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Fejrskov A, Füchtbauer JD, Davíðsdóttir LG, Halfvarson J, Høivik ML, Jensen MD, Mortensen JH, Nielsen LN, Rejler M, Repsilber D, Söderholm JD, Aalykke C, Andersen V, Christensen R, Kjeldsen J. Novel biomarker profiles to improve individual diagnosis and prognosis in patients with suspected inflammatory bowel disease: protocol for the Nordic inception cohort study (NORDTREAT). BMJ Open 2024; 14:e083144. [PMID: 38754881 PMCID: PMC11097809 DOI: 10.1136/bmjopen-2023-083144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/25/2024] [Indexed: 05/18/2024] Open
Abstract
INTRODUCTION Inflammatory bowel disease (IBD), including ulcerative colitis and Crohn's disease, can be challenging to diagnose, and treatment outcomes are difficult to predict. In the NORDTREAT cohort study, a Nordic prospective multicentre study, we aim to identify novel molecular biomarkers of diagnostic value by assessing the diagnostic test accuracy (cross-sectionally), as well as the prognostic utility when used as prognostic markers in the long-term (cohort study). In the diagnostic test accuracy study, the primary outcome is a successful diagnosis using one or more novel index tests at baseline compared with the ECCO criteria as the reference standard. The composite outcome of the prognostic utility study is 'severe IBD' within 52 weeks from inclusion, defined as one or more of the following three events: IBD-related surgery, IBD-related hospitalisation or IBD-related death. METHODS AND ANALYSIS We aim to recruit 800 patients referred on suspicion of IBD to this longitudinal observational study, a collaboration between 11 inclusion sites in Denmark, Iceland, Norway and Sweden. Inclusion will occur from February 2022 until December 2023 with screening and baseline visits for all participants and three outcome visits at weeks 12, 26 and 52 after baseline for IBD-diagnosed patients. Biological material (blood, faeces, biopsies, urine and hair), clinical data and lifestyle information will be collected during these scheduled visits. ETHICS AND DISSEMINATION This study will explore novel biomarkers to improve diagnostic accuracy and prediction of disease progression, thereby improving medical therapy and the quality of life for patients with IBD.The study is approved by the Ethics Committee (DK: S-20200051, v1.4, 16.10.2021; IS: VSNb2021070006/03.01, NO: 193064; SE: DNR 2021-05090) and the Danish Data Protecting Agency (20/54594). Results will be disseminated through peer-reviewed journals, patient associations and presentations at international conferences. CLINICAL TRIAL REGISTRATION NUMBER NCT05414578; Pre-results.
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Affiliation(s)
- Anja Fejrskov
- Department of Medical Gastroenterology, Odense University Hospital, Odense, Denmark
- Department of Internal Medicine, Molecular Diagnostics and Clinical Research Unit, Institute of Regional Health Research, University Hospital of Southern Denmark, Aabenraa, Denmark
- Section for Biostatistics and Evidence-Based Research, Parker Institute, Frederiksberg, Denmark
| | - Johannes David Füchtbauer
- Department of Medical Gastroenterology, Odense University Hospital, Odense, Denmark
- Research Unit of Medical Gastroenterology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- Internal Medicine and Emergency Department, Odense University Hospital, Svendborg, Denmark
| | - Lóa G Davíðsdóttir
- Department of Gastroenterology, Landspitali National University Hospital of Iceland, Reykjavik, Iceland
| | - Jonas Halfvarson
- Department of Internal Medicine, Örebro University Hospital, Örebro, Region Örebro län, Sweden
| | - Marte Lie Høivik
- Department of Gastroenterology, Oslo University Hospital, Oslo, Norway
- University of Oslo Institute for Clinical Medicine, Oslo, Norway
| | - Michael Dam Jensen
- Department of Internal Medicine-Gastroenterology, Lillebaelt Hospital, University Hospital of Southern Denmark, Vejle, Denmark
- Institute of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | | | - Lene Nyholm Nielsen
- Research Unit of Medical Gastroenterology and Hepatology, Hospital South West Jutland, Esbjerg, Denmark
| | - Martin Rejler
- Jönköping Academy for Improvement in Health and Welfare, Jönköping University, Jönköping, Sweden
- Futurum-Academy for Healthcare, Futurum Academy of Health and Care, Jönköping, Region Jönköping County, Sweden
| | - Dirk Repsilber
- School of Health and Medical Sciences, Örebro University, Örebro, Sweden
| | - Johan D Söderholm
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Östergötland, Sweden
| | - Claus Aalykke
- Internal Medicine and Emergency Department, Odense University Hospital, Svendborg, Denmark
| | - Vibeke Andersen
- Department of Internal Medicine, Molecular Diagnostics and Clinical Research Unit, Institute of Regional Health Research, University Hospital of Southern Denmark, Aabenraa, Denmark
- Institute of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
- Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
- OPEN, Open Patient data Explorative Network, University of Southern Denmark, Odense, Denmark
| | - Robin Christensen
- Section for Biostatistics and Evidence-Based Research, Parker Institute, Frederiksberg, Denmark
- Research Unit of Rheumatology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Jens Kjeldsen
- Department of Medical Gastroenterology, Odense University Hospital, Odense, Denmark
- Research Unit of Medical Gastroenterology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
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Belete MA, Tadesse S, Tilahun M, Gedefie A, Shibabaw A, Mulatie Z, Wudu MA, Gebremichael S, Debash H, Alebachew M, Alemayehu E. Long noncoding RNAs and circular RNAs as potential diagnostic biomarkers of inflammatory bowel diseases: a systematic review and meta-analysis. Front Immunol 2024; 15:1362437. [PMID: 38524131 PMCID: PMC10957631 DOI: 10.3389/fimmu.2024.1362437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 02/27/2024] [Indexed: 03/26/2024] Open
Abstract
Introduction Inflammatory bowel disease (IBD) poses a growing global burden, necessitating the discovery of reliable biomarkers for early diagnosis. The clinical significance of dysregulated expression of long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) in diagnosing IBD has not been well established. Thus, our study aimed to investigate the diagnostic value of lncRNAs and circRNAs for IBD based on currently available studies. Methods A comprehensive search was carried out in diverse electronic databases, such as PubMed, Embase, Scopus, Science Direct and Wiley Online Library to retrieve articles published until October 30, 2023. Stata 17.0 software was employed to determine pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic ratio (DOR), and area under the curve (AUC). Heterogeneity, subgroup analysis, and meta-regression were explored, and publication bias was assessed using Deeks' funnel plot. Fagan's nomogram and likelihood ratio scattergram were employed to evaluate the clinical validity. Result A total of 11 articles encompassing 21 studies which involved 1239 IBD patients and 985 healthy controls were investigated. The findings revealed lncRNAs exhibit high level of pooled sensitivity 0.94 (95% CI: 0.87-0.97) and specificity 0.99 (95% CI: 0.89-1.00), along with PLR, NLR, DOR, and AUC values of 64.25 (95% CI: 7.39-558.66), 0.06 (95% CI: 0.03-0.13), 1055.25 (95% CI: 70.61-15770.77), and 0.99 (95% CI: 0.97-0.99), respectively. Conversely, CircRNAs showed moderate accuracy in IBD diagnosis, with sensitivity of 0.68 (95% CI: 0.61-0.73), specificity of 0.73 (95% CI: 0.65-0.79), PLR of 2.47 (95% CI: 1.94-3.16), NLR of 0.45 (95% CI: 0.38-0.53), DOR of 5.54 (95% CI: 3.88-7.93), and AUC value of 0.75 (95% CI: 0.71-0.79). Moreover, findings from subgroup analysis depicted heightened diagnostic efficacy when employing lncRNA H19 and a large sample size (≥100), with notable efficacy in diagnosing both ulcerative colitis (UC) and Crohn's disease (CD). Conclusion LncRNAs exhibit high diagnostic accuracy in distinguishing patients with IBD from healthy controls signifying their possible use as potential biomarkers, while circRNAs showed moderate diagnostic accuracy. Nevertheless, to validate our findings and confirm the clinical utility of lncRNAs and circRNAs in IBD diagnosis, a large pool of prospective and multi-center studies should be undertaken. Systematic review registration https://www.crd.york.ac.uk/PROSPERO, identifier CRD42023491840.
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Affiliation(s)
- Melaku Ashagrie Belete
- Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia
| | - Selamyhun Tadesse
- Department of Medical Laboratory Science, College of Health Sciences, Woldia University, Woldia, Ethiopia
| | - Mihret Tilahun
- Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia
| | - Alemu Gedefie
- Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia
| | - Agumas Shibabaw
- Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia
| | - Zewudu Mulatie
- Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia
| | - Muluken Amare Wudu
- Department of Pediatric and Child Health Nursing, School of Nursing and Midwifery, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia
| | - Saba Gebremichael
- Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia
| | - Habtu Debash
- Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia
| | - Mihreteab Alebachew
- Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia
| | - Ermiyas Alemayehu
- Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia
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Fabian O, Bajer L, Drastich P, Harant K, Sticova E, Daskova N, Modos I, Tichanek F, Cahova M. A Current State of Proteomics in Adult and Pediatric Inflammatory Bowel Diseases: A Systematic Search and Review. Int J Mol Sci 2023; 24:ijms24119386. [PMID: 37298338 DOI: 10.3390/ijms24119386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/23/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are systemic immune-mediated conditions with predilection for the gastrointestinal tract and include Crohn's disease and ulcerative colitis. Despite the advances in the fields of basic and applied research, the etiopathogenesis remains largely unknown. As a result, only one third of the patients achieve endoscopic remission. A substantial portion of the patients also develop severe clinical complications or neoplasia. The need for novel biomarkers that can enhance diagnostic accuracy, more precisely reflect disease activity, and predict a complicated disease course, thus, remains high. Genomic and transcriptomic studies contributed substantially to our understanding of the immunopathological pathways involved in disease initiation and progression. However, eventual genomic alterations do not necessarily translate into the final clinical picture. Proteomics may represent a missing link between the genome, transcriptome, and phenotypical presentation of the disease. Based on the analysis of a large spectrum of proteins in tissues, it seems to be a promising method for the identification of new biomarkers. This systematic search and review summarize the current state of proteomics in human IBD. It comments on the utility of proteomics in research, describes the basic proteomic techniques, and provides an up-to-date overview of available studies in both adult and pediatric IBD.
