1
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Wang J, Novick S. Peptide set test: a peptide-centric strategy to infer differentially expressed proteins. BIOINFORMATICS (OXFORD, ENGLAND) 2024; 40:btae270. [PMID: 38632081 DOI: 10.1093/bioinformatics/btae270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 03/20/2024] [Accepted: 04/16/2024] [Indexed: 04/19/2024]
Abstract
MOTIVATION The clinical translation of mass spectrometry-based proteomics has been challenging due to limited statistical power caused by large technical variability and inter-patient heterogeneity. Bottom-up proteomics provides an indirect measurement of proteins through digested peptides. This raises the question whether peptide measurements can be used directly to better distinguish differentially expressed proteins. RESULTS We present a novel method called the peptide set test, which detects coordinated changes in the expression of peptides originating from the same protein and compares them to the rest of the peptidome. Applying our method to data from a published spike-in experiment and simulations demonstrates improved sensitivity without compromising precision, compared to aggregation-based approaches. Additionally, applying the peptide set test to compare the tumor proteomes of tamoxifen-sensitive and tamoxifen-resistant breast cancer patients reveals significant alterations in peptide levels of collagen XII, suggesting an association between collagen XII-mediated matrix reassembly and tamoxifen resistance. Our study establishes the peptide set test as a powerful peptide-centric strategy to infer differential expression in proteomics studies. AVAILABILITY AND IMPLEMENTATION Peptide set test (PepSetTest) is publicly available at https://github.com/JmWangBio/PepSetTest.
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Affiliation(s)
- Junmin Wang
- Data Sciences and Quantitative Biology, Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, United States
| | - Steven Novick
- Global Statistical Sciences, Eli Lilly, Indianapolis, IN 46285, United States
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2
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Joshi N, Garapati K, Ghose V, Kandasamy RK, Pandey A. Recent progress in mass spectrometry-based urinary proteomics. Clin Proteomics 2024; 21:14. [PMID: 38389064 PMCID: PMC10885485 DOI: 10.1186/s12014-024-09462-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 02/12/2024] [Indexed: 02/24/2024] Open
Abstract
Serum or plasma is frequently utilized in biomedical research; however, its application is impeded by the requirement for invasive sample collection. The non-invasive nature of urine collection makes it an attractive alternative for disease characterization and biomarker discovery. Mass spectrometry-based protein profiling of urine has led to the discovery of several disease-associated biomarkers. Proteomic analysis of urine has not only been applied to disorders of the kidney and urinary bladder but also to conditions affecting distant organs because proteins excreted in the urine originate from multiple organs. This review provides a progress update on urinary proteomics carried out over the past decade. Studies summarized in this review have expanded the catalog of proteins detected in the urine in a variety of clinical conditions. The wide range of applications of urine analysis-from characterizing diseases to discovering predictive, diagnostic and prognostic markers-continues to drive investigations of the urinary proteome.
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Affiliation(s)
- Neha Joshi
- Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Kishore Garapati
- Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Vivek Ghose
- Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
| | - Richard K Kandasamy
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India.
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA.
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.
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3
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Giansanti P, Samaras P, Bian Y, Meng C, Coluccio A, Frejno M, Jakubowsky H, Dobiasch S, Hazarika RR, Rechenberger J, Calzada-Wack J, Krumm J, Mueller S, Lee CY, Wimberger N, Lautenbacher L, Hassan Z, Chang YC, Falcomatà C, Bayer FP, Bärthel S, Schmidt T, Rad R, Combs SE, The M, Johannes F, Saur D, de Angelis MH, Wilhelm M, Schneider G, Kuster B. Mass spectrometry-based draft of the mouse proteome. Nat Methods 2022; 19:803-811. [PMID: 35710609 DOI: 10.1038/s41592-022-01526-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 05/17/2022] [Indexed: 01/06/2023]
Abstract
The laboratory mouse ranks among the most important experimental systems for biomedical research and molecular reference maps of such models are essential informational tools. Here, we present a quantitative draft of the mouse proteome and phosphoproteome constructed from 41 healthy tissues and several lines of analyses exemplify which insights can be gleaned from the data. For instance, tissue- and cell-type resolved profiles provide protein evidence for the expression of 17,000 genes, thousands of isoforms and 50,000 phosphorylation sites in vivo. Proteogenomic comparison of mouse, human and Arabidopsis reveal common and distinct mechanisms of gene expression regulation and, despite many similarities, numerous differentially abundant orthologs that likely serve species-specific functions. We leverage the mouse proteome by integrating phenotypic drug (n > 400) and radiation response data with the proteomes of 66 pancreatic ductal adenocarcinoma (PDAC) cell lines to reveal molecular markers for sensitivity and resistance. This unique atlas complements other molecular resources for the mouse and can be explored online via ProteomicsDB and PACiFIC.
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Affiliation(s)
- Piero Giansanti
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Patroklos Samaras
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Yangyang Bian
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.,College of Life Science, Northwest University, Xi'an, China
| | - Chen Meng
- Bavarian Biomolecular Mass Spectrometry Center, Technical University of Munich, Freising, Germany
| | - Andrea Coluccio
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Chair of Translational Cancer Research and Institute for Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Martin Frejno
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Hannah Jakubowsky
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Chair of Translational Cancer Research and Institute for Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Sophie Dobiasch
- Department of Radiation Oncology, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Institute of Radiation Medicine, Department of Radiation Sciences, Helmholtz Zentrum München, Neuherberg, Germany.,German Cancer Consortium (DKTK), Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rashmi R Hazarika
- Population epigenetics and epigenomics, Technical University of Munich, Freising, Germany.,Institute of Advanced Study (IAS), Technical University of Munich, Freising, Germany
| | - Julia Rechenberger
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Julia Calzada-Wack
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Johannes Krumm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Sebastian Mueller
- Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.,Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Chien-Yun Lee
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Nicole Wimberger
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Chair of Translational Cancer Research and Institute for Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Ludwig Lautenbacher
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Zonera Hassan
- Medical Clinic and Policlinic II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Yun-Chien Chang
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Chiara Falcomatà
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Chair of Translational Cancer Research and Institute for Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Florian P Bayer
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Stefanie Bärthel
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Chair of Translational Cancer Research and Institute for Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Tobias Schmidt
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Roland Rad
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.,Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Stephanie E Combs
- Department of Radiation Oncology, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Institute of Radiation Medicine, Department of Radiation Sciences, Helmholtz Zentrum München, Neuherberg, Germany.,German Cancer Consortium (DKTK), Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthew The
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Frank Johannes
- Population epigenetics and epigenomics, Technical University of Munich, Freising, Germany.,Institute of Advanced Study (IAS), Technical University of Munich, Freising, Germany
| | - Dieter Saur
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Chair of Translational Cancer Research and Institute for Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Martin Hrabe de Angelis
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Chair of Experimental Genetics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.,Computational Mass Spectrometry, Technical University of Munich, Freising, Germany
| | - Günter Schneider
- Medical Clinic and Policlinic II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,University Medical Center Göttingen, Department of General, Visceral and Pediatric Surgery, Göttingen, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany. .,Bavarian Biomolecular Mass Spectrometry Center, Technical University of Munich, Freising, Germany. .,German Cancer Consortium (DKTK), Munich, Germany. .,German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Institute of Advanced Study (IAS), Technical University of Munich, Freising, Germany.
