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1
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Mach N. The forecasting power of the mucin-microbiome interplay in livestock respiratory diseases. Vet Q 2024; 44:1-18. [PMID: 38606662 PMCID: PMC11018052 DOI: 10.1080/01652176.2024.2340003] [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: 05/23/2023] [Accepted: 03/31/2024] [Indexed: 04/13/2024] Open
Abstract
Complex respiratory diseases are a significant challenge for the livestock industry worldwide. These diseases considerably impact animal health and welfare and cause severe economic losses. One of the first lines of pathogen defense combines the respiratory tract mucus, a highly viscous material primarily composed of mucins, and a thriving multi-kingdom microbial ecosystem. The microbiome-mucin interplay protects from unwanted substances and organisms, but its dysfunction may enable pathogenic infections and the onset of respiratory disease. Emerging evidence also shows that noncoding regulatory RNAs might modulate the structure and function of the microbiome-mucin relationship. This opinion paper unearths the current understanding of the triangular relationship between mucins, the microbiome, and noncoding RNAs in the context of respiratory infections in animals of veterinary interest. There is a need to look at these molecular underpinnings that dictate distinct health and disease outcomes to implement effective prevention, surveillance, and timely intervention strategies tailored to the different epidemiological contexts.
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Affiliation(s)
- Núria Mach
- IHAP, Université de Toulouse, INRAE, ENVT, Toulouse, France
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2
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Marie AL, Gao Y, Ivanov AR. Native N-glycome profiling of single cells and ng-level blood isolates using label-free capillary electrophoresis-mass spectrometry. Nat Commun 2024; 15:3847. [PMID: 38719792 PMCID: PMC11079027 DOI: 10.1038/s41467-024-47772-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 04/12/2024] [Indexed: 05/12/2024] Open
Abstract
The development of reliable single-cell dispensers and substantial sensitivity improvement in mass spectrometry made proteomic profiling of individual cells achievable. Yet, there are no established methods for single-cell glycome analysis due to the inability to amplify glycans and sample losses associated with sample processing and glycan labeling. In this work, we present an integrated platform coupling online in-capillary sample processing with high-sensitivity label-free capillary electrophoresis-mass spectrometry for N-glycan profiling of single mammalian cells. Direct and unbiased quantitative characterization of single-cell surface N-glycomes are demonstrated for HeLa and U87 cells, with the detection of up to 100 N-glycans per single cell. Interestingly, N-glycome alterations are unequivocally detected at the single-cell level in HeLa and U87 cells stimulated with lipopolysaccharide. The developed workflow is also applied to the profiling of ng-level amounts (5-500 ng) of blood-derived protein, extracellular vesicle, and total plasma isolates, resulting in over 170, 220, and 370 quantitated N-glycans, respectively.
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Affiliation(s)
- Anne-Lise Marie
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, US
| | - Yunfan Gao
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, US
| | - Alexander R Ivanov
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, US.
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3
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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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4
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Sebek M, Menichetti G. Network Science and Machine Learning for Precision Nutrition. PRECISION NUTRITION 2024:367-402. [DOI: 10.1016/b978-0-443-15315-0.00012-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2025]
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5
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Clark A, Mach N. The gut mucin-microbiota interactions: a missing key to optimizing endurance performance. Front Physiol 2023; 14:1284423. [PMID: 38074323 PMCID: PMC10703311 DOI: 10.3389/fphys.2023.1284423] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/27/2023] [Indexed: 01/22/2025] Open
Abstract
Endurance athletes offer unique physiology and metabolism compared to sedentary individuals. Athletes training at high intensities for prolonged periods are at risk for gastrointestinal disturbances. An important factor in endurance performance is the integrity and function of the gut barrier, which primarily depends on heavily O-glycosylated mucins. Emerging evidence shows a complex bidirectional dialogue between glycans on mucins and gut microorganisms. This review emphasizes the importance of the crosstalk between the gut microbiome and host mucus mucins and some of the mechanisms underlying this symbiosis. The contribution of mucin glycans to the composition and functionality of the gut microbiome is discussed, as well as the persuasive impact of the gut microbiome on mucin composition, thickness, and immune and metabolic functions. Lastly, we propose natural and synthetic glycans supplements to improve intestinal mucus production and barrier function, offering new opportunities to enhance endurance athletes' performance and gut health.