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Affiliation(s)
- Ondrej Fabian
- Clinical and Transplant Pathology Centre, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
- Department of Pathology and Molecular Medicine, 3rd Faculty of Medicine, Charles University and Thomayer Hospital, 140 59 Prague, Czech Republic
| | - Lukas Bajer
- Department of Gastroenterology and Hepatology, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
- Institute of Microbiology, Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Pavel Drastich
- Department of Gastroenterology and Hepatology, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
| | - Karel Harant
- Proteomics Core Facility, Faculty of Science, Charles University, 252 50 Vestec, Czech Republic
| | - Eva Sticova
- Clinical and Transplant Pathology Centre, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
- Department of Pathology, Royal Vinohrady Teaching Hospital, Srobarova 1150/50, 100 00 Prague, Czech Republic
| | - Nikola Daskova
- Experimental Medicine Centre, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
| | - Istvan Modos
- Department of Informatics, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
| | - Filip Tichanek
- Department of Informatics, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
| | - Monika Cahova
- Experimental Medicine Centre, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
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Jensen SB, Sheikh MA, Akkouh IA, Szabo A, O’Connell KS, Lekva T, Engh JA, Agartz I, Elvsåshagen T, Ormerod MBEG, Weibell MA, Johnsen E, Kroken RA, Melle I, Drange OK, Nærland T, Vaaler AE, Westlye LT, Aukrust P, Djurovic S, Eiel Steen N, Andreassen OA, Ueland T. Elevated Systemic Levels of Markers Reflecting Intestinal Barrier Dysfunction and Inflammasome Activation Are Correlated in Severe Mental Illness. Schizophr Bull 2023; 49:635-645. [PMID: 36462169 PMCID: PMC10154716 DOI: 10.1093/schbul/sbac191] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
BACKGROUND AND HYPOTHESIS Gut microbiota alterations have been reported in severe mental illness (SMI) but fewer studies have probed for signs of gut barrier disruption and inflammation. We hypothesized that gut leakage of microbial products due to intestinal inflammation could contribute to systemic inflammasome activation in SMI. STUDY DESIGN We measured plasma levels of the chemokine CCL25 and soluble mucosal vascular addressin cell adhesion molecule-1 (sMAdCAM-1) as markers of T cell homing, adhesion and inflammation in the gut, lipopolysaccharide binding protein (LBP) and intestinal fatty acid binding protein (I-FABP) as markers of bacterial translocation and gut barrier dysfunction, in a large SMI cohort (n = 567) including schizophrenia (SCZ, n = 389) and affective disorder (AFF, n = 178), relative to healthy controls (HC, n = 418). We assessed associations with plasma IL-18 and IL-18BPa and leukocyte mRNA expression of NLRP3 and NLRC4 as markers of inflammasome activation. STUDY RESULTS Our main findings were: (1) higher levels of sMAdCAM-1 (P = .002), I-FABP (P = 7.6E-11), CCL25 (P = 9.6E-05) and LBP (P = 2.6E-04) in SMI compared to HC in age, sex, BMI, CRP and freezer storage time adjusted analysis; (2) the highest levels of sMAdCAM-1 and CCL25 (both P = 2.6E-04) were observed in SCZ and I-FABP (P = 2.5E-10) and LBP (3) in AFF; and (3), I-FABP correlated with IL-18BPa levels and LBP correlated with NLRC4. CONCLUSIONS Our findings support that intestinal barrier inflammation and dysfunction in SMI could contribute to systemic inflammation through inflammasome activation.
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Affiliation(s)
- Søren B Jensen
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway
| | - Mashhood A Sheikh
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway
| | - Ibrahim A Akkouh
- Division of Mental Health and Addiction, Norwegian Centre for Mental Disorders Research, NORMENT, Oslo University Hospital, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Attila Szabo
- Division of Mental Health and Addiction, Norwegian Centre for Mental Disorders Research, NORMENT, Oslo University Hospital, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- K.G. Jebsen Center for Neurodevelopmental disorders, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Kevin S O’Connell
- Division of Mental Health and Addiction, Norwegian Centre for Mental Disorders Research, NORMENT, Oslo University Hospital, Oslo, Norway
| | - Tove Lekva
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway
| | - John A Engh
- Division of Mental Health and Addiction, Norwegian Centre for Mental Disorders Research, NORMENT, Oslo University Hospital, Oslo, Norway
- Division of Mental health and Addiction, Vestfold Hospital Trust, Tønsberg, Norway
| | - Ingrid Agartz
- K.G. Jebsen Center for Neurodevelopmental disorders, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Clinical Neuroscience, Centre for Psychiatry Research, Karolinska Institutet and Stockholm Health Care Services, Stockholm County Council, Stockholm, Sweden
- Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway
- Norwegian Centre for Mental Disorders Research, NORMENT, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Torbjørn Elvsåshagen
- Division of Mental Health and Addiction, Norwegian Centre for Mental Disorders Research, NORMENT, Oslo University Hospital, Oslo, Norway
| | - Monica B E G Ormerod
- Division of Mental Health and Addiction, Norwegian Centre for Mental Disorders Research, NORMENT, Oslo University Hospital, Oslo, Norway
- Norwegian Centre for Mental Disorders Research, NORMENT, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Melissa A Weibell
- Division of Psychiatry, Network for Clinical Psychosis Research, Stavanger University Hospital, Stavanger, Norway
- Network for Medical Sciences, Faculty of Health, University of Stavanger, Stavanger, Norway
| | - Erik Johnsen
- Division of Psychiatry, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- NORMENT Center of Excellence, University of Bergen and Haukeland University Hospital, Bergen, Norway
| | - Rune A Kroken
- Division of Psychiatry, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- NORMENT Center of Excellence, University of Bergen and Haukeland University Hospital, Bergen, Norway
| | - Ingrid Melle
- Division of Mental Health and Addiction, Norwegian Centre for Mental Disorders Research, NORMENT, Oslo University Hospital, Oslo, Norway
- Norwegian Centre for Mental Disorders Research, NORMENT, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ole K Drange
- Department of Mental Health, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Østmarka, Division of Mental Health, St. Olavs University Hospital, Trondheim, Norway
- Department of Psychiatry, Sørlandet Hospital, Kristiansand, Norway
| | - Terje Nærland
- K.G. Jebsen Center for Neurodevelopmental disorders, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Rare Disorders, Division of Child and Adolescent medicine, Oslo University Hospital, Oslo, Norway
| | - Arne E Vaaler
- Department of Mental Health, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Østmarka, Division of Mental Health, St. Olavs University Hospital, Trondheim, Norway
| | - Lars T Westlye
- Division of Mental Health and Addiction, Norwegian Centre for Mental Disorders Research, NORMENT, Oslo University Hospital, Oslo, Norway
- K.G. Jebsen Center for Neurodevelopmental disorders, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Psychology, University of Oslo, Oslo, Norway
| | - Pål Aukrust
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway
- Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Srdjan Djurovic
- Division of Mental Health and Addiction, Norwegian Centre for Mental Disorders Research, NORMENT, Oslo University Hospital, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- K.G. Jebsen Center for Neurodevelopmental disorders, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Psychology, University of Oslo, Oslo, Norway
| | - Nils Eiel Steen
- Division of Mental Health and Addiction, Norwegian Centre for Mental Disorders Research, NORMENT, Oslo University Hospital, Oslo, Norway
- Norwegian Centre for Mental Disorders Research, NORMENT, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ole A Andreassen
- Division of Mental Health and Addiction, Norwegian Centre for Mental Disorders Research, NORMENT, Oslo University Hospital, Oslo, Norway
- K.G. Jebsen Center for Neurodevelopmental disorders, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Norwegian Centre for Mental Disorders Research, NORMENT, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Thor Ueland
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- K.G. Jebsen Thrombosis Research and Expertise Center, University of Tromsø, Tromsø, Norway
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Warpechowski M, Warpechowski J, Pieńkowska A, Sagała S, Milewski R. Neutrophil-to-Platelet Ratio in Patients with Ulcerative Colitis Treated with Infliximab or Vedolizumab: A Retrospective, Single-Center Study in Poland. Med Sci Monit 2023; 29:e938827. [PMID: 36721357 PMCID: PMC9901171 DOI: 10.12659/msm.938827] [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] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND This retrospective study from a single center in Poland was undertaken to evaluate the clinical utility of neutrophil-to-platelet ratio in therapy of 35 ulcerative colitis (UC) patients with infliximab or vedolizumab. MATERIAL AND METHODS This study included 35 patients: 16 were treated with infliximab and 19 were treated with vedolizumab. Treatment response was evaluated using partial Mayo score. Treatment response was defined as a reduction of partial Mayo score of ≥3 points followed by a decrease of a minimum of 30% from the baseline, decrease in the rectal bleeding subscore of ≥1, or an absolute rectal bleeding subscore of 0 or 1. During the maintenance period, we diagnosed 13 patients with loss of response (LOR) (5 with infliximab and 8 with vedolizumab). The Mann-Whitney U test was performed to assess differences between the groups. Statistical significance was defined as P<0.05. The median was used to describe the value of the parameter. Analysis of the receiver operating characteristic (ROC) curve with the determination of area under the curve (AUC) was performed for the neutrophil-to-platelet parameter during the induction period. RESULTS The median value of the neutrophil-to-platelet ratio for the treatment response group was lower than in the LOR group (median=13.18 and median=19.49, respectively). Calculation of AUC curve for neutrophil-to-platelet ratio during the induction period showed best sensitivity and specificity for values ≥32.511. There were no other significant findings. CONCLUSIONS Neutrophil-to-platelet ratio might be a promising biomarker of LOR in biologic therapy of UC. However, to fully prove this, further studies are needed.