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4
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Metaproteomics Approach and Pathway Modulation in Obesity and Diabetes: A Narrative Review. Nutrients 2021; 14:nu14010047. [PMID: 35010920 PMCID: PMC8746330 DOI: 10.3390/nu14010047] [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: 10/28/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 12/14/2022] Open
Abstract
Low-grade inflammatory diseases revealed metabolic perturbations that have been linked to various phenotypes, including gut microbiota dysbiosis. In the last decade, metaproteomics has been used to investigate protein composition profiles at specific steps and in specific healthy/pathologic conditions. We applied a rigorous protocol that relied on PRISMA guidelines and filtering criteria to obtain an exhaustive study selection that finally resulted in a group of 10 studies, based on metaproteomics and that aim at investigating obesity and diabetes. This batch of studies was used to discuss specific microbial and human metaproteome alterations and metabolic patterns in subjects affected by diabetes (T1D and T2D) and obesity. We provided the main up- and down-regulated protein patterns in the inspected pathologies. Despite the available results, the evident paucity of metaproteomic data is to be considered as a limiting factor in drawing objective considerations. To date, ad hoc prepared metaproteomic databases collecting pathologic data and related metadata, together with standardized analysis protocols, are required to increase our knowledge on these widespread pathologies.
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5
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Wang J, Delfarah A, Gelbach PE, Fong E, Macklin P, Mumenthaler SM, Graham NA, Finley SD. Elucidating tumor-stromal metabolic crosstalk in colorectal cancer through integration of constraint-based models and LC-MS metabolomics. Metab Eng 2021; 69:175-187. [PMID: 34838998 PMCID: PMC8818109 DOI: 10.1016/j.ymben.2021.11.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 10/07/2021] [Accepted: 11/09/2021] [Indexed: 12/28/2022]
Abstract
Colorectal cancer (CRC) is a major cause of morbidity and mortality in the United States. Tumor-stromal metabolic crosstalk in the tumor microenvironment promotes CRC development and progression, but exactly how stromal cells, in particular cancer-associated fibroblasts (CAFs), affect the metabolism of tumor cells remains unknown. Here we take a data-driven approach to investigate the metabolic interactions between CRC cells and CAFs, integrating constraint-based modeling and metabolomic profiling. Using metabolomics data, we perform unsteady-state parsimonious flux balance analysis to infer flux distributions for central carbon metabolism in CRC cells treated with or without CAF-conditioned media. We find that CAFs reprogram CRC metabolism through stimulation of glycolysis, the oxidative arm of the pentose phosphate pathway (PPP), and glutaminolysis, as well as inhibition of the tricarboxylic acid cycle. To identify potential therapeutic targets, we simulate enzyme knockouts and find that CAF-treated CRC cells are especially sensitive to inhibitions of hexokinase and glucose-6-phosphate, the rate limiting steps of glycolysis and oxidative PPP. Our work gives mechanistic insights into the metabolic interactions between CRC cells and CAFs and provides a framework for testing hypotheses towards CRC-targeted therapies.
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Affiliation(s)
- Junmin Wang
- Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, 90089, USA
| | - Alireza Delfarah
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, 90089, USA
| | - Patrick E Gelbach
- Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, 90089, USA
| | - Emma Fong
- Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA, 90064, USA
| | - Paul Macklin
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, 46202, USA
| | - Shannon M Mumenthaler
- Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA, 90064, USA; Division of Medical Oncology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90033, USA
| | - Nicholas A Graham
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, 90089, USA
| | - Stacey D Finley
- Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, 90089, USA; Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, 90089, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA.
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6
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Yu Y, Singh H, Tsitrin T, Bekele S, Lin YH, Sikorski P, Moncera KJ, Torralba MG, Morrow L, Wolcott R, Nelson KE, Pieper R. Urethral Catheter Biofilms Reveal Plasticity in Bacterial Composition and Metabolism and Withstand Host Immune Defenses in Hypoxic Environment. Front Med (Lausanne) 2021; 8:667462. [PMID: 34249966 PMCID: PMC8260951 DOI: 10.3389/fmed.2021.667462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 05/06/2021] [Indexed: 11/18/2022] Open
Abstract
Biofilms composed of multiple microorganisms colonize the surfaces of indwelling urethral catheters that are used serially by neurogenic bladder patients and cause chronic infections. Well-adapted pathogens in this niche are Escherichia coli, Proteus, and Enterococcus spp., species that cycle through adhesion and multilayered cell growth, trigger host immune responses, are starved off nutrients, and then disperse. Viable microbial foci retained in the urinary tract recolonize catheter surfaces. The molecular adaptations of bacteria in catheter biofilms (CBs) are not well-understood, promising new insights into this pathology based on host and microbial meta-omics analyses from clinical specimens. We examined catheters from nine neurogenic bladder patients longitudinally over up to 6 months. Taxonomic analyses from 16S rRNA gene sequencing and liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomics revealed that 95% of all catheter and corresponding urinary pellet (UP) samples contained bacteria. CB biomasses were dominated by Enterobacteriaceae spp. and often accompanied by lactic acid and anaerobic bacteria. Systemic antibiotic drug treatments of patients resulted in either transient or lasting microbial community perturbations. Neutrophil effector proteins were abundant not only in UP but also CB samples, indicating their penetration of biofilm surfaces. In the context of one patient who advanced to a kidney infection, Proteus mirabilis proteomic data suggested a combination of factors associated with this disease complication: CB biomasses were high; the bacteria produced urease alkalinizing the pH and triggering urinary salt deposition on luminal catheter surfaces; P. mirabilis utilized energy-producing respiratory systems more than in CBs from other patients. The NADH:quinone oxidoreductase II (Nqr), a Na+ translocating enzyme not operating as a proton pump, and the nitrate reductase A (Nar) equipped the pathogen with electron transport chains promoting growth under hypoxic conditions. Both P. mirabilis and E. coli featured repertoires of transition metal ion acquisition systems in response to human host-mediated iron and zinc sequestration. We discovered a new drug target, the Nqr respiratory system, whose deactivation may compromise P. mirabilis growth in a basic pH milieu. Animal models would not allow such molecular-level insights into polymicrobial biofilm metabolism and interactions because the complexity cannot be replicated.