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Affiliation(s)
- Allison Clark
- Universitat Oberta de Catalunya, Universitat de Catalunya, Barcelona, Spain
| | - Núria Mach
- Interactions hôtes-agents pathogènes, Université de Toulouse, Institut national de recherche pour l’agriculture, l’alimentation et l’environnement, École nationale vétérinaire de Toulouse, Toulouse, France
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6
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Ivanov A, Marie AL, Gao Y. In-capillary sample processing coupled to label-free capillary electrophoresis-mass spectrometry to decipher the native N-glycome of single mammalian cells and ng-level blood isolates. RESEARCH SQUARE 2023:rs.3.rs-3500983. [PMID: 38014012 PMCID: PMC10680937 DOI: 10.21203/rs.3.rs-3500983/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The development of reliable single-cell dispensers and substantial sensitivity improvement in mass spectrometry made proteomic profiling of individual cells achievable. Yet, there are no established methods for single-cell glycome analysis due to the inability to amplify glycans and sample losses associated with sample processing and glycan labeling. In this work, we developed an integrated platform coupling online in-capillary sample processing with high-sensitivity label-free capillary electrophoresis-mass spectrometry for N-glycan profiling of single mammalian cells. Direct and unbiased characterization and quantification of single-cell surface N-glycomes were demonstrated for HeLa and U87 cells, with the detection of up to 100 N-glycans per single cell. Interestingly, N-glycome alterations were unequivocally detected at the single-cell level in HeLa and U87 cells stimulated with lipopolysaccharide. The developed workflow was also applied to the profiling of ng-level amounts of blood-derived protein, extracellular vesicle, and total plasma isolates, resulting in over 170, 220, and 370 quantitated N-glycans, respectively.
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7
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dos Reis JS, Rodrigues da Costa Santos MA, Mendonça DP, Martins do Nascimento SI, Barcelos PM, Correia de Lima RG, da Costa KM, Freire-de-Lima CG, Morrot A, Previato JO, Mendonça Previato L, da Fonseca LM, Freire-de-Lima L. Glycobiology of Cancer: Sugar Drives the Show. MEDICINES 2022; 9:medicines9060034. [PMID: 35736247 PMCID: PMC9229842 DOI: 10.3390/medicines9060034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 11/16/2022]
Abstract
Cancer development and progression is associated with aberrant changes in cellular glycosylation. Cells expressing altered glycan-structures are recognized by cells of the immune system, favoring the induction of inhibitory immune processes which subsequently promote tumor growth and spreading. Here, we discuss about the importance of glycobiology in modern medicine, taking into account the impact of altered glycan structures expressed in cancer cells as potential glycobiomarkers of disease, as well as on cancer development and progression.
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Affiliation(s)
- Jhenifer Santos dos Reis
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Marcos André Rodrigues da Costa Santos
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Daniella Pereira Mendonça
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Stefani Ingrid Martins do Nascimento
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Pedro Marçal Barcelos
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Rafaela Gomes Correia de Lima
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Kelli Monteiro da Costa
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Celio Geraldo Freire-de-Lima
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Alexandre Morrot
- Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro 21040-360, Brazil;
- Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21044-020, Brazil
| | - Jose Osvaldo Previato
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Lucia Mendonça Previato
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Leonardo Marques da Fonseca
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
| | - Leonardo Freire-de-Lima
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil; (J.S.d.R.); (M.A.R.d.C.S.); (D.P.M.); (S.I.M.d.N.); (P.M.B.); (R.G.C.d.L.); (K.M.d.C.); (C.G.F.-d.-L.); (J.O.P.); (L.M.P.); (L.M.d.F.)
