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Joglekar MV, Kaur S, Pociot F, Hardikar AA. Prediction of progression to type 1 diabetes with dynamic biomarkers and risk scores. Lancet Diabetes Endocrinol 2024; 12:483-492. [PMID: 38797187 DOI: 10.1016/s2213-8587(24)00103-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/31/2024] [Accepted: 04/02/2024] [Indexed: 05/29/2024]
Abstract
Identifying biomarkers of functional β-cell loss is an important step in the risk stratification of type 1 diabetes. Genetic risk scores (GRS), generated by profiling an array of single nucleotide polymorphisms, are a widely used type 1 diabetes risk-prediction tool. Type 1 diabetes screening studies have relied on a combination of biochemical (autoantibody) and GRS screening methodologies for identifying individuals at high-risk of type 1 diabetes. A limitation of these screening tools is that the presence of autoantibodies marks the initiation of β-cell loss, and is therefore not the best biomarker of progression to early-stage type 1 diabetes. GRS, on the other hand, represents a static biomarker offering a single risk score over an individual's lifetime. In this Personal View, we explore the challenges and opportunities of static and dynamic biomarkers in the prediction of progression to type 1 diabetes. We discuss future directions wherein newer dynamic risk scores could be used to predict type 1 diabetes risk, assess the efficacy of new and emerging drugs to retard, or prevent type 1 diabetes, and possibly replace or further enhance the predictive ability offered by static biomarkers, such as GRS.
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Affiliation(s)
- Mugdha V Joglekar
- School of Medicine, Western Sydney University, Sydney, NSW, Australia
| | | | - Flemming Pociot
- Steno Diabetes Center Copenhagen, Herlev, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.
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Bhosale SD, Moulder R, Suomi T, Ruohtula T, Honkanen J, Virtanen SM, Ilonen J, Elo LL, Knip M, Lahesmaa R. Serum proteomics of mother-infant dyads carrying HLA-conferred type 1 diabetes risk. iScience 2024; 27:110048. [PMID: 38883825 PMCID: PMC11176638 DOI: 10.1016/j.isci.2024.110048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 03/22/2024] [Accepted: 05/17/2024] [Indexed: 06/18/2024] Open
Abstract
In-utero and dietary factors make important contributions toward health and development in early childhood. In this respect, serum proteomics of maturing infants can provide insights into studies of childhood diseases, which together with perinatal proteomes could reveal further biological perspectives. Accordingly, to determine differences between feeding groups and changes in infancy, serum proteomics analyses of mother-infant dyads with HLA-conferred susceptibility to type 1 diabetes (n = 22), weaned to either an extensively hydrolyzed or regular cow's milk formula, were made. The LC-MS/MS analyses included samples from the beginning of third trimester, the time of delivery, 3 months postpartum, cord blood, and samples from the infants at 3, 6, 9, and 12 months. Correlations between ranked protein intensities were detected within the dyads, together with perinatal and age-related changes. Comparison with intestinal permeability data revealed a number of significant correlations, which could merit further consideration in this context.
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Affiliation(s)
- Santosh D Bhosale
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Robert Moulder
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Tomi Suomi
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Terhi Ruohtula
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jarno Honkanen
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Suvi M Virtanen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Unit of Health Sciences, Faculty of Social Sciences, Tampere University, Tampere, Finland
- Center for Child Health Research and Research, Development and Innovation Center, Tampere University Hospital, Tampere, Finland
| | - Jorma Ilonen
- Immunogenetics Laboratory, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Laura L Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Mikael Knip
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Center for Child Health Research and Research, Development and Innovation Center, Tampere University Hospital, Tampere, Finland
| | - Riitta Lahesmaa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
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Ngo D, Benson MD, Long JZ, Chen ZZ, Wang R, Nath AK, Keyes MJ, Shen D, Sinha S, Kuhn E, Morningstar JE, Shi X, Peterson BD, Chan C, Katz DH, Tahir UA, Farrell LA, Melander O, Mosley JD, Carr SA, Vasan RS, Larson MG, Smith JG, Wang TJ, Yang Q, Gerszten RE. Proteomic profiling reveals biomarkers and pathways in type 2 diabetes risk. JCI Insight 2021; 6:144392. [PMID: 33591955 PMCID: PMC8021115 DOI: 10.1172/jci.insight.144392] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 01/28/2021] [Indexed: 01/14/2023] Open
Abstract
Recent advances in proteomic technologies have made high-throughput profiling of low-abundance proteins in large epidemiological cohorts increasingly feasible. We investigated whether aptamer-based proteomic profiling could identify biomarkers associated with future development of type 2 diabetes (T2DM) beyond known risk factors. We identified dozens of markers with highly significant associations with future T2DM across 2 large longitudinal cohorts (n = 2839) followed for up to 16 years. We leveraged proteomic, metabolomic, genetic, and clinical data from humans to nominate 1 specific candidate to test for potential causal relationships in model systems. Our studies identified functional effects of aminoacylase 1 (ACY1), a top protein association with future T2DM risk, on amino acid metabolism and insulin homeostasis in vitro and in vivo. Furthermore, a loss-of-function variant associated with circulating levels of the biomarker WAP, Kazal, immunoglobulin, Kunitz, and NTR domain-containing protein 2 (WFIKKN2) was, in turn, associated with fasting glucose, hemoglobin A1c, and HOMA-IR measurements in humans. In addition to identifying potentially novel disease markers and pathways in T2DM, we provide publicly available data to be leveraged for insights about gene function and disease pathogenesis in the context of human metabolism.