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Affiliation(s)
- Yanbao Yu
- J. Craig Venter Institute, Rockville, MD, United States
| | | | | | | | - Yi-Han Lin
- J. Craig Venter Institute, Rockville, MD, United States
| | | | | | | | - Lisa Morrow
- Southwest Regional Wound Care Center, Lubbock, TX, United States
| | - Randall Wolcott
- Southwest Regional Wound Care Center, Lubbock, TX, United States
| | - Karen E. Nelson
- J. Craig Venter Institute, Rockville, MD, United States
- J. Craig Venter Institute, La Jolla, CA, United States
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7
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Yu Y, Singh H, Kwon K, Tsitrin T, Petrini J, Nelson KE, Pieper R. Protein signatures from blood plasma and urine suggest changes in vascular function and IL-12 signaling in elderly with a history of chronic diseases compared with an age-matched healthy cohort. GeroScience 2021. [PMID: 32974878 DOI: 10.1007/s11357-020-00269-y/figures/10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023] Open
Abstract
Key processes characterizing human aging are immunosenescence and inflammaging. The capacity of the immune system to adequately respond to external perturbations (e.g., pathogens, injuries, and biochemical irritants) and to repair somatic mutations that may cause cancers or cellular senescence declines. An important goal remains to identify genetic or biochemical, predictive biomarkers for healthy aging. We recruited two cohorts in the age range 70 to 82, one afflicted by chronic illnesses (non-healthy aging, NHA) and the other in good health (healthy aging, HA). NHA criteria included major cardiovascular, neurodegenerative, and chronic pulmonary diseases, diabetes, and cancers. Quantitative analysis of forty proinflammatory cytokines in blood plasma and more than 500 proteins in urine was performed to identify candidate biomarkers for and biological pathway implications of healthy aging. Nine cytokines revealed lower quantities in blood plasma for the NHA compared with the HA groups (fold change > 1.5; p value < 0.025) including IL-12p40 and IL-12p70. We note that, sampling at two timepoints, intra-individual cytokine abundance patterns clustered in 86% of all 60 cases, indicative of person-specific, highly controlled multi-cytokine signatures in blood plasma. Twenty-three urinary proteins were differentially abundant (HA versus NHA; fold change > 1.5; p value < 0.01). Among the proteins increased in abundance in the HA cohort were glycoprotein MUC18, ephrin type-B receptor 4, matrix remodeling-associated protein 8, angiopoietin-related protein 2, K-cadherin, and plasma protease C1 inhibitor. These proteins have been linked to the extracellular matrix, cell adhesion, and vascular remodeling and repair processes. In silico network analysis identified the regulation of coagulation, antimicrobial humoral immune responses, and the IL-12 signaling pathway as enriched GO terms. To validate links of these preliminary biomarkers and IL-12 signaling with healthy aging, clinical studies using larger cohorts and functional characterization of the genes/proteins in cellular models of aging need to be conducted.
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Affiliation(s)
- Yanbao Yu
- J. Craig Venter Institute, 9605 Medical Center Drive, Rockville, MD, 20850, USA
| | - Harinder Singh
- J. Craig Venter Institute, 9605 Medical Center Drive, Rockville, MD, 20850, USA
| | - Keehwan Kwon
- J. Craig Venter Institute, 9605 Medical Center Drive, Rockville, MD, 20850, USA
| | - Tamara Tsitrin
- J. Craig Venter Institute, 9605 Medical Center Drive, Rockville, MD, 20850, USA
| | - Joann Petrini
- Western Connecticut Health Network, 24 Hospital Avenue, Danbury, CT, 06810, USA
| | - Karen E Nelson
- J. Craig Venter Institute, 9605 Medical Center Drive, Rockville, MD, 20850, USA
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Rembert Pieper
- J. Craig Venter Institute, 9605 Medical Center Drive, Rockville, MD, 20850, USA.
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8
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Yu Y, Singh H, Kwon K, Tsitrin T, Petrini J, Nelson KE, Pieper R. Protein signatures from blood plasma and urine suggest changes in vascular function and IL-12 signaling in elderly with a history of chronic diseases compared with an age-matched healthy cohort. GeroScience 2020; 43:593-606. [PMID: 32974878 PMCID: PMC8110643 DOI: 10.1007/s11357-020-00269-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/14/2020] [Indexed: 01/02/2023] Open
Abstract
Key processes characterizing human aging are immunosenescence and inflammaging. The capacity of the immune system to adequately respond to external perturbations (e.g., pathogens, injuries, and biochemical irritants) and to repair somatic mutations that may cause cancers or cellular senescence declines. An important goal remains to identify genetic or biochemical, predictive biomarkers for healthy aging. We recruited two cohorts in the age range 70 to 82, one afflicted by chronic illnesses (non-healthy aging, NHA) and the other in good health (healthy aging, HA). NHA criteria included major cardiovascular, neurodegenerative, and chronic pulmonary diseases, diabetes, and cancers. Quantitative analysis of forty proinflammatory cytokines in blood plasma and more than 500 proteins in urine was performed to identify candidate biomarkers for and biological pathway implications of healthy aging. Nine cytokines revealed lower quantities in blood plasma for the NHA compared with the HA groups (fold change > 1.5; p value < 0.025) including IL-12p40 and IL-12p70. We note that, sampling at two timepoints, intra-individual cytokine abundance patterns clustered in 86% of all 60 cases, indicative of person-specific, highly controlled multi-cytokine signatures in blood plasma. Twenty-three urinary proteins were differentially abundant (HA versus NHA; fold change > 1.5; p value < 0.01). Among the proteins increased in abundance in the HA cohort were glycoprotein MUC18, ephrin type-B receptor 4, matrix remodeling-associated protein 8, angiopoietin-related protein 2, K-cadherin, and plasma protease C1 inhibitor. These proteins have been linked to the extracellular matrix, cell adhesion, and vascular remodeling and repair processes. In silico network analysis identified the regulation of coagulation, antimicrobial humoral immune responses, and the IL-12 signaling pathway as enriched GO terms. To validate links of these preliminary biomarkers and IL-12 signaling with healthy aging, clinical studies using larger cohorts and functional characterization of the genes/proteins in cellular models of aging need to be conducted.