- Correspondence: ; Tel./Fax: +55-21-3938-6646
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8
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Cvetko A, Tijardović M, Bilandžija-Kuš I, Gornik O. Comparison of self-sampling blood collection for N-glycosylation analysis. BMC Res Notes 2022; 15:61. [PMID: 35172879 PMCID: PMC8849020 DOI: 10.1186/s13104-022-05958-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 02/07/2022] [Indexed: 11/27/2022] Open
Abstract
Objective Self-sampling of capillary blood provides easier sample collection, handling, and shipping compared to more invasive blood sampling via venepuncture. Recently, other means of capillary blood collection were introduced to the market, such as Neoteryx sticks and Noviplex cards. We tested the comparability of these two self-sampling methods, alongside dried blood spots (DBS), with plasma acquired from venepunctured blood in N-glycoprofiling of total proteins. We have also tested the intra-day repeatability of the three mentioned self-sampling methods. Capillary blood collection with Neoteryx, Noviplex and DBS was done following the manufacturers’ instructions and N-glycoprofiling of released, fluorescently labelled N-glycans was performed with ultra-performance liquid chromatography. Results Comparability with plasma was assessed by calculating the relative deviance, which was 0.674 for DBS, 0.092 for Neoteryx sticks, and 0.069 for Noviplex cards. In repeatability testing, similar results were obtained, with Noviplex cards and Neoteryx sticks performing substantially better than DBS (CVs = 4.831% and 7.098%, compared to 14.305%, respectively). Our preliminary study on the use of Neoteryx and Noviplex self-sampling devices in glycoanalysis demonstrates their satisfactory performance in both the comparability and repeatability testing, however, they should be further tested in larger collaborations and cohorts. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-022-05958-9.
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Affiliation(s)
- Ana Cvetko
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Ante Kovačića 1, 10000, Zagreb, Croatia
| | - Marko Tijardović
- 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.
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Gao L, Zhang J, Ran X, Jia X, Xing Y, Dai T, Song W, Wu Z, Sun W, Shan D. Urinary Proteomics for Noninvasive Prenatal Screening of Trisomy 21: New Biomarker Candidates. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:738-744. [PMID: 34714146 DOI: 10.1089/omi.2021.0154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Trisomy 21 is a common birth defect in humans. Screening for trisomy 21 is one of the most important tasks in routine prenatal care and robust noninvasive diagnostics are needed in clinical practice. Urinary proteomics offers a new research platform for diagnostics innovation in this context. We report here new biomarker candidates using urinary proteomics profiling. Specifically, we used liquid chromatography-tandem mass spectrometry (LC-MS/MS) to analyze the proteomes of urine samples from 19 pregnant women (aged 28-44 years) carrying fetuses with trisomy 21 and 22 healthy pregnant women (aged 27-42 years) carrying fetuses with normal karyotype. We identified more than 50 differentially expressed proteins between the trisomy 21 group and healthy group, and most of these proteins were associated with the embryonic development. Importantly, tissue inhibitor of metalloproteinases 2 (TIMP2) and lysosomal-associated membrane protein 2 (LAMP2) were further selected as potential urinary protein biomarkers. We found that the combination of TIMP2 and LAMP2 could differentiate fetuses with trisomy 21 from healthy controls with a sensitivity of 74%, a specificity of 82%, and an area under the receiver operating characteristic curves (AUC) value of 0.82 (95% confidence interval, 0.69-0.95). We conclude that TIMP2 and LAMP2 offer promise as biomarker candidates and warrant further clinical research in larger study samples. These findings further our understanding of the pathological processes involved in fetal trisomy 21 and are poised to accelerate the development of new noninvasive potential biomarkers for trisomy 21 prenatal screening.
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Affiliation(s)
- Lei Gao
- Beijing Obstetrics and Gynecology Hospital, Capital Medical University. Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Jian Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Xiaoju Ran
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.,School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Xue Jia
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Yiyi Xing
- Beijing Obstetrics and Gynecology Hospital, Capital Medical University. Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Tianyi Dai
- Beijing Obstetrics and Gynecology Hospital, Capital Medical University. Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Wei Song
- Beijing Obstetrics and Gynecology Hospital, Capital Medical University. Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Ze Wu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Wei Sun
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.,School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Dan Shan
- Beijing Obstetrics and Gynecology Hospital, Capital Medical University. Beijing Maternal and Child Health Care Hospital, Beijing, China
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10
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Banerjee S, Prabhu Basrur N, Rai PS. Omics technologies in personalized combination therapy for cardiovascular diseases: challenges and opportunities. Per Med 2021; 18:595-611. [PMID: 34689602 DOI: 10.2217/pme-2021-0087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The primary purpose of 'omics' technologies is to understand the intricacy of genomics, proteomics, metabolomics and other molecular mechanisms to reveal the complex traits of human diseases. The significant use of omics technologies and their applications in medicine gear up the study of the pathogenesis of several disorders. The detection of biomarkers in the early onset of diseases is challenging; still, omics can discover novel molecular mechanisms and biomarkers. In this review, the different types of omics and their technologies are explicated and aimed to provide their emerging applications in cardiovascular precision medicine. These technologies significantly impact optimizing medical treatment for individuals to reach a higher level in precision medicine.