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Affiliation(s)
- Marcin Warpechowski
- Department of Biostatistics and Medical Informatics, Medical University of Białystok, Białystok, Poland
| | - Jędrzej Warpechowski
- Student Scientific Group at the Department of Biostatistics and Medical Informatics, Medical University of Białystok, Białystok, Poland
| | - Anita Pieńkowska
- Student Scientific Group at the Department of Biostatistics and Medical Informatics, Medical University of Białystok, Białystok, Poland
| | - Szymon Sagała
- Student Scientific Group at the Department of Biostatistics and Medical Informatics, Medical University of Białystok, Białystok, Poland
| | - Robert Milewski
- Department of Biostatistics and Medical Informatics, Medical University of Białystok, Białystok, Poland
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Bourgonje AR, Kloska D, Grochot-Przęczek A, Feelisch M, Cuadrado A, van Goor H. Personalized redox medicine in inflammatory bowel diseases: an emerging role for HIF-1α and NRF2 as therapeutic targets. Redox Biol 2023; 60:102603. [PMID: 36634466 PMCID: PMC9841059 DOI: 10.1016/j.redox.2023.102603] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 01/05/2023] [Accepted: 01/05/2023] [Indexed: 01/07/2023] Open
Abstract
Inflammatory bowel diseases (IBD), encompassing Crohn's disease (CD) and ulcerative colitis (UC), are intimately associated with inflammation and overproduction of reactive oxygen species (ROS). Temporal and inter-individual variabilities in disease activity and response to therapy pose significant challenges to diagnosis and patient care. Discovery and validation of truly integrative biomarkers would benefit from embracing redox metabolomics approaches with prioritization of central regulatory hubs. We here make a case for applying a personalized redox medicine approach that aims to selectively inhibit pathological overproduction and/or altered expression of specific enzymatic sources of ROS without compromising physiological function. To this end, improved 'clinical-omics integration' may help to better understand which particular redox signaling pathways are disrupted in what patient. Pharmacological interventions capable of activating endogenous antioxidant defense systems may represent viable therapeutic options to restore local/systemic redox status, with HIF-1α and NRF2 holding particular promise in this context. Achieving the implementation of clinically meaningful mechanism-based biomarkers requires development of easy-to-use, robust and cost-effective tools for secure diagnosis and monitoring of treatment efficacy. Ultimately, matching redox-directed pharmacological interventions to individual patient phenotypes using predictive biomarkers may offer new opportunities to break the therapeutic ceiling in IBD.
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Affiliation(s)
- Arno R. Bourgonje
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands,Corresponding author.
| | - Damian Kloska
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Anna Grochot-Przęczek
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Martin Feelisch
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Antonio Cuadrado
- Instituto de Investigaciones Biomédicas “Alberto Sols” UAM-CSIC. Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid, Spain
| | - Harry van Goor
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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Zheng J, Sun Q, Zhang J, Ng SC. The role of gut microbiome in inflammatory bowel disease diagnosis and prognosis. United European Gastroenterol J 2022; 10:1091-1102. [PMID: 36461896 PMCID: PMC9752296 DOI: 10.1002/ueg2.12338] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/05/2022] [Indexed: 12/04/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic immune-mediated intestinal disease consisting of ulcerative colitis and Crohn's disease. Inflammatory bowel disease is believed to be developed as a result of interactions between environmental, immune-mediated and microbial factors in a genetically susceptible host. Recent advances in high-throughput sequencing technologies have aided the identification of consistent alterations of the gut microbiome in patients with IBD. Preclinical and murine models have also shed light on the role of beneficial and pathogenic bacteria in IBD. These findings have stimulated interest in development of non-invasive microbial and metabolite biomarkers for predicting disease risk, disease progression, recurrence after surgery and responses to therapeutics. This review briefly summarizes the current evidence on the role of gut microbiome in IBD pathogenesis and mainly discusses the latest literature on the utilization of potential microbial biomarkers in disease diagnosis and prognosis.
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Affiliation(s)
- Jiaying Zheng
- Microbiota I-Center (MagIC), Hong Kong, China.,Department of Medicine and Therapeutics, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China.,Li Ka Shing Institute of Health Science, State Key Laboratory of Digestive Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Qianru Sun
- Microbiota I-Center (MagIC), Hong Kong, China.,Department of Medicine and Therapeutics, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China.,Li Ka Shing Institute of Health Science, State Key Laboratory of Digestive Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Jingwan Zhang
- Microbiota I-Center (MagIC), Hong Kong, China.,Department of Medicine and Therapeutics, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China.,Li Ka Shing Institute of Health Science, State Key Laboratory of Digestive Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Siew C Ng
- Microbiota I-Center (MagIC), Hong Kong, China.,Department of Medicine and Therapeutics, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China.,Li Ka Shing Institute of Health Science, State Key Laboratory of Digestive Diseases, The Chinese University of Hong Kong, Hong Kong, China
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Piestansky J, Olesova D, Matuskova M, Cizmarova I, Chalova P, Galba J, Majerova P, Mikus P, Kovac A. Amino acids in inflammatory bowel diseases: Modern diagnostic tools and methodologies. Adv Clin Chem 2022; 107:139-213. [PMID: 35337602 DOI: 10.1016/bs.acc.2021.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Amino acids are crucial building blocks of living organisms. Together with their derivatives, they participate in many intracellular processes to act as hormones, neuromodulators, and neurotransmitters. For several decades amino acids have been studied for their potential as markers of various diseases, including inflammatory bowel diseases. Subsequent improvements in sample pretreatment, separation, and detection methods have enabled the specific and very sensitive determination of these molecules in multicomponent matrices-biological fluids and tissues. The information obtained from targeted amino acid analysis (biomarker-based analytical strategy) can be further used for early diagnostics, to monitor the course of the disease or compliance of the patients. This review will provide an insight into current knowledge about inflammatory bowel diseases, the role of proteinogenic amino acids in intestinal inflammation and modern analytical techniques used in its diagnosis and disease activity monitoring. Current advances in the analysis of amino acids focused on sample pretreatment, separation strategy, or detection methods are highlighted, and their potential in clinical laboratories is discussed. In addition, the latest clinical data obtained from the metabolomic profiling of patients suffering from inflammatory bowel diseases are summarized with a focus on proteinogenic amino acids.
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Affiliation(s)
- Juraj Piestansky
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovakia; Toxicological and Antidoping Center, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovakia
| | - Dominika Olesova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Michaela Matuskova
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovakia
| | - Ivana Cizmarova
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovakia
| | - Petra Chalova
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovakia
| | - Jaroslav Galba
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovakia
| | - Petra Majerova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Peter Mikus
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovakia; Toxicological and Antidoping Center, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovakia
| | - Andrej Kovac
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia.
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9
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Di Narzo AF, Houten SM, Kosoy R, Huang R, Vaz FM, Hou R, Wei G, Wang WH, Comella PH, Dodatko T, Rogatsky E, Stojmirovic A, Brodmerkel C, Perrigoue J, Hart A, Curran M, Friedman JR, Zhu J, Agrawal M, Cho J, Ungaro R, Dubinsky M, Sands BE, Suárez-Fariñas M, Schadt EE, Colombel JF, Kasarskis A, Hao K, Argmann C. Integrative Analysis of the Inflammatory Bowel Disease Serum Metabolome Improves Our Understanding of Genetic Etiology and Points to Novel Putative Therapeutic Targets. Gastroenterology 2022; 162:828-843.e11. [PMID: 34780722 PMCID: PMC9214725 DOI: 10.1053/j.gastro.2021.11.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 11/01/2021] [Accepted: 11/07/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND & AIMS Polygenic and environmental factors are underlying causes of inflammatory bowel disease (IBD). We hypothesized that integration of the genetic loci controlling a metabolite's abundance, with known IBD genetic susceptibility loci, may help resolve metabolic drivers of IBD. METHODS We measured the levels of 1300 metabolites in the serum of 484 patients with ulcerative colitis (UC) and 464 patients with Crohn's disease (CD) and 365 controls. Differential metabolite abundance was determined for disease status, subtype, clinical and endoscopic disease activity, as well as IBD phenotype including disease behavior, location, and extent. To inform on the genetic basis underlying metabolic diversity, we integrated metabolite and genomic data. Genetic colocalization and Mendelian randomization analyses were performed using known IBD risk loci to explore whether any metabolite was causally associated with IBD. RESULTS We found 173 genetically controlled metabolites (metabolite quantitative trait loci, 9 novel) within 63 non-overlapping loci (7 novel). Furthermore, several metabolites significantly associated with IBD disease status and activity as defined using clinical and endoscopic indexes. This constitutes a resource for biomarker discovery and IBD biology insights. Using this resource, we show that a novel metabolite quantitative trait locus for serum butyrate levels containing ACADS was not supported as causal for IBD; replicate the association of serum omega-6 containing lipids with the fatty acid desaturase 1/2 locus and identify these metabolites as causal for CD through Mendelian randomization; and validate a novel association of serum plasmalogen and TMEM229B, which was predicted as causal for CD. CONCLUSIONS An exploratory analysis combining genetics and unbiased serum metabolome surveys can reveal novel biomarkers of disease activity and potential mediators of pathology in IBD.
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Affiliation(s)
- Antonio F. Di Narzo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Sema4, Stamford, CT, 06902, USA,Corresponding Author: Carmen Argmann,
| | - Sander M. Houten
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Roman Kosoy
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Ruiqi Huang
- Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Frédéric M. Vaz
- Department of Clinical Chemistry, Amsterdam Gastroenterology & Metabolism, Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Ruixue Hou
- Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gabrielle Wei
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Wen-hui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Phillip H. Comella
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Tetyana Dodatko
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Eduard Rogatsky
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | | | | | | | - Amy Hart
- Janssen R&D, LLC, 1400 McKean Road, Spring House, PA, USA
| | - Mark Curran
- Janssen R&D, LLC, 1400 McKean Road, Spring House, PA, USA
| | | | - Jun Zhu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Sema4, Stamford, CT, 06902, USA,Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Manasi Agrawal
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judy Cho
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ryan Ungaro
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marla Dubinsky
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bruce E Sands
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mayte Suárez-Fariñas
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric E. Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Sema4, Stamford, CT, 06902, USA,Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Jean-Frederic Colombel
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrew Kasarskis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Sema4, Stamford, CT, 06902, USA,Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA,Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Sema4, Stamford, CT, 06902, USA,Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, New York, New York.
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10
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Cao Y, Dai Y, Zhang L, Wang D, Hu W, Yu Q, Wang X, Yu P, Liu W, Ping Y, Sun T, Sang Y, Liu Z, Chen Y, Tao Z. Combined Use of Fecal Biomarkers in Inflammatory Bowel Diseases: Oncostatin M and Calprotectin. J Inflamm Res 2021; 14:6409-6419. [PMID: 34880643 PMCID: PMC8647726 DOI: 10.2147/jir.s342846] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/20/2021] [Indexed: 12/12/2022] Open
Abstract
Background Fecal biomarkers have emerged as one of the most useful tools for clinical management of inflammatory bowel disease (IBD). Oncostatin M (OSM), like fecal calprotectin (FC), is highly expressed in the inflamed intestinal mucosa which may have potential usefulness. We aimed to evaluate the additional utility of these two fecal biomarkers for IBD diagnosis, activity, and prediction of infliximab response over FC alone. Methods In group 1, 236 IBD patients (145 Crohn’s disease, 91 ulcerative colitis), 50 disease controls, and 32 healthy controls were recruited for IBD diagnosis and activity. In group 2, baseline stool samples were collected from 62 patients to predict infliximab response at week 28 and 52. The performance of fecal biomarkers for IBD management was assessed by the area under the receiver operating characteristic curve (AUC). Results Fecal OSM and FC levels were increased in IBD patients and were positively correlated with clinical and endoscopic activity. Their combination showed a better ability for disease diagnosis (AUC = 0.93) and slightly improved the capability to identify mucosal healing (AUC = 0.923). Baseline OSM and FC levels were elevated in non-responders at week 28 and 52. The AUCs of OSM, FC, and their combination to predict therapeutic response were 0.763, 0.834, and 0.859 at week 28, 0.638, 0.661, and 0.704 at week 52, respectively. Combined use of fecal and blood biomarkers improved predictive accuracy with an AUC of 0.919 at week 28 and 0.887 at week 52. Conclusion In addition to FC, OSM is a novel fecal biomarker, and their combination is more beneficial for disease diagnosis and prediction of infliximab response but not for disease activity in IBD patients. Further larger-scale studies are required to confirm our findings.