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Affiliation(s)
- Debby Ngo
- Cardiovascular Institute
- Division of Pulmonary, Critical Care and Sleep Medicine, and
| | - Mark D. Benson
- Cardiovascular Institute
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center (BIDMC), Boston, Massachusetts, USA
| | - Jonathan Z. Long
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Zsu-Zsu Chen
- Cardiovascular Institute
- Division of Endocrinology, Diabetes and Metabolism, BIDMC, Boston, Massachusetts, USA
| | - Ruiqi Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | | | | | | | | | - Eric Kuhn
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | | | | | | | | | - Daniel H. Katz
- Cardiovascular Institute
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center (BIDMC), Boston, Massachusetts, USA
| | - Usman A. Tahir
- Cardiovascular Institute
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center (BIDMC), Boston, Massachusetts, USA
| | | | - Olle Melander
- Department of Cardiology, Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden
| | - Jonathan D. Mosley
- Departments of Medicine and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Steven A. Carr
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Ramachandran S. Vasan
- Department of Medicine, Divisions of Preventive Medicine and Cardiology, Boston University School of Medicine, Boston, Massachusetts, USA
- The National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, Massachusetts, USA
| | - Martin G. Larson
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
- The National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, Massachusetts, USA
| | - J. Gustav Smith
- Department of Cardiology, Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden
- Wallenberg Center for Molecular Medicine and Diabetes Center, Lund University, Lund, Sweden
- Department of Cardiology and Wallenberg Laboratory, Gothenburg University and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Thomas J. Wang
- Department of Medicine, University of Texas, Southwestern Medical Center, Dallas, Texas, USA
| | - Qiong Yang
- Division of Endocrinology, Diabetes and Metabolism, BIDMC, Boston, Massachusetts, USA
| | - Robert E. Gerszten
- Cardiovascular Institute
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center (BIDMC), Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
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Pappa E, Vougas K, Zoidakis J, Vastardis H. Proteomic advances in salivary diagnostics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140494. [DOI: 10.1016/j.bbapap.2020.140494] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/21/2020] [Accepted: 06/29/2020] [Indexed: 12/17/2022]
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Moulder R, Bhosale SD, Goodlett DR, Lahesmaa R. Analysis of the plasma proteome using iTRAQ and TMT-based Isobaric labeling. MASS SPECTROMETRY REVIEWS 2018; 37:583-606. [PMID: 29120501 DOI: 10.1002/mas.21550] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 09/26/2017] [Indexed: 05/23/2023]
Abstract
Over the past decade, chemical labeling with isobaric tandem mass tags, such as isobaric tags for relative and absolute quantification reagents (iTRAQ) and tandem mass tag (TMT) reagents, has been employed in a wide range of different clinically orientated serum and plasma proteomics studies. In this review the scope of these works is presented with attention to the areas of research, methods employed and performance limitations. These applications have covered a wide range of diseases, disorders and infections, and have implemented a variety of different preparative and mass spectrometric approaches. In contrast to earlier works, which struggled to quantify more than a few hundred proteins, increasingly these studies have provided deeper insight into the plasma proteome extending the numbers of quantified proteins to over a thousand.