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Affiliation(s)
- Saradindu Banerjee
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Navya Prabhu Basrur
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Padmalatha S Rai
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
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11
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Wang S, Yong H, He XD. Multi-omics: Opportunities for research on mechanism of type 2 diabetes mellitus. World J Diabetes 2021; 12:1070-1080. [PMID: 34326955 PMCID: PMC8311486 DOI: 10.4239/wjd.v12.i7.1070] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 03/22/2021] [Accepted: 05/22/2021] [Indexed: 02/06/2023] Open
Abstract
Type 2 diabetes mellitus (T2DM) is a burdensome global disease. In-depth understanding of its mechanism will help to optimize diagnosis and treatment, which reduces the burden. Multi-omics research has unparalleled advantages in contributing to the overall understanding of the mechanism of this chronic metabolic disease. In the past two decades, the study of multi-omics on T2DM-related intestinal flora perturbation and plasma dyslipidemia has shown tremendous potential and is expected to achieve major breakthroughs. The regulation of intestinal flora in diabetic patients has been confirmed by multiple studies. The use of metagenomics, 16S RNA sequencing, and metabolomics has comprehensively identified the overall changes in the intestinal flora and the metabolic disturbances that could directly or indirectly participate in the intestinal flora-host interactions. Lipidomics combined with other “omics” has characterized lipid metabolism disorders in T2DM. The combined application and cross-validation of multi-omics can screen for dysregulation in T2DM, which will provide immense opportunities to understand the mechanisms behind T2DM.
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Affiliation(s)
- Shuai Wang
- Institute of Toxicology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong Province, China
| | - Hui Yong
- Institute of Toxicology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong Province, China
| | - Xiao-Dong He
- Department of Physical and Chemical Inspection, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong Province, China
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12
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Wang X, Zhong Z, Wang W. COVID-19 and Preparing Planetary Health for Future Ecological Crises: Hopes from Glycomics for Vaccine Innovation. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:234-241. [PMID: 33794117 DOI: 10.1089/omi.2021.0011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
A key lesson emerging from COVID-19 is that pandemic proofing planetary health against future ecological crises calls for systems science and preventive medicine innovations. With greater proximity of the human and animal natural habitats in the 21st century, it is also noteworthy that zoonotic infections such as COVID-19 that jump from animals to humans are increasingly plausible in the coming decades. In this context, glycomics technologies and the third alphabet of life, the sugar code, offer veritable prospects to move omics systems science from discovery to diverse applications of relevance to global public health and preventive medicine. In this expert review, we discuss the science of glycomics, its importance in vaccine development, and the recent progress toward discoveries on the sugar code that can help prevent future infectious outbreaks that are looming on the horizon in the 21st century. Glycomics offers veritable prospects to boost planetary health, not to mention the global scientific capacity for vaccine innovation against novel and existing infectious agents.
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Affiliation(s)
- Xueqing Wang
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
- Centre for Precision Health, ECU Strategic Research Centre, Edith Cowan University, Perth, Australia
| | - Zhaohua Zhong
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
- School of Basic Medicine, Harbin Medical University, Harbin, China
| | - Wei Wang
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
- Centre for Precision Health, ECU Strategic Research Centre, Edith Cowan University, Perth, Australia
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Martins ÁM, Ramos CC, Freitas D, Reis CA. Glycosylation of Cancer Extracellular Vesicles: Capture Strategies, Functional Roles and Potential Clinical Applications. Cells 2021; 10:cells10010109. [PMID: 33430152 PMCID: PMC7827205 DOI: 10.3390/cells10010109] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/29/2020] [Accepted: 01/04/2021] [Indexed: 12/12/2022] Open
Abstract
Glycans are major constituents of extracellular vesicles (EVs). Alterations in the glycosylation pathway are a common feature of cancer cells, which gives rise to de novo or increased synthesis of particular glycans. Therefore, glycans and glycoproteins have been widely used in the clinic as both stratification and prognosis cancer biomarkers. Interestingly, several of the known tumor-associated glycans have already been identified in cancer EVs, highlighting EV glycosylation as a potential source of circulating cancer biomarkers. These particles are crucial vehicles of cell–cell communication, being able to transfer molecular information and to modulate the recipient cell behavior. The presence of particular glycoconjugates has been described to be important for EV protein sorting, uptake and organ-tropism. Furthermore, specific EV glycans or glycoproteins have been described to be able to distinguish tumor EVs from benign EVs. In this review, the application of EV glycosylation in the development of novel EV detection and capture methodologies is discussed. In addition, we highlight the potential of EV glycosylation in the clinical setting for both cancer biomarker discovery and EV therapeutic delivery strategies.