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Affiliation(s)
- Ying Cao
- Department of Laboratory Medicine, Zhejiang University School of Medicine Second Affiliated Hospital, Hangzhou, People's Republic of China
| | - Yibei Dai
- Department of Laboratory Medicine, Zhejiang University School of Medicine Second Affiliated Hospital, Hangzhou, People's Republic of China
| | - Lingyu Zhang
- Department of Laboratory Medicine, Zhejiang University School of Medicine Second Affiliated Hospital, Hangzhou, People's Republic of China
| | - Danhua Wang
- Department of Laboratory Medicine, Zhejiang University School of Medicine Second Affiliated Hospital, Hangzhou, People's Republic of China
| | - Wen Hu
- National Clinical Research Center for Infectious Diseases, Zhejiang University School of Medicine First Affiliated Hospital, Hangzhou, People's Republic of China
| | - Qiao Yu
- Center for Inflammatory Bowel Diseases, Department of Gastroenterology, Zhejiang University School of Medicine Second Affiliated Hospital, Hangzhou, People's Republic of China
| | - Xuchu Wang
- Department of Laboratory Medicine, Zhejiang University School of Medicine Second Affiliated Hospital, Hangzhou, People's Republic of China
| | - Pan Yu
- Department of Laboratory Medicine, Zhejiang University School of Medicine Second Affiliated Hospital, Hangzhou, People's Republic of China
| | - Weiwei Liu
- Department of Laboratory Medicine, Zhejiang University School of Medicine Second Affiliated Hospital, Hangzhou, People's Republic of China
| | - Ying Ping
- Department of Laboratory Medicine, Zhejiang University School of Medicine Second Affiliated Hospital, Hangzhou, People's Republic of China
| | - Tao Sun
- Department of Laboratory Medicine, Zhejiang University School of Medicine Second Affiliated Hospital, Hangzhou, People's Republic of China
| | - Yiwen Sang
- Department of Laboratory Medicine, Zhejiang University School of Medicine Second Affiliated Hospital, Hangzhou, People's Republic of China
| | - Zhenping Liu
- Department of Laboratory Medicine, the First People's Hospital of Yuhang District, Hangzhou, People's Republic of China
| | - Yan Chen
- Center for Inflammatory Bowel Diseases, Department of Gastroenterology, Zhejiang University School of Medicine Second Affiliated Hospital, Hangzhou, People's Republic of China
| | - Zhihua Tao
- Department of Laboratory Medicine, Zhejiang University School of Medicine Second Affiliated Hospital, Hangzhou, People's Republic of China
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11
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Kozik A, Pavlova M, Petrov I, Bychkov V, Kim L, Dorozhko E, Cheng C, Rodriguez RD, Sheremet E. A review of surface-enhanced Raman spectroscopy in pathological processes. Anal Chim Acta 2021; 1187:338978. [PMID: 34753586 DOI: 10.1016/j.aca.2021.338978] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 12/17/2022]
Abstract
With the continuous growth of the human population and new challenges in the quality of life, it is more important than ever to diagnose diseases and pathologies with high accuracy, sensitivity and in different scenarios from medical implants to the operation room. Although conventional methods of diagnosis revolutionized healthcare, alternative analytical methods are making their way out of academic labs into clinics. In this regard, surface-enhanced Raman spectroscopy (SERS) developed immensely with its capability to achieve single-molecule sensitivity and high-specificity in the last two decades, and now it is well on its way to join the arsenal of physicians. This review discusses how SERS is becoming an essential tool for the clinical investigation of pathologies including inflammation, infections, necrosis/apoptosis, hypoxia, and tumors. We critically discuss the strategies reported so far in nanoparticle assembly, functionalization, non-metallic substrates, colloidal solutions and how these techniques improve SERS characteristics during pathology diagnoses like sensitivity, selectivity, and detection limit. Moreover, it is crucial to introduce the most recent developments and future perspectives of SERS as a biomedical analytical method. We finally discuss the challenges that remain as bottlenecks for a routine SERS implementation in the medical room from in vitro to in vivo applications. The review showcases the adaptability and versatility of SERS to resolve pathological processes by covering various experimental and analytical methods and the specific spectral features and analysis results achieved by these methods.
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Affiliation(s)
- Alexey Kozik
- Tomsk Polytechnic University, Lenin Ave, 30, Tomsk, 634050, Russia; Siberian Medical State University, Moskovskiy Trakt, 2, Tomsk, 634050, Russia
| | - Marina Pavlova
- Tomsk Polytechnic University, Lenin Ave, 30, Tomsk, 634050, Russia; Siberian Medical State University, Moskovskiy Trakt, 2, Tomsk, 634050, Russia
| | - Ilia Petrov
- Tomsk Polytechnic University, Lenin Ave, 30, Tomsk, 634050, Russia
| | - Vyacheslav Bychkov
- Tomsk National Research Medical Center of the Russian Academy of Sciences, Cancer Research Institute, 5 Kooperativny Street, Tomsk, 634009, Russia
| | - Larissa Kim
- Tomsk Polytechnic University, Lenin Ave, 30, Tomsk, 634050, Russia
| | - Elena Dorozhko
- Tomsk Polytechnic University, Lenin Ave, 30, Tomsk, 634050, Russia
| | - Chong Cheng
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Raul D Rodriguez
- Tomsk Polytechnic University, Lenin Ave, 30, Tomsk, 634050, Russia.
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12
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Lee EG, Yoon YC, Yoon J, Lee SJ, Oh YK, Kwon SW. Systematic Review of Recent Lipidomics Approaches Toward Inflammatory Bowel Disease. Biomol Ther (Seoul) 2021; 29:582-595. [PMID: 34565718 PMCID: PMC8551739 DOI: 10.4062/biomolther.2021.125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 02/06/2023] Open
Abstract
Researchers have endeavored to identify the etiology of inflammatory bowel diseases, including Crohn’s disease and ulcerative colitis. Though the pathogenesis of inflammatory bowel diseases remains unknown, dysregulation of the immune system in the host gastrointestinal tract is believed to be the major causative factor. Omics is a powerful methodological tool that can reveal biochemical information stored in clinical samples. Lipidomics is a subset of omics that explores the lipid classes associated with inflammation. One objective of the present systematic review was to facilitate the identification of biochemical targets for use in future lipidomic studies on inflammatory bowel diseases. The use of high-resolution mass spectrometry to observe alterations in global lipidomics might help elucidate the immunoregulatory mechanisms involved in inflammatory bowel diseases and discover novel biomarkers for them. Assessment of the characteristics of previous clinical trials on inflammatory bowel diseases could help researchers design and establish patient selection and analytical method criteria for future studies on these conditions. In this study, we curated literature exclusively from four databases and extracted lipidomics-related data from literature, considering criteria. This paper suggests that the lipidomics approach toward research in inflammatory bowel diseases can clarify their pathogenesis and identify clinically valuable biomarkers to predict and monitor their progression.
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Affiliation(s)
- Eun Goo Lee
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Young Cheol Yoon
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jihyun Yoon
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Seul Ji Lee
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yu-Kyoung Oh
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sung Won Kwon
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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13
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Bin Masud S, Jenkins C, Hussey E, Elkin-Frankston S, Mach P, Dhummakupt E, Aeron S. Utilizing machine learning with knockoff filtering to extract significant metabolites in Crohn's disease with a publicly available untargeted metabolomics dataset. PLoS One 2021; 16:e0255240. [PMID: 34324558 PMCID: PMC8320926 DOI: 10.1371/journal.pone.0255240] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/12/2021] [Indexed: 12/26/2022] Open
Abstract
Metabolomic data processing pipelines have been improving in recent years, allowing for greater feature extraction and identification. Lately, machine learning and robust statistical techniques to control false discoveries are being incorporated into metabolomic data analysis. In this paper, we introduce one such recently developed technique called aggregate knockoff filtering to untargeted metabolomic analysis. When applied to a publicly available dataset, aggregate knockoff filtering combined with typical p-value filtering improves the number of significantly changing metabolites by 25% when compared to conventional untargeted metabolomic data processing. By using this method, features that would normally not be extracted under standard processing would be brought to researchers’ attention for further analysis.
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Affiliation(s)
- Shoaib Bin Masud
- Department of Electrical and Computer Engineering, Tufts University, Medford, MA, United States of America
| | - Conor Jenkins
- DEVCOM Chemical Biological Center, Aberdeen Proving Ground, Aberdeen, MD, United States of America
| | - Erika Hussey
- DEVCOM Soldier Center, Natick, MA, United States of America
| | | | - Phillip Mach
- DEVCOM Chemical Biological Center, Aberdeen Proving Ground, Aberdeen, MD, United States of America
| | - Elizabeth Dhummakupt
- DEVCOM Chemical Biological Center, Aberdeen Proving Ground, Aberdeen, MD, United States of America
- * E-mail: (ED); (SA)
| | - Shuchin Aeron
- Department of Electrical and Computer Engineering, Tufts University, Medford, MA, United States of America
- * E-mail: (ED); (SA)
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14
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Caio G, Lungaro L, Caputo F, Zoli E, Giancola F, Chiarioni G, De Giorgio R, Zoli G. Nutritional Treatment in Crohn's Disease. Nutrients 2021; 13:nu13051628. [PMID: 34066229 PMCID: PMC8151495 DOI: 10.3390/nu13051628] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 12/12/2022] Open
Abstract
Crohn's disease (CD) is a chronic inflammatory bowel disease (IBD) which can affect any part of the whole gastrointestinal tract (from mouth to anus). Malnutrition affects 65-75% of CD patients, and it is now well acknowledged that diet is of paramount importance in the management of the disease. In this review, we would like to highlight the most recent findings in the field of nutrition for the treatment of CD. Our analysis will cover a wide range of topics, from the well-established diets to the new nutritional theories, along with the recent progress in emerging research fields, such as nutrigenomics.