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Affiliation(s)
- Yanbao Yu
- J. Craig Venter Institute, 9605 Medical Center Drive, Rockville, MD, 20850, USA
| | - Harinder Singh
- J. Craig Venter Institute, 9605 Medical Center Drive, Rockville, MD, 20850, USA
| | - Keehwan Kwon
- J. Craig Venter Institute, 9605 Medical Center Drive, Rockville, MD, 20850, USA
| | - Tamara Tsitrin
- J. Craig Venter Institute, 9605 Medical Center Drive, Rockville, MD, 20850, USA
| | - Joann Petrini
- Western Connecticut Health Network, 24 Hospital Avenue, Danbury, CT, 06810, USA
| | - Karen E Nelson
- J. Craig Venter Institute, 9605 Medical Center Drive, Rockville, MD, 20850, USA.,J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Rembert Pieper
- J. Craig Venter Institute, 9605 Medical Center Drive, Rockville, MD, 20850, USA.
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9
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Ding H, Lin C, Cai J, Guo Q, Dai M, Mohan C, Shen N. Urinary activated leukocyte cell adhesion molecule as a novel biomarker of lupus nephritis histology. Arthritis Res Ther 2020; 22:122. [PMID: 32460901 PMCID: PMC7251704 DOI: 10.1186/s13075-020-02209-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/01/2020] [Indexed: 12/31/2022] Open
Abstract
Background Lupus nephritis (LN) is one of the most severe complications of SLE patients. We aim to validate urinary ALCAM as a biomarker in predicting renal disease histpathology in a Chinese lupus cohort. Methods In this cross-sectional study, a total of 256 patients and controls were recruited. Urinary levels of ALCAM were determined by ELISA. Renal histopathology was reviewed by an experienced renal pathologist. Results Urinary ALCAM levels were significantly increased in active LN patients when compared to active SLE patients without renal involvement (p < 0.001), inactive LN patients (p = 0.023), inactive SLE patients without renal involvement (p < 0.001), and healthy controls (p < 0.001). Correlation analysis revealed a positive correlation between urinary ALCAM and general disease activity—SLEDAI score (r = 0.487, p < 0.001), as well as renal disease activity—rSLEDAI (r = 0.552, p < 0.001) and SLICC RAS (r = 0.584, p < 0.001). Urinary ALCAM also correlated with lab parameters including 24-h urine protein, hemoglobin, and complement 3. Moreover, urinary ALCAM levels were significantly increased in class III and IV (proliferative) LN as compared to those in class V (membranous) LN. It outperformed conventional biomarkers (anti-dsDNA antibody, C3, C4, proteinuria) in discriminating the two groups of LN. On renal histopathology, urinary ALCAM levels correlated positively with activity index (r = 0.405, p < 0.001) but not chronicity index (r = 0.079, p = 0.448). Conclusion Urinary ALCAM is a potential biomarker for predicting renal pathology activity in LN and may serve as a valuable surrogate marker of renal histopathology.
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Affiliation(s)
- Huihua Ding
- Department of Rheumatology, Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 145 Shandong (M) Rd, Shanghai, 200001, China
| | - Cheng Lin
- Department of Rheumatology, Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 145 Shandong (M) Rd, Shanghai, 200001, China
| | - Jingyi Cai
- Department of Rheumatology, Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 145 Shandong (M) Rd, Shanghai, 200001, China
| | - Qiang Guo
- Department of Rheumatology, Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 145 Shandong (M) Rd, Shanghai, 200001, China
| | - Min Dai
- Department of Rheumatology, Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 145 Shandong (M) Rd, Shanghai, 200001, China
| | - Chandra Mohan
- Department of Biomedical Engineering, University of Houston, 3517 Cullen Blvd, Room 2027, Houston, TX, 77204-5060, USA.
| | - Nan Shen
- Department of Rheumatology, Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 145 Shandong (M) Rd, Shanghai, 200001, China. .,China-Australia Centre for Personalized Immunology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China. .,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200032, China. .,Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040, China. .,Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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10
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Van JAD, Clotet-Freixas S, Hauschild AC, Batruch I, Jurisica I, Elia Y, Mahmud FH, Sochett E, Diamandis EP, Scholey JW, Konvalinka A. Urinary proteomics links keratan sulfate degradation and lysosomal enzymes to early type 1 diabetes. PLoS One 2020; 15:e0233639. [PMID: 32453760 PMCID: PMC7250451 DOI: 10.1371/journal.pone.0233639] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/09/2020] [Indexed: 01/09/2023] Open
Abstract
Diabetes is the leading cause of end-stage renal disease worldwide. Our understanding of the early kidney response to chronic hyperglycemia remains incomplete. To address this, we first investigated the urinary proteomes of otherwise healthy youths with and without type 1 diabetes and subsequently examined the enriched pathways that might be dysregulated in early disease using systems biology approaches. This cross-sectional study included two separate cohorts for the discovery (N = 30) and internal validation (N = 30) of differentially excreted proteins. Discovery proteomics was performed on a Q Exactive Plus hybrid quadrupole-orbitrap mass spectrometer. We then searched the pathDIP, KEGG, and Reactome databases to identify enriched pathways in early diabetes; the Integrated Interactions Database to retrieve protein-protein interaction data; and the PubMed database to compare fold changes of our signature proteins with those published in similarly designed studies. Proteins were selected for internal validation based on pathway enrichment and availability of commercial enzyme-linked immunosorbent assay kits. Of the 2451 proteins identified, 576 were quantified in all samples from the discovery cohort; 34 comprised the urinary signature for early diabetes after Benjamini-Hochberg adjustment (Q < 0.05). The top pathways associated with this signature included lysosome, glycosaminoglycan degradation, and innate immune system (Q < 0.01). Notably, all enzymes involved in keratan sulfate degradation were significantly elevated in urines from youths with diabetes (|fold change| > 1.6). Increased urinary excretion of monocyte differentiation antigen CD14, hexosaminidase A, and lumican was also observed in the validation cohort (P < 0.05). Twenty-one proteins from our signature have been reported elsewhere as potential mediators of early diabetes. In this study, we identified a urinary proteomic signature for early type 1 diabetes, of which lysosomal enzymes were major constituents. Our findings highlight novel pathways such as keratan sulfate degradation in the early kidney response to hyperglycemia.