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Affiliation(s)
- Álvaro M. Martins
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal; (Á.M.M.); (C.C.R.)
- Institute of Molecular Pathology and Immunology (IPATIMUP), University of Porto, 4200-135 Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
| | - Cátia C. Ramos
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal; (Á.M.M.); (C.C.R.)
- Institute of Molecular Pathology and Immunology (IPATIMUP), University of Porto, 4200-135 Porto, Portugal
- Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Daniela Freitas
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal; (Á.M.M.); (C.C.R.)
- Institute of Molecular Pathology and Immunology (IPATIMUP), University of Porto, 4200-135 Porto, Portugal
- Correspondence: (D.F.); (C.A.R.); Tel.:+351-225-570-786 (C.A.R.)
| | - Celso A. Reis
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal; (Á.M.M.); (C.C.R.)
- Institute of Molecular Pathology and Immunology (IPATIMUP), University of Porto, 4200-135 Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal
- Correspondence: (D.F.); (C.A.R.); Tel.:+351-225-570-786 (C.A.R.)
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14
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Bonnardel F, Mariethoz J, Pérez S, Imberty A, Lisacek F. LectomeXplore, an update of UniLectin for the discovery of carbohydrate-binding proteins based on a new lectin classification. Nucleic Acids Res 2021; 49:D1548-D1554. [PMID: 33174598 PMCID: PMC7778903 DOI: 10.1093/nar/gkaa1019] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/13/2020] [Accepted: 10/16/2020] [Indexed: 12/22/2022] Open
Abstract
Lectins are non-covalent glycan-binding proteins mediating cellular interactions but their annotation in newly sequenced organisms is lacking. The limited size of functional domains and the low level of sequence similarity challenge usual bioinformatics tools. The identification of lectin domains in proteomes requires the manual curation of sequence alignments based on structural folds. A new lectin classification is proposed. It is built on three levels: (i) 35 lectin domain folds, (ii) 109 classes of lectins sharing at least 20% sequence similarity and (iii) 350 families of lectins sharing at least 70% sequence similarity. This information is compiled in the UniLectin platform that includes the previously described UniLectin3D database of curated lectin 3D structures. Since its first release, UniLectin3D has been updated with 485 additional 3D structures. The database is now complemented by two additional modules: PropLec containing predicted β-propeller lectins and LectomeXplore including predicted lectins from sequences of the NBCI-nr and UniProt for every curated lectin class. UniLectin is accessible at https://www.unilectin.eu/.
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Affiliation(s)
- François Bonnardel
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, CH-1227 Geneva, Switzerland
- Computer Science Department, University of Geneva, CH-1227 Geneva, Switzerland
| | - Julien Mariethoz
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, CH-1227 Geneva, Switzerland
- Computer Science Department, University of Geneva, CH-1227 Geneva, Switzerland
- Section of Biology, University of Geneva, CH-1205 Geneva, Switzerland
| | - Serge Pérez
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
| | - Anne Imberty
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
| | - Frédérique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, CH-1227 Geneva, Switzerland
- Computer Science Department, University of Geneva, CH-1227 Geneva, Switzerland
- Section of Biology, University of Geneva, CH-1205 Geneva, Switzerland
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Abstract
Glycobiology is a glycan-based field of study that focuses on the structure, function, and biology of carbohydrates, and glycomics is a sub-study of the field of glycobiology that aims to define structure/function of glycans in living organisms. With the popularity of the glycobiology and glycomics, application of computational modeling expanded in the scientific area of glycobiology over the last decades. The recent availability of progressive Wet-Lab methods in the field of glycobiology and glycomics is promising for the impact of systems biology on the research area of the glycome, an emerging field that is termed “systems glycobiology.” This chapter will summarize the up-to-date leading edge in the use of bioinformatics tools in the field of glycobiology. The chapter provides basic knowledge both for glycobiologists interested in the application of bioinformatics tools and scientists of computational biology interested in studying the glycome.