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Affiliation(s)
- Giacomo Caio
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy; (L.L.); (F.C.); (E.Z.); (F.G.); (R.D.G.)
- Center for the Study and Treatment of Chronic Inflammatory Intestinal Diseases (IBD) and Gastroenterological Manifestations of Rare Diseases, Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Center for the Study and Treatment of Alcohol-Related Diseases, Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital-Harvard Medical School, Boston, MA 02114, USA
- Correspondence: (G.C.); (G.Z.); Tel.: +39-0532-236823 (G.C.); +39-051-6838307 (G.Z.)
| | - Lisa Lungaro
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy; (L.L.); (F.C.); (E.Z.); (F.G.); (R.D.G.)
- Department of Internal Medicine, Santissima Annunziata Hospital, Cento (Ferrara), University of Ferrara, 44042 Ferrara, Italy
| | - Fabio Caputo
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy; (L.L.); (F.C.); (E.Z.); (F.G.); (R.D.G.)
- Center for the Study and Treatment of Chronic Inflammatory Intestinal Diseases (IBD) and Gastroenterological Manifestations of Rare Diseases, Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Center for the Study and Treatment of Alcohol-Related Diseases, Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Department of Internal Medicine, Santissima Annunziata Hospital, Cento (Ferrara), University of Ferrara, 44042 Ferrara, Italy
| | - Eleonora Zoli
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy; (L.L.); (F.C.); (E.Z.); (F.G.); (R.D.G.)
- Department of Internal Medicine, Santissima Annunziata Hospital, Cento (Ferrara), University of Ferrara, 44042 Ferrara, Italy
| | - Fiorella Giancola
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy; (L.L.); (F.C.); (E.Z.); (F.G.); (R.D.G.)
| | - Giuseppe Chiarioni
- Division of Gastroenterology of the University of Verona, A.O.U.I. Verona, 37126 Verona, Italy;
- Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7080, USA
| | - Roberto De Giorgio
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy; (L.L.); (F.C.); (E.Z.); (F.G.); (R.D.G.)
- Center for the Study and Treatment of Chronic Inflammatory Intestinal Diseases (IBD) and Gastroenterological Manifestations of Rare Diseases, Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Center for the Study and Treatment of Alcohol-Related Diseases, Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Giorgio Zoli
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy; (L.L.); (F.C.); (E.Z.); (F.G.); (R.D.G.)
- Center for the Study and Treatment of Chronic Inflammatory Intestinal Diseases (IBD) and Gastroenterological Manifestations of Rare Diseases, Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Center for the Study and Treatment of Alcohol-Related Diseases, Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Department of Internal Medicine, Santissima Annunziata Hospital, Cento (Ferrara), University of Ferrara, 44042 Ferrara, Italy
- Correspondence: (G.C.); (G.Z.); Tel.: +39-0532-236823 (G.C.); +39-051-6838307 (G.Z.)
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15
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Derkacz A, Olczyk P, Jura-Półtorak A, Olczyk K, Komosinska-Vassev K. The Diagnostic Usefulness of Circulating Profile of Extracellular Matrix Components: Sulfated Glycosaminoglycans (sGAG), Hyaluronan (HA) and Extracellular Part of Syndecan-1 (sCD138) in Patients with Crohn's Disease and Ulcerative Colitis. J Clin Med 2021; 10:jcm10081722. [PMID: 33923501 PMCID: PMC8073401 DOI: 10.3390/jcm10081722] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/07/2021] [Accepted: 04/14/2021] [Indexed: 12/14/2022] Open
Abstract
The described research focused on the diagnostic usefulness of sulfated glycosaminoglycans (sGAG), hyaluronan (HA), and extracellular part of syndecan-1 (sCD138) as new markers related to extracellular matrix (ECM) remodeling in the intestine during the two most common forms of inflammatory bowel diseases (IBD), i.e., ulcerative colitis (UC) and Crohn’ disease (CD). Inflammatory markers belonging to ECM components were assessed in serum of patients with IBD using an immunoenzymatic method (HA and sCD138) and a method based on the reaction with dimethylmethylene blue (sulfated GAG). Measurements were carried out twice: at baseline and after one year of therapy with prednisone (patients with CD) or adalimumab (patients with UC). No quantitative changes were observed in serum sGAG, HA, and sCD138 concentrations between patients newly diagnosed with CD and the healthy group. In the case of patients with UC, the parameter which significantly differentiated healthy subjects and patients with IBD before biological therapy was HA. Significant correlation between serum HA level and inflammation activity, expressed as Mayo score, was also observed in patients with UC. Moreover, the obtained results have confirmed that steroid therapy with prednisone significantly influenced the circulating profile of all examined ECM components (sGAG, HA, and sCD138), whereas adalimumab therapy in patients with UC led to a significant change in only circulating sGAG levels. Moreover, the significant differences in serum HA levels between patients with UC and CD indicate that quantification of circulating HA may be useful in the differential diagnosis of CD and UC.
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Affiliation(s)
- Alicja Derkacz
- Department of Clinical Chemistry and Laboratory Diagnostics, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 41-200 Sosnowiec, Poland; (A.D.); (A.J.-P.); (K.O.)
| | - Paweł Olczyk
- Department of Community Pharmacy, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 41-200 Sosnowiec, Poland;
| | - Agnieszka Jura-Półtorak
- Department of Clinical Chemistry and Laboratory Diagnostics, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 41-200 Sosnowiec, Poland; (A.D.); (A.J.-P.); (K.O.)
| | - Krystyna Olczyk
- Department of Clinical Chemistry and Laboratory Diagnostics, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 41-200 Sosnowiec, Poland; (A.D.); (A.J.-P.); (K.O.)
| | - Katarzyna Komosinska-Vassev
- Department of Clinical Chemistry and Laboratory Diagnostics, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 41-200 Sosnowiec, Poland; (A.D.); (A.J.-P.); (K.O.)
- Correspondence: ; Tel.: +48-32-364-1150
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Comprehensive multi-omics analysis of G6PC3 deficiency-related congenital neutropenia with inflammatory bowel disease. iScience 2021; 24:102214. [PMID: 33748703 PMCID: PMC7960940 DOI: 10.1016/j.isci.2021.102214] [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: 06/02/2020] [Revised: 08/29/2020] [Accepted: 02/17/2021] [Indexed: 11/26/2022] Open
Abstract
Autosomal recessive mutations in G6PC3 cause isolated and syndromic congenital neutropenia which includes congenital heart disease and atypical inflammatory bowel disease (IBD). In a highly consanguineous pedigree with novel mutations in G6PC3 and MPL, we performed comprehensive multi-omics analyses. Structural analysis of variant G6PC3 and MPL proteins suggests a damaging effect. A distinct molecular cytokine profile (cytokinome) in the affected proband with IBD was detected. Liquid chromatography-mass spectrometry-based proteomics analysis of the G6PC3-deficient plasma samples identified 460 distinct proteins including 75 upregulated and 73 downregulated proteins. Specifically, the transcription factor GATA4 and LST1 were downregulated while platelet factor 4 (PF4) was upregulated. GATA4 and PF4 have been linked to congenital heart disease and IBD respectively, while LST1 may have perturbed a variety of essential cell functions as it is required for normal cell-cell communication. Together, these studies provide potentially novel insights into the pathogenesis of syndromic congenital G6PC3 deficiency. Multi-omics approaches identify unique signatures Whole-exome sequencing reveals distinct cytokine profiles Expression of GATA4, PF4, and LST1 is dysregulated
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17
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Abstract
Background and aim: The diagnosis of Crohn's disease (CD) is challenging. Ongoing search for biomarkers to facilitate the diagnosis is a worthwhile endeavor. The aim of this study was to explore the role of serological markers in the diagnosis of CD at an inflammatory bowel disease (IBD) referral center.Methods: This was a retrospective study including 196 suspected CD patients. The expression of ASCA-IgG, ASCA-IgA, AYMA-IgG, AYCA-IgA, FI2Y-IgG, and pANCA in the patient's serum was determined by enzyme-linked immunosorbent assay (ELISA) and indirect immunofluorescence (IF).Results: ASCA was a relatively specific marker for CD (p = 0.0005), but not AYMA-IgG, AYCA-IgA, F12Y-IgG (p = 0.5936, 0.7974, 0.1085, respectively). However, a high sensitivity of 96.77% (95% CI 90.19%-99.83%) was noted for ASCA+/FI2Y+ to identify CD patients among the suspected cases, albeit with low PPV. The more combinations of serological markers, the higher sensitivity, and NPV. No correlation was found between the age of onset or disease location and the expression of ASCA, AYMA, AYCA, FI2Y, or pANCA. There was no significant difference between the expression of ASCA and the disease behavior at diagnosis (p = 0.3307). However, a decreased proportion of AYMA+ CD patients was found in those who received surgery compared with their non-surgical counterparts (p = 0.0488).Conclusions: ASCA was found to be the most accurate serological marker for the differential diagnosis of CD. Combinations of ASCA, AYMA, AYCA, and FI2Y improved diagnostic accuracy of CD.
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Affiliation(s)
- Xin Gao
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Yan Zhang
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
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Vitorino R, Guedes S, Vitorino C, Ferreira R, Amado F, Van Eyk JE. Elucidating Citrullination by Mass Spectrometry and Its Role in Disease Pathogenesis. J Proteome Res 2021; 20:38-48. [PMID: 32966086 PMCID: PMC11009872 DOI: 10.1021/acs.jproteome.0c00474] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This review focuses on discussing key mechanisms in disease pathogenesis mediated by the protein post-translational modification citrullination. These processes are discussed in depth in the context of complex diseases such as rheumatoid arthritis, cancer, central nervous system disorders, and cardiovascular disease. Additionally, a critical evaluation of challenges in laboratory detection of citrullination sites is also outlined. In this context, the role of mass spectrometry is discussed with a focus on contemporary techniques that offer promising options to detect the exact site of protein citrullination. Novel methods described in the paper have the potential to detect and quantify the occurrence of post-translational modification sites for diagnosis and therapeutic purposes with a high degree of specificity and sensitivity. Furthermore, they offer a much faster performance than traditional techniques making them ideal for large-scale experimentation.