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Affiliation(s)
- Robert Moulder
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Santosh D Bhosale
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | | | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
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Abstract
PURPOSE OF REVIEW The immunosuppressive agent cyclosporine was first reported to lower daily insulin dose and improve glycemic control in patients with new-onset type 1 diabetes (T1D) in 1984. While renal toxicity limited cyclosporine's extended use, this observation ignited collaborative efforts to identify immunotherapeutic agents capable of safely preserving β cells in patients with or at risk for T1D. RECENT FINDINGS Advances in T1D prediction and early diagnosis, together with expanded knowledge of the disease mechanisms, have facilitated trials targeting specific immune cell subsets, autoantigens, and pathways. In addition, clinical responder and non-responder subsets have been defined through the use of metabolic and immunological readouts. Herein, we review emerging T1D biomarkers within the context of recent and ongoing T1D immunotherapy trials. We also discuss responder/non-responder analyses in an effort to identify therapeutic mechanisms, define actionable pathways, and guide subject selection, drug dosing, and tailored combination drug therapy for future T1D trials.
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Affiliation(s)
- Laura M Jacobsen
- Department of Pediatrics, College of Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Brittney N Newby
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida Diabetes Institute, 1275 Center Drive, Biomedical Sciences Building J-589, Box 100275, Gainesville, FL, 32610, USA
| | - Daniel J Perry
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida Diabetes Institute, 1275 Center Drive, Biomedical Sciences Building J-589, Box 100275, Gainesville, FL, 32610, USA
| | - Amanda L Posgai
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida Diabetes Institute, 1275 Center Drive, Biomedical Sciences Building J-589, Box 100275, Gainesville, FL, 32610, USA
| | - Michael J Haller
- Department of Pediatrics, College of Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Todd M Brusko
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida Diabetes Institute, 1275 Center Drive, Biomedical Sciences Building J-589, Box 100275, Gainesville, FL, 32610, USA.
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Moulder R, Schvartz D, Goodlett DR, Dayon L. Proteomics of Diabetes, Obesity, and Related Disorders. Proteomics Clin Appl 2018; 12. [DOI: 10.1002/prca.201600134] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Robert Moulder
- Turku Centre for Biotechnology; University of Turku and Åbo Akademi University; Turku Finland
| | - Domitille Schvartz
- Human Protein Sciences Department; Centre Medical Universitaire; University of Geneva; Geneva, Switzerland
| | - David R. Goodlett
- Turku Centre for Biotechnology; University of Turku and Åbo Akademi University; Turku Finland
- Department of Pharmaceutical Sciences; University of Maryland; Baltimore MD USA
| | - Loïc Dayon
- Nestlé Institute of Health Sciences; EPFL Innovation Park; Lausanne Switzerland
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Lepper MF, Ohmayer U, von Toerne C, Maison N, Ziegler AG, Hauck SM. Proteomic Landscape of Patient-Derived CD4+ T Cells in Recent-Onset Type 1 Diabetes. J Proteome Res 2017; 17:618-634. [PMID: 29182335 DOI: 10.1021/acs.jproteome.7b00712] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The pathophysiology underlying the autoimmune disease type 1 diabetes (T1D) is poorly understood. Obtaining an accurate proteomic profile of the T helper cell population is essential for understanding the pathogenesis of T1D. Here, we performed in-depth proteomic profiling of peripheral CD4+ T cells in a pediatric cohort to identify cellular signatures associated with the onset of T1D. Using only 250 000 CD4+ T cells per patient, isolated from biobanked PBMC samples, we identified nearly 6000 proteins using deep-proteome profiling with LC-MS/MS data-independent acquisition. Our analysis revealed an inflammatory signature in patients with T1D; this signature is characterized by circulating mediators of neutrophils, platelets, and the complement system. This signature likely reflects the inflammatory extracellular milieu, which suggests that activation of the innate immune system plays an important role in disease onset. Our results emphasize the potential value of using high-resolution LC-MS/MS to investigate limited quantities of biobanked samples to identify disease-relevant proteomic patterns. Proteomic profiles of 114 individuals have been deposited in a comprehensive portable repository serving as a unique resource for CD4+ T cell expression in the context of both health and T1D disease.
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Affiliation(s)
- Marlen F Lepper
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | | | | | | | | | - Stefanie M Hauck
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
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Crèvecoeur I, Vig S, Mathieu C, Overbergh L. Understanding type 1 diabetes through proteomics. Expert Rev Proteomics 2017. [DOI: 10.1080/14789450.2017.1345633] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Inne Crèvecoeur
- Laboratory for Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
| | - Saurabh Vig
- Laboratory for Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
| | - Chantal Mathieu
- Laboratory for Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
| | - Lut Overbergh
- Laboratory for Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
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