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16
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Wesch D, Kabelitz D, Oberg HH. Tumor resistance mechanisms and their consequences on γδ T cell activation. Immunol Rev 2020; 298:84-98. [PMID: 33048357 DOI: 10.1111/imr.12925] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/28/2020] [Accepted: 09/03/2020] [Indexed: 12/22/2022]
Abstract
Human γδ T lymphocytes are predominated by two major subsets, defined by the variable domain of the δ chain. Both, Vδ1 and Vδ2 T cells infiltrate in tumors and have been implicated in cancer immunosurveillance. Since the localization and distribution of tumor-infiltrating γδ T cell subsets and their impact on survival of cancer patients are not completely defined, this review summarizes the current knowledge about this issue. Different intrinsic tumor resistance mechanisms and immunosuppressive molecules of immune cells in the tumor microenvironment have been reported to negatively influence functional properties of γδ T cell subsets. Here, we focus on selected tumor resistance mechanisms including overexpression of cyclooxygenase (COX)-2 and indolamine-2,3-dioxygenase (IDO)-1/2, regulation by tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)/TRAIL-R4 pathway and the release of galectins. These inhibitory mechanisms play important roles in the cross-talk of γδ T cell subsets and tumor cells, thereby influencing cytotoxicity or proliferation of γδ T cells and limiting a successful γδ T cell-based immunotherapy. Possible future directions of a combined therapy of adoptively transferred γδ T cells together with γδ-targeting bispecific T cell engagers and COX-2 or IDO-1/2 inhibitors or targeting sialoglycan-Siglec pathways will be discussed and considered as attractive therapeutic options to overcome the immunosuppressive tumor microenvironment.
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Affiliation(s)
- Daniela Wesch
- Institute of Immunology, University Hospital Schleswig-Holstein, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Dieter Kabelitz
- Institute of Immunology, University Hospital Schleswig-Holstein, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Hans-Heinrich Oberg
- Institute of Immunology, University Hospital Schleswig-Holstein, Christian-Albrechts University of Kiel, Kiel, Germany
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17
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Dzobo K, Chiririwa H, Dandara C, Dzobo W. Coronavirus Disease-2019 Treatment Strategies Targeting Interleukin-6 Signaling and Herbal Medicine. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 25:13-22. [PMID: 32857671 DOI: 10.1089/omi.2020.0122] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Coronavirus disease-2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is evolving across the world and new treatments are urgently needed as with vaccines to prevent the illness and stem the contagion. The virus affects not only the lungs but also other tissues, thus lending support to the idea that COVID-19 is a systemic disease. The current vaccine and treatment development strategies ought to consider such systems medicine perspectives rather than a narrower focus on the lung infection only. COVID-19 is associated with elevated levels of the inflammatory cytokines such as interleukin-6 (IL-6), IL-10, and interferon-gamma (IFN-γ). Elevated levels of cytokines and the cytokine storm have been linked to fatal disease. This suggests new therapeutic strategies through blocking the cytokine storm. IL-6 is one of the major cytokines associated with the cytokine storm. IL-6 is also known to display pleiotropic/diverse pathophysiological effects. We suggest the blockage of IL-6 signaling and its downstream mediators such as Janus kinases (JAKs), and signal transducer and activators of transcription (STATs) offer potential hope for the treatment of severe cases of COVID-19. Thus, repurposing of already approved IL-6-JAK-STAT signaling inhibitors as well as other anti-inflammatory drugs, including dexamethasone, is under development for severe COVID-19 cases. We conclude this expert review by highlighting the potential role of precision herbal medicines, for example, the Cannabis sativa, provided that omics technologies can be utilized to build a robust scientific evidence base on their clinical safety and efficacy. Precision herbal medicine buttressed by omics systems science would also help identify new molecular targets for drug discovery against COVID-19.