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Affiliation(s)
- Rui Vitorino
- QOPNA & LAQV-REQUIMTE, Departamento de Qúimica, Universidade de Aveiro, Aveiro, Portugal; iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal; Unidade de Investigação Cardiovascular, Departamento de Cirurgia e Fisiologia, Faculdade de Medicina, Universidade do Porto, Porto, Portugal
| | - Sofia Guedes
- QOPNA & LAQV-REQUIMTE, Departamento de Qúimica, Universidade de Aveiro, Aveiro, Portugal
| | - Carla Vitorino
- Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Rita Ferreira
- QOPNA & LAQV-REQUIMTE, Departamento de Qúimica, Universidade de Aveiro, Aveiro, Portugal
| | - Francisco Amado
- QOPNA & LAQV-REQUIMTE, Departamento de Qúimica, Universidade de Aveiro, Aveiro, Portugal
| | - Jennifer E. Van Eyk
- Advanced Clinical Biosystems Research Institute, The Smidt Heart Institute, Cedars-Sinia Medical Center, Los Angeles, California, United States
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Lin Y, Xiong W, Xiao S, Li F, Lu Z, Yan J, Fang X, Cui X, Wen Y, Liang J, Yu K. Pharmacoproteomics reveals the mechanism of Chinese dragon's blood in regulating the RSK/TSC2/mTOR/ribosome pathway in alleviation of DSS-induced acute ulcerative colitis. JOURNAL OF ETHNOPHARMACOLOGY 2020; 263:113221. [PMID: 32783984 DOI: 10.1016/j.jep.2020.113221] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 06/11/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Chinese dragon's blood (CDB), a crude drug extracted from Dracaena cochinchinensis (Lour.) S.C. Chen, has been historically applied for the treatment of various diseases, including ulcerative colitis (UC). Unfortunately, the underlying molecular mechanism remains unclear. MATERIALS AND METHODS In this paper, the effects of CDB treatment on a mouse model of acute UC and proteomic variation in colonic tissue were investigated. The acute UC model in Balb/c mice was induced by administration of 2.5% (wt/vol) dextran sulfate sodium (DSS) in drinking water for 8 days. After the mice with UC were intragastrically administered CDB and intraperitoneally injected with rapamycin (RAPA, a specific inhibitor of mTORC1), the disease activity index (DAI) and histopathological score were recorded. An isobaric tags for relative and absolute quantification (iTRAQ) based LC-MS/MS proteomic technique was adopted to identify the differentially expressed proteins (DEPs) in colonic tissue. Bioinformatics analysis was used to discover the molecular functions and pathways of the DEPs. Finally, Western blot analysis and immunohistochemistry were used to verify the protein expression. RESULTS The results showed that CDB treatment significantly ameliorated the symptoms and intestinal damage in acute UC, while RAPA treatment led to severe symptoms and intestinal damage. A total of 489 DEPs were reversed in the control check (CK) group and the CDB group. Most DEPs were enriched in the structural constituents of ribosomes and the ribosome pathway. CDB treatment significantly upregulated the expression of the mTOR, p-mTOR and p70S6K proteins and downregulated the expression of the Akt, p-Akt, and p4EBP1 proteins. However, RAPA treatment, unlike CDB, did not return the levels of mTOR, Akt, and their phosphorylated forms to nearly normal. CONCLUSIONS In conclusion, the dysfunction of the mTOR/ribosome pathway resulting in the inhibition of ribosome synthesis played an important role in the development of acute UC in mice, and CDB, but not RAPA, was an alternative drug for the treatment of acute UC by enhancing ribosome synthesis via the mTOR/ribosome pathway and further promoting protein synthesis.
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Affiliation(s)
- Yilong Lin
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, 530200, China
| | - Wanna Xiong
- Department of Pharmacy, Guangxi Medical College, Nanning, 530021, China
| | - Simeng Xiao
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, 530200, China
| | - Fang Li
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, 530200, China
| | - Zhuo Lu
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, 530200, China
| | - Jiongyi Yan
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, 530200, China
| | - Xuewan Fang
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, 530200, China
| | - Xiaojuan Cui
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, 530200, China
| | - Yilei Wen
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, 530200, China
| | - Jianqin Liang
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, 530200, China.
| | - Kai Yu
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, China.
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20
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Identification of Differential Intestinal Mucosa Transcriptomic Biomarkers for Ulcerative Colitis by Bioinformatics Analysis. DISEASE MARKERS 2020; 2020:8876565. [PMID: 33144895 PMCID: PMC7596466 DOI: 10.1155/2020/8876565] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/05/2020] [Accepted: 09/23/2020] [Indexed: 02/07/2023]
Abstract
Background Ulcerative colitis (UC) is a complicated disease caused by the interaction between genetic and environmental factors that affect mucosal homeostasis and triggers inappropriate immune response. The purpose of the study was to identify significant biomarkers with potential therapeutic targets and the underlying mechanisms. Methods The gene expression profiles of GSE48958, GSE73661, and GSE59071 are from the GEO database. Differentially expressed genes (DEGs) were screened by the GEO2R tool. Next, the Database for Annotation, Visualization and Integrated Discovery (DAVID) was applied to analyze gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. Then, protein-protein interaction (PPI) was visualized by Cytoscape with Search Tool for the Retrieval of Interacting Genes (STRING). Results There were a total of 128 common DEGs genes, including 86 upregulated genes enriched in extracellular space, regulation of inflammatory response, chemokine-mediated signaling pathway, response to lipopolysaccharide, and cell proliferation, while 42 downregulated genes enriched in the integral component of the membrane, the integral component of the plasma membrane, apical plasma membrane, symporter activity, and chloride channel activity. The KEGG pathway analysis results demonstrated that DEGs were particularly enriched in cytokine-cytokine receptor interaction, TNF signaling pathway, chemokine signaling pathway, pertussis, and rheumatoid arthritis. 18 central modules of the PPI networks were selected with Cytotype MCODE. Furthermore, 18 genes were found to significantly enrich in the extracellular space, inflammatory response, chemokine-mediated signaling pathway, TNF signaling pathway, regulation of cell proliferation, and immune response via reanalysis of DAVID. Conclusion The study identified DEGs, key target genes, functional pathways, and pathway analysis of UC, which may provide potential molecular targets and diagnostic biomarkers for UC.
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21
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Ocansey DKW, Zhang L, Wang Y, Yan Y, Qian H, Zhang X, Xu W, Mao F. Exosome-mediated effects and applications in inflammatory bowel disease. Biol Rev Camb Philos Soc 2020; 95:1287-1307. [PMID: 32410383 PMCID: PMC7540363 DOI: 10.1111/brv.12608] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 12/15/2022]
Abstract
Gut mucosal barriers, including chemical and physical barriers, spatially separate the gut microbiota from the host immune system to prevent unwanted immune responses that could lead to intestinal inflammation. In inflammatory bowel disease (IBD), there is mucosal barrier dysfunction coupled with immune dysregulation and dysbiosis. The discovery of exosomes as regulators of vital functions in both physiological and pathological processes has generated much research interest. Interestingly, exosomes not only serve as natural nanocarriers for the delivery of functional RNAs, proteins, and synthetic drugs or molecules, but also show potential for clinical applications in tissue repair and regeneration as well as disease diagnosis and prognosis. Biological or chemical modification of exosomes can broaden, change and enhance their therapeutic capability. We review the modulatory effects of exosomal proteins, RNAs and lipids on IBD components such as immune cells, the gut microbiota and the intestinal mucosal barrier. Mechanisms involved in regulating these factors towards attenuating IBD have been explored in several studies employing exosomes derived from different sources. We discuss the potential utility of exosomes as diagnostic markers and drug delivery systems, as well as the application of modified exosomes in IBD.
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Affiliation(s)
- Dickson K. W. Ocansey
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of MedicineJiangsu University301 Xuefu RoadZhenjiangJiangsu212013China
- Directorate of University Health Services, University of Cape Coast, PMBCape CoastGhana
| | - Li Zhang
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of MedicineJiangsu University301 Xuefu RoadZhenjiangJiangsu212013China
- Nanjing Lishui People's Hospital, Zhongda Hospital Lishui BranchSoutheast UniversityNanjingJiangsu211200China
| | - Yifei Wang
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of MedicineJiangsu University301 Xuefu RoadZhenjiangJiangsu212013China
| | - Yongmin Yan
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of MedicineJiangsu University301 Xuefu RoadZhenjiangJiangsu212013China
| | - Hui Qian
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of MedicineJiangsu University301 Xuefu RoadZhenjiangJiangsu212013China
| | - Xu Zhang
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of MedicineJiangsu University301 Xuefu RoadZhenjiangJiangsu212013China
| | - Wenrong Xu
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of MedicineJiangsu University301 Xuefu RoadZhenjiangJiangsu212013China
| | - Fei Mao
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of MedicineJiangsu University301 Xuefu RoadZhenjiangJiangsu212013China
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Hendrickx JO, van Gastel J, Leysen H, Martin B, Maudsley S. High-dimensionality Data Analysis of Pharmacological Systems Associated with Complex Diseases. Pharmacol Rev 2020; 72:191-217. [PMID: 31843941 DOI: 10.1124/pr.119.017921] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
It is widely accepted that molecular reductionist views of highly complex human physiologic activity, e.g., the aging process, as well as therapeutic drug efficacy are largely oversimplifications. Currently some of the most effective appreciation of biologic disease and drug response complexity is achieved using high-dimensionality (H-D) data streams from transcriptomic, proteomic, metabolomics, or epigenomic pipelines. Multiple H-D data sets are now common and freely accessible for complex diseases such as metabolic syndrome, cardiovascular disease, and neurodegenerative conditions such as Alzheimer's disease. Over the last decade our ability to interrogate these high-dimensionality data streams has been profoundly enhanced through the development and implementation of highly effective bioinformatic platforms. Employing these computational approaches to understand the complexity of age-related diseases provides a facile mechanism to then synergize this pathologic appreciation with a similar level of understanding of therapeutic-mediated signaling. For informative pathology and drug-based analytics that are able to generate meaningful therapeutic insight across diverse data streams, novel informatics processes such as latent semantic indexing and topological data analyses will likely be important. Elucidation of H-D molecular disease signatures from diverse data streams will likely generate and refine new therapeutic strategies that will be designed with a cognizance of a realistic appreciation of the complexity of human age-related disease and drug effects. We contend that informatic platforms should be synergistic with more advanced chemical/drug and phenotypic cellular/tissue-based analytical predictive models to assist in either de novo drug prioritization or effective repurposing for the intervention of aging-related diseases. SIGNIFICANCE STATEMENT: All diseases, as well as pharmacological mechanisms, are far more complex than previously thought a decade ago. With the advent of commonplace access to technologies that produce large volumes of high-dimensionality data (e.g., transcriptomics, proteomics, metabolomics), it is now imperative that effective tools to appreciate this highly nuanced data are developed. Being able to appreciate the subtleties of high-dimensionality data will allow molecular pharmacologists to develop the most effective multidimensional therapeutics with effectively engineered efficacy profiles.
