, cancer) has recently gained interest and mucins are being investigated as a therapeutic target. A better understanding of the production and function of mucin macromolecules may lead to novel pharmaceutical approaches, e.g., inhibitors of mucin granule exocytosis and/or mucolytic agents. Therefore, consistent and reliable protocols to investigate mucin biology are critical for scientific advancement. Here, we describe conventional methods to separate mucin macromolecules by electrophoresis using an agarose gel, transfer protein into nitrocellulose membrane, and detect signal with mucin-specific antibodies as well as infrared fluorescent gel reader. These techniques are widely applicable to determine mucin quantitation, multimerization and to test the effects of pharmacological compounds on mucins.
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Affiliation(s)
- Kathryn A Ramsey
- Marsico Lung Institute/CF Center, University of North Carolina at Chapel Hill; Telethon Kids Institute, University of Western Australia
| | - Zachary L Rushton
- Marsico Lung Institute/CF Center, University of North Carolina at Chapel Hill
| | - Camille Ehre
- Marsico Lung Institute/CF Center, University of North Carolina at Chapel Hill; Department of Pediatrics, University of North Carolina at Chapel Hill;
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Linke D, Koudelka T, Becker A, Tholey A. Identification and relative quantification of phosphopeptides by a combination of multi-protease digestion and isobaric labeling. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:919-926. [PMID: 26407306 DOI: 10.1002/rcm.7185] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/18/2015] [Accepted: 02/25/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE The identification and the determination of the extent of protein phosphorylation are major prerequisites for the comparative analysis of this important posttranslational modification of proteins in different biological situations. High sequence coverages and the availability of straightforward quantification methods are necessary to achieve these goals. METHODS Phosphoproteins and non-phosphorylated analogues separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) were digested using four different proteases (trypsin, chymotrypsin, elastase and GluC) and the digests were isobarically labeled using eight-plex iTRAQ. The combined labeled digests were subsequently enriched using titanium dioxide and both the phosphorylated and non-phosphorylated fractions were analyzed by liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS). The influence of different data analysis algorithms (Percolator or False Discovery Rate) on the outcome of analysis was investigated. RESULTS Almost complete sequence coverage could be achieved upon application of a multi-protease approach. The formation of peptides of different lengths and physicochemical properties allowed the identification and the mapping of all phosphorylation sites in the investigated model proteins. The introduction of isobaric labels allowed quantification of different peptides of the same phosphorylation site with more than one peptide, leading to significantly improved statistical confidence. CONCLUSIONS A workflow for the straightforward comparative analysis of protein phosphorylation in samples of low complexity, e.g. isolated proteins, was developed. The workflow is transferable to other posttranslational modifications.
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Affiliation(s)
- Dennis Linke
- Institut für Experimentelle Medizin - AG Systematische Proteomforschung und Bioanalytik, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany
| | - Tomas Koudelka
- Institut für Experimentelle Medizin - AG Systematische Proteomforschung und Bioanalytik, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany
| | - Alexander Becker
- Institut für Experimentelle Medizin - AG Systematische Proteomforschung und Bioanalytik, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany
| | - Andreas Tholey
- Institut für Experimentelle Medizin - AG Systematische Proteomforschung und Bioanalytik, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany
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