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Affiliation(s)
- Kevin Dzobo
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town, South Africa.,Division of Medical Biochemistry and Institute of Infectious Disease and Molecular Medicine, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Harry Chiririwa
- Department of Chemical Engineering, Vaal University of Technology, Vanderbijlpark, South Africa
| | - Collet Dandara
- Division of Human Genetics, Department of Pathology, Institute for Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Witness Dzobo
- Immunology Department, Pathology, University Hospital Southampton, Southampton, United Kingdom.,Faculty of Science, University of Portsmouth, Portsmouth, United Kingdom
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18
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Meng Z, Li C, Ding G, Cao W, Xu X, Heng Y, Deng Y, Li Y, Zhang X, Li D, Wang W, Wang Y, Xing W, Hou H. Glycomics: Immunoglobulin G N-Glycosylation Associated with Mammary Gland Hyperplasia in Women. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 24:551-558. [PMID: 32833579 DOI: 10.1089/omi.2020.0091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Mammary gland hyperplasia (MGH) is very common, especially among young and middle-aged women. New diagnostics and biomarkers for MGH are needed for rational clinical management and precision medicine. We report, in this study, new findings using a glycomics approach, with a focus on immunoglobulin G (IgG) N-glycosylation. A cross-sectional study was conducted in a community-based population sample in Beijing, China. A total of 387 participants 40-65 years of age were enrolled in this study, including 194 women with MGH (cases) and 193 women who had no MGH (controls). IgG N-glycans were characterized in the serum by ultra-performance liquid chromatography. The levels of the glycan peaks (GPs) GP2, GP5, GP6, and GP7 were lower in the MGH group compared with the control group, whereas GP14 was significantly higher in the MGH group (p < 0.05). A predictive model using GP5, GP21, and age was established and a receiver operating characteristic curve analysis was performed. The sensitivity and specificity of the model for MGH was 61.3% and 63.2%, respectively, likely owing to receptor mechanisms and/or inflammation regulation. To the best of our knowledge, this is the first study reporting on an association between IgG N-glycosylation and MGH. We suggest person-to-person variations in IgG N-glycans and their combination with multiomics biomarker strategies offer a promising avenue to identify novel diagnostics and individuals at increased risk of MGH.
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Affiliation(s)
- Zixiu Meng
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China
| | - Cancan Li
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China
| | - Guoyong Ding
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China
| | - Weijie Cao
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Xizhu Xu
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China
| | - Yuanyuan Heng
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China
| | - Yang Deng
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China
| | - Yuejin Li
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China
| | - Xiaoyu Zhang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Dong Li
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China
| | - Wei Wang
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China.,School of Medical and Health Sciences, Edith Cowan University, Perth, Western Australia, Australia
| | - Youxin Wang
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China.,School of Medical and Health Sciences, Edith Cowan University, Perth, Western Australia, Australia.,School of Public Health and Management, Binzhou Medical University, Yantai, China
| | - Weijia Xing
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China
| | - Haifeng Hou
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China.,School of Medical and Health Sciences, Edith Cowan University, Perth, Western Australia, Australia
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19
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Dávila AM. Rethinking Omics Education in Brazil and South America: From Genomics to Multiomics and Critical Policy Studies. OMICS: A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 24:391-393. [PMID: 32412823 PMCID: PMC7368383 DOI: 10.1089/omi.2020.0064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Alberto M.R. Dávila
- Computational and Systems Biology Laboratory, Graduate Program in Biodiversity and Health, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
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20