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Affiliation(s)
- Jhana O Hendrickx
- Receptor Biology Laboratory, Department of Biomedical Research (J.O.H., J.v.G., H.L., S.M.) and Faculty of Pharmacy, Biomedical and Veterinary Sciences (J.O.H., J.v.G., H.L., B.M., S.M.), University of Antwerp, Antwerp, Belgium
| | - Jaana van Gastel
- Receptor Biology Laboratory, Department of Biomedical Research (J.O.H., J.v.G., H.L., S.M.) and Faculty of Pharmacy, Biomedical and Veterinary Sciences (J.O.H., J.v.G., H.L., B.M., S.M.), University of Antwerp, Antwerp, Belgium
| | - Hanne Leysen
- Receptor Biology Laboratory, Department of Biomedical Research (J.O.H., J.v.G., H.L., S.M.) and Faculty of Pharmacy, Biomedical and Veterinary Sciences (J.O.H., J.v.G., H.L., B.M., S.M.), University of Antwerp, Antwerp, Belgium
| | - Bronwen Martin
- Receptor Biology Laboratory, Department of Biomedical Research (J.O.H., J.v.G., H.L., S.M.) and Faculty of Pharmacy, Biomedical and Veterinary Sciences (J.O.H., J.v.G., H.L., B.M., S.M.), University of Antwerp, Antwerp, Belgium
| | - Stuart Maudsley
- Receptor Biology Laboratory, Department of Biomedical Research (J.O.H., J.v.G., H.L., S.M.) and Faculty of Pharmacy, Biomedical and Veterinary Sciences (J.O.H., J.v.G., H.L., B.M., S.M.), University of Antwerp, Antwerp, Belgium
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23
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Longo S, Chieppa M, Cossa LG, Spinelli CC, Greco M, Maffia M, Giudetti AM. New Insights into Inflammatory Bowel Diseases from Proteomic and Lipidomic Studies. Proteomes 2020; 8:proteomes8030018. [PMID: 32784952 PMCID: PMC7565982 DOI: 10.3390/proteomes8030018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 08/04/2020] [Accepted: 08/07/2020] [Indexed: 12/19/2022] Open
Abstract
Ulcerative colitis (UC) and Crohn's disease (CD) represent the two main forms of chronic inflammatory bowel diseases (IBD). The exact IBD etiology is not yet revealed but CD and UC are likely induced by an excessive immune response against normal constituents of the intestinal microbial flora. IBD diagnosis is based on clinical symptoms often combined with invasive and costly procedures. Thus, the need for more non-invasive markers is urgent. Several routine laboratory investigations have been explored as indicators of intestinal inflammation in IBD, including blood testing for C-reactive protein, erythrocyte sedimentation rate, and specific antibodies, in addition to stool testing for calprotectin and lactoferrin. However, none has been universally adopted, some have been well-characterized, and others hold great promise. In recent years, the technological developments within the field of mass spectrometry (MS) and bioinformatics have greatly enhanced the ability to retrieve, characterize, and analyze large amounts of data. High-throughput research allowed enhancing the understanding of the biology of IBD permitting a more accurate biomarker discovery than ever before. In this review, we summarize currently used IBD serological and stool biomarkers and how proteomics and lipidomics are contributing to the identification of IBD biomarkers.
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Affiliation(s)
- Serena Longo
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Monteroni 165, 73100 Lecce, Italy; (S.L.); (L.G.C.); (C.C.S.)
| | - Marcello Chieppa
- National Institute of Gastroenterology “S. de Bellis”, Institute of Research, Via Turi, 27, 70013 Castellana Grotte, Italy;
| | - Luca G. Cossa
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Monteroni 165, 73100 Lecce, Italy; (S.L.); (L.G.C.); (C.C.S.)
| | - Chiara C. Spinelli
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Monteroni 165, 73100 Lecce, Italy; (S.L.); (L.G.C.); (C.C.S.)
| | - Marco Greco
- Department of Mathematics and Physics “Ennio De Giorgi”, University of Salento, via Monteroni, 73100 Lecce, Italy;
| | - Michele Maffia
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Monteroni 165, 73100 Lecce, Italy; (S.L.); (L.G.C.); (C.C.S.)
- Correspondence: (M.M.); (A.M.G.)
| | - Anna M. Giudetti
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Monteroni 165, 73100 Lecce, Italy; (S.L.); (L.G.C.); (C.C.S.)
- Correspondence: (M.M.); (A.M.G.)
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24
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Spp24 is associated with endocytic signalling, lipid metabolism, and discrimination of tissue integrity for 'leaky-gut' in inflammatory bowel disease. Sci Rep 2020; 10:12932. [PMID: 32737354 PMCID: PMC7395150 DOI: 10.1038/s41598-020-69746-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 07/06/2020] [Indexed: 11/14/2022] Open
Abstract
Epithelial barrier injury allows contaminants to cross-over into the blood stream and trigger an inflammatory response, contributing to inflammatory bowel disease (IBD). Currently there is no single test that can reliably diagnose intestinal mucosal barrier function or measure impaired epithelial cell integrity associated with increasing permeability. Here, we assess the association between serum proteins and small intestinal permeability as detected by confocal laser endomicroscopy (CLE); in particular the known IBD marker—secreted phosphoprotein 24 (SPP24) and its binding partners; and use developed monoclonal antibodies to assess the role of SPP24 in mucosal healing. Sera were obtained from 28 IBD patients and non-IBD controls undergoing CLE with scores ranging from low to high permeability, as well as active ulcerative colitis from 53 patients undergoing fecal microbiota transplant therapy (FMT). Higher permeability associated with altered lipid metabolism, heightened innate immune response and junctional protein signalling in UC patients. A correlation between increasing leak and SPP24 peptide was observed. There is a strong indication of the novel role of SPP24 in gut barrier dysfunction particularly in ulcerative colitis. Its correlation to the established CLE for monitoring permeability has the potential to provide a blood based parallel to monitor and guide therapy more readily across a broad spectrum of illnesses for which ‘leak’ dominates the pathology.
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25
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Edwards JA, Tan N, Toussaint N, Ou P, Mueller C, Stanek A, Zinsou V, Roudnitsky S, Sagal M, Dresner L, Schwartzman A, Huan C. Role of regenerating islet-derived proteins in inflammatory bowel disease. World J Gastroenterol 2020; 26:2702-2714. [PMID: 32550748 PMCID: PMC7284176 DOI: 10.3748/wjg.v26.i21.2702] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/26/2020] [Accepted: 05/13/2020] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease (IBD) is an inflammatory disorder of the gastrointestinal tract that affects millions of patients worldwide. It has a complex and multifactorial etiology leading to excessive exposure of intestinal epithelium to microbial antigens, inappropriate activation of the immune system and ultimately to the damage of intestinal tissues. Although numerous efforts have been made to improve the disease management, IBD remains persistently recurring and beyond cure. This is due largely to the gaps in our understanding of the pathogenesis of IBD that hamper the development of timely diagnoses and effective treatment. However, some recent discoveries, including the beneficial effects of interleukin-22 (IL-22) on the inflamed intestine, have shed light on a self-protective mechanism in IBD. Regenerating islet-derived (REG/Reg) proteins are small secretory proteins which function as IL-22's downstream effectors. Mounting studies have demonstrated that IBD patients have significantly increased REG expressions in the injured intestine, but with undefined mechanisms and roles. The reported functions of REG/Reg proteins in intestinal homeostasis, such as those of antibacterial, anti-inflammatory and tissue repair, lead us to discuss their potential mechanisms and clinical relevance in IBD in order to advance IBD research and management.
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Affiliation(s)
- Jodi-Ann Edwards
- Department of Surgery, State University of New York, Downstate Health Sciences University, Brooklyn, NY 11203, United States
| | - Nicholas Tan
- College of Medicine, State University of New York, Downstate Health Sciences University, Brooklyn, NY 11203, United States
| | - Nadlie Toussaint
- College of Medicine, State University of New York, Downstate Health Sciences University, Brooklyn, NY 11203, United States
| | - Peiqi Ou
- MCB program, School of Graduate Studies, State University of New York, Downstate Health Sciences University, Brooklyn, NY 11203, United States
| | - Cathy Mueller
- Department of Surgery, State University of New York, Downstate Health Sciences University, Brooklyn, NY 11203, United States
| | - Albert Stanek
- Department of Surgery, State University of New York, Downstate Health Sciences University, Brooklyn, NY 11203, United States
| | - Vladimir Zinsou
- College of Medicine, State University of New York, Downstate Health Sciences University, Brooklyn, NY 11203, United States
| | - Sean Roudnitsky
- Department of Surgery, State University of New York, Downstate Health Sciences University, Brooklyn, NY 11203, United States
| | - Michelle Sagal
- Department of Surgery, State University of New York, Downstate Health Sciences University, Brooklyn, NY 11203, United States
| | - Lisa Dresner
- Department of Surgery, State University of New York, Downstate Health Sciences University, Brooklyn, NY 11203, United States
| | - Alexander Schwartzman
- Department of Surgery, State University of New York, Downstate Health Sciences University, Brooklyn, NY 11203, United States
| | - Chongmin Huan
- Department of Surgery and Cell Biology, State University of New York, Downstate Health Sciences University, Brooklyn, NY 11203, United States
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Diagnostic utility of the neutrophil-platelet ratio as a novel marker of activity in patients with Ulcerative Colitis. PLoS One 2020; 15:e0231988. [PMID: 32315368 PMCID: PMC7173773 DOI: 10.1371/journal.pone.0231988] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/03/2020] [Indexed: 12/12/2022] Open
Abstract
Background Ulcerative colitis (UC) is a chronic disease characterized by periods of activity and remission. The platelet, one of the main activators of neutrophils, contains Interleukin 8 (IL-8), a potent neutrophil chemo-attractant and P-selectin that induces excretion of superoxide in the neutrophils, forming platelet-neutrophil aggregates that are increased in individuals with active UC, hence an index of both cells could produce a monitoring tool. No previous studies have evaluated this ratio in UC. Goal To evaluate the clinical utility of the Neutrophil-Platelet (NeuPla) ratio in patients with UC. Study A total of 158 patients with a diagnosis of UC. This index was based on the ratio between platelets and the neutrophil differential in blood count. The activity was classified using Mayo endoscopic sub-score, histological (Riley score) and for clinical was used the Truelove-Witts, Montreal, Mayo and Yamamoto-Furusho scores. Results The correlation of the NeuPla ratio with activity scales were significant (P <0.05). An optimal cut-off point to classify patients with clinical activity was 14.94 with a sensitivity 87.95% and specificity 63.5 and endoscopy activity with a cut-off 14.64 with a sensibility of 70.5% and specificity of 61.8%. Conclusions The NeuPla ratio showed an adequate diagnostic utility to identify UC patients with clinical and endoscopy activity without the use of invasive studies like a colonoscopy or expensive fecal biomarkers such as calprotectin and have a better diagnostic performance in comparison to other serum biomarkers (C reactive protein, erythrocyte sedimentation rate and albumin).