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Affiliation(s)
- Julie A. D. Van
- Institute of Medical Science, University of Toronto, Toronto, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
- * E-mail:
| | - Sergi Clotet-Freixas
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
| | - Anne-Christin Hauschild
- Krembil Research Institute, University Health Network, Toronto, Canada
- Department of Mathematics & Computer Science, University of Marburg, Marburg, Germany
| | - Ihor Batruch
- Department of Laboratory Medicine and Pathobiology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Canada
| | - Igor Jurisica
- Krembil Research Institute, University Health Network, Toronto, Canada
- Department of Computer Science, University of Toronto, Toronto, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Yesmino Elia
- Hospital for Sick Children, Toronto, Ontario, Canada
| | | | | | - Eleftherios P. Diamandis
- Department of Laboratory Medicine and Pathobiology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Canada
- Department of Clinical Biochemistry, University Health Network, University of Toronto, Toronto, Canada
| | - James W. Scholey
- Institute of Medical Science, University of Toronto, Toronto, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
- Division of Nephrology, Department of Medicine, University Health Network, Toronto, Ontario, Canada
| | - Ana Konvalinka
- Institute of Medical Science, University of Toronto, Toronto, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
- Division of Nephrology, Department of Medicine, University Health Network, Toronto, Ontario, Canada
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11
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Van JAD, Clotet-Freixas S, Zhou J, Batruch I, Sun C, Glogauer M, Rampoldi L, Elia Y, Mahmud FH, Sochett E, Diamandis EP, Scholey JW, Konvalinka A. Peptidomic Analysis of Urine from Youths with Early Type 1 Diabetes Reveals Novel Bioactivity of Uromodulin Peptides In Vitro. Mol Cell Proteomics 2020; 19:501-517. [PMID: 31879271 PMCID: PMC7050109 DOI: 10.1074/mcp.ra119.001858] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/20/2019] [Indexed: 12/17/2022] Open
Abstract
Chronic hyperglycemia is known to disrupt the proteolytic milieu, initiating compensatory and maladaptive pathways in the diabetic kidney. Such changes in intrarenal proteolysis are captured by the urinary peptidome. To elucidate the early kidney response to chronic hyperglycemia, we conducted a peptidomic investigation into urines from otherwise healthy youths with type 1 diabetes and their non-diabetic peers using unbiased and targeted mass spectrometry-based techniques. This cross-sectional study included two separate cohorts for the discovery (n = 30) and internal validation (n = 30) of differential peptide excretion. Peptide bioactivity was predicted using PeptideRanker and subsequently verified in vitro Proteasix and the Nephroseq database were used to identify putative proteases responsible for peptide generation and examine their expression in diabetic nephropathy. A total of 6550 urinary peptides were identified in the discovery analysis. We further examined the subset of 162 peptides, which were quantified across all thirty samples. Of the 15 differentially excreted peptides (p < 0.05), seven derived from a C-terminal region (589SGSVIDQSRVLNLGPITRK607) of uromodulin, a kidney-specific protein. Increased excretion of five uromodulin peptides was replicated in the validation cohort using parallel reaction monitoring (p < 0.05). One of the validated peptides (SGSVIDQSRVLNLGPI) activated NFκB and AP-1 signaling, stimulated cytokine release, and enhanced neutrophil migration in vitro. In silico analyses highlighted several potential proteases such as hepsin, meprin A, and cathepsin B to be responsible for generating these peptides. In summary, we identified a urinary signature of uromodulin peptides associated with early type 1 diabetes before clinical manifestations of kidney disease and discovered novel bioactivity of uromodulin peptides in vitro Our present findings lay the groundwork for future studies to validate peptide excretion in larger and broader populations, to investigate the role of bioactive uromodulin peptides in high glucose conditions, and to examine proteases that cleave uromodulin.
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Affiliation(s)
- Julie A D Van
- Institute of Medical Science, University of Toronto, Toronto, Canada; Toronto General Hospital Research Institute, University Health Network, Toronto, Canada.
| | - Sergi Clotet-Freixas
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
| | - Joyce Zhou
- Institute of Medical Science, University of Toronto, Toronto, Canada
| | - Ihor Batruch
- Department of Laboratory Medicine and Pathobiology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Canada
| | - Chunxiang Sun
- Faculty of Dentistry, University of Toronto, Toronto, Canada
| | | | - Luca Rampoldi
- Molecular Genetics of Renal Disorders Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
| | | | | | | | - Eleftherios P Diamandis
- Department of Laboratory Medicine and Pathobiology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Canada; Department of Clinical Biochemistry, University Health Network, University of Toronto, Toronto, Canada
| | - James W Scholey
- Institute of Medical Science, University of Toronto, Toronto, Canada; Toronto General Hospital Research Institute, University Health Network, Toronto, Canada; Department of Medicine, Division of Nephrology, University Health Network, Toronto, Canada
| | - Ana Konvalinka
- Institute of Medical Science, University of Toronto, Toronto, Canada; Toronto General Hospital Research Institute, University Health Network, Toronto, Canada; Department of Medicine, Division of Nephrology, University Health Network, Toronto, Canada
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12
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Johar D, Ahmed SM, El Hayek S, Al-Dewik N, Bahbah EI, Omar NH, Mustafa M, Salman DO, Fahmey A, Mottawea M, Azouz RAM, Bernstein L. Diabetes-induced Proteome Changes Throughout Development. Endocr Metab Immune Disord Drug Targets 2020; 19:732-743. [PMID: 31038056 DOI: 10.2174/1871530319666190305153810] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 10/31/2018] [Accepted: 11/25/2018] [Indexed: 12/31/2022]
Abstract
BACKGROUND Diabetes Mellitus (DM) is a multisystemic disease involving the homeostasis of insulin secretion by the pancreatic islet beta cells (β-cells). It is associated with hypertension, renal disease, and arterial and arteriolar vascular diseases. DISCUSSION The classification of diabetes is identified as type 1 (gene linked β-cell destruction in childhood) and type 2 (late onset associated with β-cell overload and insulin resistance in peripheral tissues. Type 1 diabetes is characterized by insulin deficiency, type 2 diabetes by both insulin deficiency and insulin resistance. The former is a genetically programmed loss of insulin secretion whereas the latter constitutes a disruption of the homeostatic relationship between the opposing activity of β- cell insulin and alpha cell (α-cell) glucagon of the Islets of Langerhans. The condition could also occur in pregnancy, as a prenatal occurring event, possibly triggered by the hormonal changes of pregnancy combined with β-cell overload. This review discusses the molecular basis of the biomolecular changes that occur with respect to glucose homeostasis and related diseases in DM. The underlying link between pancreatic, renal, and microvascular diseases in DM is based on oxidative stress and the Unfolded Protein Response (UPR). CONCLUSION Studying proteome changes in diabetes can deepen our understanding of the biomolecular basis of disease and help us acquire more efficient therapies.