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Özdemir V, Arga KY, Aziz RK, Bayram M, Conley SN, Dandara C, Endrenyi L, Fisher E, Garvey CK, Hekim N, Kunej T, Şardaş S, Von Schomberg R, Yassin AS, Yılmaz G, Wang W. Digging Deeper into Precision/Personalized Medicine: Cracking the Sugar Code, the Third Alphabet of Life, and Sociomateriality of the Cell. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 24:62-80. [PMID: 32027574 DOI: 10.1089/omi.2019.0220] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Precision/personalized medicine is a hot topic in health care. Often presented with the motto "the right drug, for the right patient, at the right dose, and the right time," precision medicine is a theory for rational therapeutics as well as practice to individualize health interventions (e.g., drugs, food, vaccines, medical devices, and exercise programs) using biomarkers. Yet, an alien visitor to planet Earth reading the contemporary textbooks on diagnostics might think precision medicine requires only two biomolecules omnipresent in the literature: nucleic acids (e.g., DNA) and proteins, known as the first and second alphabet of biology, respectively. However, the precision/personalized medicine community has tended to underappreciate the third alphabet of life, the "sugar code" (i.e., the information stored in glycans, glycoproteins, and glycolipids). This article brings together experts in precision/personalized medicine science, pharmacoglycomics, emerging technology governance, cultural studies, contemporary art, and responsible innovation to critically comment on the sociomateriality of the three alphabets of life together. First, the current transformation of targeted therapies with personalized glycomedicine and glycan biomarkers is examined. Next, we discuss the reasons as to why unraveling of the sugar code might have lagged behind the DNA and protein codes. While social scientists have historically noted the importance of constructivism (e.g., how people interpret technology and build their values, hopes, and expectations into emerging technologies), life scientists relied on the material properties of technologies in explaining why some innovations emerge rapidly and are more popular than others. The concept of sociomateriality integrates these two explanations by highlighting the inherent entanglement of the social and the material contributions to knowledge and what is presented to us as reality from everyday laboratory life. Hence, we present a hypothesis based on a sociomaterial conceptual lens: because materiality and synthesis of glycans are not directly driven by a template, and thus more complex and open ended than sequencing of a finite length genome, social construction of expectations from unraveling of the sugar code versus the DNA code might have evolved differently, as being future-uncertain versus future-proof, respectively, thus potentially explaining the "sugar lag" in precision/personalized medicine diagnostics over the past decades. We conclude by introducing systems scientists, physicians, and biotechnology industry to the concept, practice, and value of responsible innovation, while glycomedicine and other emerging biomarker technologies (e.g., metagenomics and pharmacomicrobiomics) transition to applications in health care, ecology, pharmaceutical/diagnostic industries, agriculture, food, and bioengineering, among others.
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Affiliation(s)
- Vural Özdemir
- OMICS: A Journal of Integrative Biology, New Rochelle, New York.,Senior Advisor and Writer, Emerging Technology Governance and Responsible Innovation, Toronto, Ontario, Canada
| | - K Yalçın Arga
- Health Institutes of Turkey, Istanbul, Turkey.,Department of Bioengineering, Faculty of Engineering, Marmara University, İstanbul, Turkey
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt.,The Center for Genome and Microbiome Research, Cairo University, Cairo, Egypt
| | - Mustafa Bayram
- Department of Food Engineering, Faculty of Engineering, Gaziantep University, Gaziantep, Turkey
| | - Shannon N Conley
- STS Futures Lab, School of Integrated Sciences, James Madison University, Harrisonburg, Virginia
| | - Collet Dandara
- Division of Human Genetics, Department of Pathology and Institute for Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Laszlo Endrenyi
- Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Erik Fisher
- School for the Future of Innovation in Society and the Consortium for Science, Policy and Outcomes, Arizona State University, Tempe, Arizona
| | - Colin K Garvey
- Stanford Institute for Human-Centered Artificial Intelligence, Stanford University, Palo Alto, California
| | - Nezih Hekim
- Department of Biochemistry, Faculty of Medicine, İstanbul Medipol University, İstanbul, Turkey
| | - Tanja Kunej
- University of Ljubljana, Biotechnical Faculty, Department of Animal Science, Domzale, Slovenia
| | - Semra Şardaş
- Faculty of Pharmacy, İstinye University, İstanbul, Turkey
| | - Rene Von Schomberg
- Directorate General for Research and Innovation, European Commission, Brussel, Belgium.,Technical University Darmstadt, Darmstadt, Germany
| | - Aymen S Yassin
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt.,The Center for Genome and Microbiome Research, Cairo University, Cairo, Egypt
| | - Gürçim Yılmaz
- Writer and Editor, Cultural Studies, and Curator of Contemporary Arts, İstanbul, Turkey
| | - Wei Wang
- Key Municipal Laboratory of Clinical Epidemiology, Capital Medical University, Beijing, China.,School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia
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