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Affiliation(s)
- Dina Johar
- Biomedical Science Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt and Biochemistry and Nutrition Department, Ain Shams University Faculty of Women for Arts, Sciences and Education, Heliopolis, Cairo, Egypt
| | - Sara M Ahmed
- Clinical Pathology Department, Faculty of Medicine (Girls), Al-Azhar University, Nasr City, Cairo, Egypt
| | - Samer El Hayek
- Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Nader Al-Dewik
- Qatar Medical Genetic Center, Pediatrics Department, Hamad General Hospital (HGH), Hamad Medical Corporation (HMC), Doha, Qatar
| | - Eshak I Bahbah
- Faculty of Medicine, Al-Azhar University, Damietta, P.C. 34511, Egypt
| | - Nabil H Omar
- Pharmacy Department, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | | | - Doaa O Salman
- Genetics Unit, Histology and Cell biology department, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Asmaa Fahmey
- Faculty of Pharmacy, Al-Mansoura University, Al-Mansoura, Egypt
| | - Mohamed Mottawea
- Faculty of Pharmacy, Modern University for Technology and Information, Cairo, Egypt
| | - Rasha A M Azouz
- Molecular Biology Department, Genetic Engineering and Biotechnology Research Division, National Research Centre, Dokki, 12622 Giza, Egypt
| | - Larry Bernstein
- Triplex Consulting, 54 Firethorn Lane, Northampton, MA 01060, United States
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13
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Yu Y, Tsitrin T, Bekele S, Thovarai V, Torralba MG, Singh H, Wolcott R, Doerfert SN, Sizova MV, Epstein SS, Pieper R. Aerococcus urinae and Globicatella sanguinis Persist in Polymicrobial Urethral Catheter Biofilms Examined in Longitudinal Profiles at the Proteomic Level. BIOCHEMISTRY INSIGHTS 2019; 12:1178626419875089. [PMID: 31555049 PMCID: PMC6753514 DOI: 10.1177/1178626419875089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 08/13/2019] [Indexed: 11/27/2022]
Abstract
Aerococcus urinae (Au) and Globicatella
sanguinis (Gs) are gram-positive bacteria
belonging to the family Aerococcaceae and colonize the human immunocompromised
and catheterized urinary tract. We identified both pathogens in polymicrobial
urethral catheter biofilms (CBs) with a combination of 16S rDNA sequencing,
proteomic analyses, and microbial cultures. Longitudinal sampling of biofilms
from serially replaced catheters revealed that each species persisted in the
urinary tract of a patient in cohabitation with 1 or more gram-negative
uropathogens. The Gs and Au proteomes revealed
active glycolytic, heterolactic fermentation, and peptide catabolic energy
metabolism pathways in an anaerobic milieu. A few phosphotransferase system
(PTS)–based sugar uptake and oligopeptide ABC transport systems were highly
expressed, indicating adaptations to the supply of nutrients in urine and from
exfoliating squamous epithelial and urothelial cells. Differences in the
Au vs Gs metabolisms pertained to citrate
lyase and utilization and storage of glycogen (evident only in
Gs proteomes) and to the enzyme Xfp that degrades
d-xylulose-5′-phosphate and the biosynthetic pathways for 2 protein
cofactors, pyridoxal 6′-phosphate and 4′-phosphopantothenate (expressed only in
Au proteomes). A predicted ZnuA-like transition metal ion
uptake system was identified for Gs while Au
expressed 2 LPXTG-anchored surface proteins, one of which had a predicted pilin
D adhesion motif. While these proteins may contribute to fitness and virulence
in the human host, it cannot be ruled out that Au and
Gs fill a niche in polymicrobial biofilms without being the
direct cause of injury in urothelial tissues.
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Affiliation(s)
- Yanbao Yu
- J. Craig Venter Institute, Rockville, MD, USA
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14
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Nakayasu ES, Qian WJ, Evans-Molina C, Mirmira RG, Eizirik DL, Metz TO. The role of proteomics in assessing beta-cell dysfunction and death in type 1 diabetes. Expert Rev Proteomics 2019; 16:569-582. [PMID: 31232620 PMCID: PMC6628911 DOI: 10.1080/14789450.2019.1634548] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/18/2019] [Indexed: 12/17/2022]
Abstract
Introduction: Type 1 diabetes (T1D) is characterized by autoimmune-induced dysfunction and destruction of the pancreatic beta cells. Unfortunately, this process is poorly understood, and the current best treatment for type 1 diabetes is the administration of exogenous insulin. To better understand these mechanisms and to develop new therapies, there is an urgent need for biomarkers that can reliably predict disease stage. Areas covered: Mass spectrometry (MS)-based proteomics and complementary techniques play an important role in understanding the autoimmune response, inflammation and beta-cell death. MS is also a leading technology for the identification of biomarkers. This, and the technical difficulties and new technologies that provide opportunities to characterize small amounts of sample in great depth and to analyze large sample cohorts will be discussed in this review. Expert opinion: Understanding disease mechanisms and the discovery of disease-associated biomarkers are highly interconnected goals. Ideal biomarkers would be molecules specific to the different stages of the disease process that are released from beta cells to the bloodstream. However, such molecules are likely to be present in trace amounts in the blood due to the small number of pancreatic beta cells in the human body and the heterogeneity of the target organ and disease process.
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Affiliation(s)
- Ernesto S. Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Carmella Evans-Molina
- Center for Diabetes and Metabolic Diseases, Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Raghavendra G. Mirmira
- Center for Diabetes and Metabolic Diseases, Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Decio L. Eizirik
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Thomas O. Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
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15
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Actinobaculum massiliense Proteome Profiled in Polymicrobial Urethral Catheter Biofilms. Proteomes 2018; 6:proteomes6040052. [PMID: 30544882 PMCID: PMC6314084 DOI: 10.3390/proteomes6040052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/27/2018] [Accepted: 12/03/2018] [Indexed: 01/28/2023] Open
Abstract
Actinobaculum massiliense, a Gram-positive anaerobic coccoid rod colonizing the human urinary tract, belongs to the taxonomic class of Actinobacteria. We identified A. massiliense as a cohabitant of urethral catheter biofilms (CB). The CBs also harbored more common uropathogens, such as Proteus mirabilis and Aerococcus urinae, supporting the notion that A. massiliense is adapted to a life style in polymicrobial biofilms. We isolated a clinical strain from a blood agar colony and used 16S rRNA gene sequencing and shotgun proteomics to confirm its identity as A. massiliense. We characterized this species by quantitatively comparing the bacterial proteome derived from in vitro growth with that of four clinical samples. The functional relevance of proteins with emphasis on nutrient import and the response to hostile host conditions, showing evidence of neutrophil infiltration, was analyzed. Two putative subtilisin-like proteases and a heme/oligopeptide transporter were abundant in vivo and are likely important for survival and fitness in the biofilm. Proteins facilitating uptake of xylose/glucuronate and oligopeptides, also highly expressed in vivo, may feed metabolites into mixed acid fermentation and peptidolysis pathways, respectively, to generate energy. A polyketide synthase predicted to generate a secondary metabolite that interacts with either the human host or co-colonizing microbes was also identified. The product of the PKS enzyme may contribute to A. massiliense fitness and persistence in the CBs.
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16
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Spazzafumo L, Mensà E, Matacchione G, Galeazzi T, Zampini L, Recchioni R, Marcheselli F, Prattichizzo F, Testa R, Antonicelli R, Garagnani P, Boemi M, Bonafè M, Bonfigli AR, Procopio AD, Olivieri F. Age-related modulation of plasmatic beta-Galactosidase activity in healthy subjects and in patients affected by T2DM. Oncotarget 2017; 8:93338-93348. [PMID: 29212153 PMCID: PMC5706799 DOI: 10.18632/oncotarget.21848] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/04/2017] [Indexed: 01/01/2023] Open
Abstract
β-Galactosidase (β-Gal) activity has been the most extensively utilized biomarker for the detection of cellular senescence. It can be measured also in plasma, and few recent evidence showed an altered plasmatic β-Gal activity in patients affected by some age-related diseases (ARDs). Since T2DM is one of the most common ARDs, we aimed to investigate if plasmatic β-Gal activity is modulated in T2DM patients and if "age" could affect such modulation. To gain mechanistic insights we paralleled this investigation with the evaluation of β-Gal activity in young and senescent endothelial cells (HUVECs) cultured in normo- and hyper-glycaemic environment. A significant age-related increase of plasmatic β-Gal activity was observed in healthy subjects (n. 230; 55-87 years), whereas the enzymatic activity was significantly reduced in T2DM patients (n. 230; 55-96 years) compared to healthy subjects. β-Gal activity detectable both in cells and in the culture medium was significantly increased in senescent cells compared to the younger ones, both under normo- and hyper-glycaemic condition. However, the hyper-glycaemic condition was not associated with an increased β-Gal activity in milieu compared to normo-glycaemic condition. Overall our data reinforce the notion that plasmatic β-Gal activity could be a systemic biomarker of aging, whereas T2DM patients are characterized by a different age-releated trend.
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Affiliation(s)
- Liana Spazzafumo
- Center of Biostatics, INRCA-IRCCS National Institute, Ancona, Italy
| | - Emanuela Mensà
- Department of Clinical and Molecular Sciences, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy
| | - Giulia Matacchione
- Department of Clinical and Molecular Sciences, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy
| | - Tiziana Galeazzi
- Pediatric Division, Department of Clinical Sciences, Università Politecnica delle Marche, Ospedali Riuniti, Presidio Salesi, Ancona, Italy
| | - Lucia Zampini
- Pediatric Division, Department of Clinical Sciences, Università Politecnica delle Marche, Ospedali Riuniti, Presidio Salesi, Ancona, Italy
| | - Rina Recchioni
- Center of Clinical Pathology and Innovative Therapy, INRCA-IRCCS National Institute, Ancona, Italy
| | - Fiorella Marcheselli
- Center of Clinical Pathology and Innovative Therapy, INRCA-IRCCS National Institute, Ancona, Italy
| | - Francesco Prattichizzo
- Department of Cardiovascular and Metabolic Diseases, IRCCS Multimedica, Sesto San Giovanni, Italy
| | - Roberto Testa
- Clinical Laboratory and Molecular Diagnostics, INRCA-IRCCS National Institute, Ancona, Italy
| | | | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, University of Bologna, Bologna, Italy.,Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, Stockholm, Sweden
| | - Massimo Boemi
- Diabetology Unit, INRCA-IRCCS, National Institute, Ancona, Italy
| | - Massimiliano Bonafè
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | | | - Antonio Domenico Procopio
- Department of Clinical and Molecular Sciences, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy.,Center of Clinical Pathology and Innovative Therapy, INRCA-IRCCS National Institute, Ancona, Italy
| | - Fabiola Olivieri
- Department of Clinical and Molecular Sciences, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy.,Center of Clinical Pathology and Innovative Therapy, INRCA-IRCCS National Institute, Ancona, Italy
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17
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Singh H, Yu Y, Suh MJ, Torralba MG, Stenzel RD, Tovchigrechko A, Thovarai V, Harkins DM, Rajagopala SV, Osborne W, Cogen FR, Kaplowitz PB, Nelson KE, Madupu R, Pieper R. Type 1 Diabetes: Urinary Proteomics and Protein Network Analysis Support Perturbation of Lysosomal Function. Theranostics 2017; 7:2704-2717. [PMID: 28819457 PMCID: PMC5558563 DOI: 10.7150/thno.19679] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/25/2017] [Indexed: 12/11/2022] Open
Abstract
While insulin replacement therapy restores the health and prevents the onset of diabetic complications (DC) for many decades, some T1D patients have elevated hemoglobin A1c values suggesting poor glycemic control, a risk factor of DC. We surveyed the stool microbiome and urinary proteome of a cohort of 220 adolescents and children, half of which had lived with T1D for an average of 7 years and half of which were healthy siblings. Phylogenetic analysis of the 16S rRNA gene did not reveal significant differences in gut microbial alpha-diversity comparing the two cohorts. The urinary proteome of T1D patients revealed increased abundances of several lysosomal proteins that correlated with elevated HbA1c values. In silico protein network analysis linked such proteins to extracellular matrix components and the glycoprotein LRG1. LRG1 is a prominent inflammation and neovascularization biomarker. We hypothesize that these changes implicate aberrant glycation of macromolecules that alter lysosomal function and metabolism in renal tubular epithelial cells, cells that line part of the upper urinary tract.
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18
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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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An M, Ni Y, Li X, Gao Y. Effects of arginine vasopressin on the urine proteome in rats. PeerJ 2017; 5:e3350. [PMID: 28560103 PMCID: PMC5444365 DOI: 10.7717/peerj.3350] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 04/24/2017] [Indexed: 12/14/2022] Open
Abstract
Biomarkers are the measurable changes associated with a physiological or pathophysiological process. The content of urine frequently changes because it is not controlled by homeostatic mechanisms, and these alterations can be a source of biomarkers. However, urine is affected by many factors. In this study, vasoconstrictor and antidiuretic arginine vasopressin (AVP) were infused into rats using an osmotic pump. The rats’ urinary proteome after one week of infusion was analyzed by label-free LC-MS/MS. A total of 408 proteins were identified; among these proteins, eight and 10 proteins had significantly altered expression in the low and high dose groups, respectively, compared with the control group using the one-way ANOVA analysis followed by post hoc analysis with the least significant difference (LSD) test or Dunnett’s T3 test. Three differential proteins were described in prior studies as related to AVP physiological processes, and nine differential proteins are known disease biomarkers. Sixteen of the 17 differential proteins have human orthologs. These results suggest that we should consider the effects of AVP on urinary proteins in future urinary disease biomarker researches. The study data provide clues regarding underlying mechanisms associated with AVP for future physiological researches on AVP. This study provide a sensitive changes associated with AVP. However, the limitation of this result is that the candidate biomarkers should be further verified and filtered. Large clinical samples must be examined to verify the differential proteins identified in this study before these proteins are used as biomarkers for pathological AVP increased diseases, such as syndrome of inappropriate antidiuretic hormone secretion (SIADH).
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Affiliation(s)
- Manxia An
- Department of Pathophysiology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Yanying Ni
- Department of Pathophysiology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Xundou Li
- Department of Pathophysiology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Youhe Gao
- Department of Pathophysiology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China.,Department of Biochemistry and Molecular Biology, Beijing Normal University, Gene Engineering and Biotechnology Beijing Key Laboratory, Beijing, China
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Yu Y, Kwon K, Tsitrin T, Bekele S, Sikorski P, Nelson KE, Pieper R. Characterization of Early-Phase Neutrophil Extracellular Traps in Urinary Tract Infections. PLoS Pathog 2017; 13:e1006151. [PMID: 28129394 PMCID: PMC5298345 DOI: 10.1371/journal.ppat.1006151] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 02/08/2017] [Accepted: 12/24/2016] [Indexed: 12/15/2022] Open
Abstract
Neutrophils have an important role in the antimicrobial defense and resolution of urinary tract infections (UTIs). Our research suggests that a mechanism known as neutrophil extracellular trap (NET) formation is a defense strategy to combat pathogens that have invaded the urinary tract. A set of human urine specimens with very high neutrophil counts had microscopic evidence of cellular aggregation and lysis. Deoxyribonuclease I (DNase) treatment resulted in disaggregation of such structures, release of DNA fragments and a proteome enriched in histones and azurophilic granule effectors whose quantitative composition was similar to that of previously described in vitro-formed NETs. The effector proteins were further enriched in DNA-protein complexes isolated in native PAGE gels. Immunofluorescence microscopy revealed a flattened morphology of neutrophils associated with decondensed chromatin, remnants of granules in the cell periphery, and myeloperoxidase co-localized with extracellular DNA, features consistent with early-phase NETs. Nuclear staining revealed that a considerable fraction of bacterial cells in these structures were dead. The proteomes of two pathogens, Staphylococcus aureus and Escherichia coli, were indicative of adaptive responses to early-phase NETs, specifically the release of virulence factors and arrest of ribosomal protein synthesis. Finally, we discovered patterns of proteolysis consistent with widespread cleavage of proteins by neutrophil elastase, proteinase 3 and cathepsin G and evidence of citrullination in many nuclear proteins. Urinary tract infections (UTIs) are one of the world’s most widespread infectious diseases, with an estimated number of 150 million cases per year. Neutrophils play an important role in the defense of human patients against microbes causing UTIs. Molecules produced by neutrophils that migrate into the urinary tract can kill the invading microbes and resolve an infection, often without a need to treat patients with an antibiotic. Our work shows strong support for a mechanism called the formation of neutrophil extracellular traps (NETs), previously described for other infections and autoimmune conditions, which are involved in killing pathogens that have invaded the urinary tract. We show evidence of extracellular chromatin-containing structures using immunofluorescence microscopy and identified proteins that bind to the chromatin DNA and have functions to damage and kill bacterial cells or stop their growth.
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Affiliation(s)
- Yanbao Yu
- The J. Craig Venter Institute, Rockville, MD, United States of America
| | - Keehwan Kwon
- The J. Craig Venter Institute, Rockville, MD, United States of America
| | - Tamara Tsitrin
- The J. Craig Venter Institute, Rockville, MD, United States of America
| | - Shiferaw Bekele
- The J. Craig Venter Institute, Rockville, MD, United States of America
| | - Patricia Sikorski
- The J. Craig Venter Institute, Rockville, MD, United States of America
| | - Karen E. Nelson
- The J. Craig Venter Institute, Rockville, MD, United States of America
| | - Rembert Pieper
- The J. Craig Venter Institute, Rockville, MD, United States of America
- * E-mail:
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Moulder R, Bhosale SD, Lahesmaa R, Goodlett DR. The progress and potential of proteomic biomarkers for type 1 diabetes in children. Expert Rev Proteomics 2016; 14:31-41. [PMID: 27997253 DOI: 10.1080/14789450.2017.1265449] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
INTRODUCTION Although it is possible to identify the genetic risk for type 1 diabetes (T1D), it is not possible to predict who will develop the disease. New biomarkers are needed that would help understand the mechanisms of disease onset and when to administer targeted therapies and interventions. Areas covered: An overview is presented of international study efforts towards understanding the cause of T1D, including the collection of several extensive temporal sample series that follow the development of T1D in at risk children. The results of the proteomics analysis of these materials are presented, which have included bodily fluids, such as serum or plasma and urine, as well as tissue samples from the pancreas. Expert commentary: Promising recent reports have indicated detection of early proteomic changes in the serum of patients prior to diagnosis, potentially providing new measures for risk assessment. Similarly, there has been evidence that post-translational modification (PTM) may result in the recognition of islet cell proteins as autoantigens; modified proteins could thus be used as targets for immunomodulation to overcome the threat of the autoimmune response.
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Affiliation(s)
- Robert Moulder
- a Turku Centre for Biotechnology , University of Turku , Turku , Finland
| | | | - Riitta Lahesmaa
- a Turku Centre for Biotechnology , University of Turku , Turku , Finland
| | - David Robinson Goodlett
- a Turku Centre for Biotechnology , University of Turku , Turku , Finland.,b School of Pharmacy , University of Maryland , Baltimore , MD , USA
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