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Kaur A, Goggolidou P. Ulcerative colitis: understanding its cellular pathology could provide insights into novel therapies. JOURNAL OF INFLAMMATION-LONDON 2020; 17:15. [PMID: 32336953 PMCID: PMC7175540 DOI: 10.1186/s12950-020-00246-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 04/07/2020] [Indexed: 12/16/2022]
Abstract
Dynamic interactions between the gastrointestinal epithelium and the mucosal immune system normally contribute to ensuring intestinal homeostasis and optimal immunosurveillance, but destabilisation of these interactions in genetically predisposed individuals can lead to the development of chronic inflammatory diseases. Ulcerative colitis is one of the main types of inflammatory diseases that affect the bowel, but its pathogenesis has yet to be completely defined. Several genetic factors and other inflammation-related genes are implicated in mediating the inflammation and development of the disease. Some susceptibility loci associated with increased risk of ulcerative colitis are found to be implicated in mucosal barrier function. Different biomarkers that cause damage to the colonic mucosa can be detected in patients, including perinuclear ANCA, which is also useful in distinguishing ulcerative colitis from other colitides. The choice of treatment for ulcerative colitis depends on disease severity. Therapeutic strategies include anti-tumour necrosis factor alpha (TNF-α) monoclonal antibodies used to block the production of TNF-α that mediates intestinal tract inflammation, an anti-adhesion drug that prevents lymphocyte infiltration from the blood into the inflamed gut, inhibitors of JAK1 and JAK3 that suppress the innate immune cell signalling and interferons α/β which stimulate the production of anti-inflammatory cytokines, as well as faecal microbiota transplantation. Although further research is still required to fully dissect the pathophysiology of ulcerative colitis, understanding its cellular pathology and molecular mechanisms has already proven beneficial and it has got the potential to identify further novel, effective targets for therapy and reduce the burden of this chronic disease.
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Affiliation(s)
- Amandip Kaur
- Department of Biomedical Science and Physiology, Faculty of Science and Engineering, University of Wolverhampton, Wulfruna Street, Wolverhampton, WV1 1LY UK
| | - Paraskevi Goggolidou
- Department of Biomedical Science and Physiology, Faculty of Science and Engineering, University of Wolverhampton, Wulfruna Street, Wolverhampton, WV1 1LY UK
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Integrated omics profiling of dextran sodium sulfate-induced colitic mice supplemented with Wolfberry ( Lycium barbarum). NPJ Sci Food 2020; 4:5. [PMID: 32258419 PMCID: PMC7109062 DOI: 10.1038/s41538-020-0065-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 02/14/2020] [Indexed: 12/11/2022] Open
Abstract
We used a multi-omics profiling approach to investigate the suppressive effects of 2% Wolfberry (WOL)-enriched diets on dextran sodium sulfate (DSS)-induced colitis in mice. It was observed that in mice fed the WOL diet, the disease activity index, colon shortening, plasma concentrations of matrix metalloproteinase-3 and relative mesenteric fat weight were significantly improved as compared to the DSS group. Results from colon transcriptome and proteome profiles showed that WOL supplementation significantly ameliorated the expression of genes and proteins associated with the integrity of the colonic mucosal wall and colonic inflammation. Based on the hepatic transcriptome, proteome and metabolome data, genes involved in fatty acid metabolism, proteins involved in inflammation and metabolites related to glycolysis were downregulated in WOL mice, leading to lowered inflammation and changes in these molecules may have led to improvement in body weight loss. The integrated nutrigenomic approach thus revealed the molecular mechanisms underlying the ameliorative effect of whole WOL fruit consumption on inflammatory bowel disease.
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Pisani LF, Moriggi M, Gelfi C, Vecchi M, Pastorelli L. Proteomic insights on the metabolism in inflammatory bowel disease. World J Gastroenterol 2020; 26:696-705. [PMID: 32116417 PMCID: PMC7039832 DOI: 10.3748/wjg.v26.i7.696] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/02/2020] [Accepted: 02/09/2020] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic and relapsing inflammatory conditions of the gut that include Crohn's disease and ulcerative colitis. The pathogenesis of IBD is not completely unraveled, IBD are multi-factorial diseases with reported alterations in the gut microbiota, activation of different immune cell types, changes in the vascular endothelium, and alterations in the tight junctions’ structure of the colonic epithelial cells. Proteomics represents a useful tool to enhance our biological understanding and to discover biomarkers in blood and intestinal specimens. It is expected to provide reproducible and quantitative data that can support clinical assessments and help clinicians in the diagnosis and treatment of IBD. Sometimes a differential diagnosis of Crohn's disease and ulcerative colitis and the prediction of treatment response can be deducted by finding meaningful biomarkers. Although some non-invasive biomarkers have been described, none can be considered as the “gold standard” for IBD diagnosis, disease activity and therapy outcome. For these reason new studies have proposed an “IBD signature”, which consists in a panel of biomarkers used to assess IBD. The above described approach characterizes “omics” and in this review we will focus on proteomics.
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Affiliation(s)
- Laura Francesca Pisani
- Gastroenterology and Digestive Endoscopy Unit, IRCCS Policlinico San Donato, San Donato Milanese 20097, Italy
| | - Manuela Moriggi
- Gastroenterology and Digestive Endoscopy Unit, IRCCS Policlinico San Donato, San Donato Milanese 20097, Italy
| | - Cecilia Gelfi
- Department of Biomedical Science for Health, University of the Study of Milan, IRCCS Istituto Ortopedico Galeazzi, Milan 20122, Italy
| | - Maurizio Vecchi
- Gastroenterology and Endoscopy Unit, IRCCS Ca' Granda Foundation, Policlinico Hospital, University of the Study of Milan, Milan 20122, Italy
| | - Luca Pastorelli
- Gastroenterology and Digestive Endoscopy Unit, IRCCS Policlinico San Donato, San Donato Milanese 20097, Italy
- Department of Biomedical Science for Health, University of the Study of Milan, Milan 20122, Italy
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Takahashi N, Kitazawa C, Itani Y, Awaga Y, Hama A, Hayashi I, Takamatsu H. Exploratory clinical characterization of experimentally-induced ulcerative colitis nonhuman primates. Heliyon 2020; 6:e03178. [PMID: 31938753 PMCID: PMC6953712 DOI: 10.1016/j.heliyon.2020.e03178] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/27/2019] [Accepted: 01/06/2020] [Indexed: 12/03/2022] Open
Abstract
A limitation of currently used preclinical models of colitis is that disease and treatment assessment methods differ from clinically used methods. Thus, a modified Mayo score and an endoscopic index (EI) were developed for use in cynomolgus macaques with 0.25% dextran sulfate sodium (DSS)-induced ulcerative colitis. Macaques were treated with water with DSS for two weeks followed by water without DSS for two weeks. Disease activity was classified according to a modified Mayo score: stool consistency, rectal bleeding, colonoscopy examination and global assessment. Findings on colonoscopy were further graded according the Rachmilewitz EI. To demonstrate the sensitivity of the modified Mayo score and EI to therapeutic intervention, macaques were treated with the anti-inflammatory steroid prednisolone followed eight weeks later by the integrin antibody vedolizumab. Before DSS treatment, normal stool consistency and no rectal bleeding were observed. Colonoscopy demonstrated no mucosal abnormalities. Following the first DSS treatment, Mayo score and EI indicated signs of mild colitis. Following subsequent DSS treatments, mild to moderate colitis emerged with each DSS treatment and reduced signs of colitis were observed 2 weeks after DSS treatment termination. Prednisolone treatment during DSS treatment suppressed the emergence of colitis. Vedolizumab reduced signs of colitis during DSS treatment and further reduced signs of colitis that persisted after termination of DSS treatment. The current study demonstrated the potential of utilizing clinical outcome measures to assess experimentally-induced colitis in the macaque. Furthermore, signs of colitis, as assessed with the current methods, were reduced following therapeutic treatment. The current findings suggest that clinically relevant outcome measures in the macaque model of ulcerative colitis could be used to test novel treatments.
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Affiliation(s)
- Nobuyuki Takahashi
- Hamamatsu Pharma Research, Inc., Pharmacology, Hamamatsu, 431-2103 Japan
| | - Chinatsu Kitazawa
- Hamamatsu Pharma Research, Inc., Pharmacology, Hamamatsu, 431-2103 Japan
| | - Yoshitaka Itani
- Hamamatsu Pharma Research, Inc., Pharmacology, Hamamatsu, 431-2103 Japan
| | - Yuji Awaga
- Hamamatsu Pharma Research, Inc., Pharmacology, Hamamatsu, 431-2103 Japan
| | - Aldric Hama
- Hamamatsu Pharma Research, Inc., Pharmacology, Hamamatsu, 431-2103 Japan
- Corresponding author.
| | - Ikuo Hayashi
- Hamamatsu Pharma Research USA, Inc., San Diego, CA 92122, USA
| | - Hiroyuki Takamatsu
- Hamamatsu Pharma Research, Inc., Pharmacology, Hamamatsu, 431-2103 Japan
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Rice MW, Pandya JD, Shear DA. Gut Microbiota as a Therapeutic Target to Ameliorate the Biochemical, Neuroanatomical, and Behavioral Effects of Traumatic Brain Injuries. Front Neurol 2019; 10:875. [PMID: 31474930 PMCID: PMC6706789 DOI: 10.3389/fneur.2019.00875] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 07/29/2019] [Indexed: 12/21/2022] Open
Abstract
Current efficacious treatments for traumatic brain injury (TBI) are lacking. Establishment of a protective gut microbiota population offers a compelling therapeutic avenue, as brain injury induces disruptions in the composition of the gut microbiota, i.e., gut dysbiosis, which has been shown to contribute to TBI-related neuropathology and impaired behavioral outcomes. The gut microbiome is involved in the modulation of a multitude of cellular and molecular processes fundamental to the progression of TBI-induced pathologies including neuroinflammation, blood brain barrier permeability, immune system response, microglial activation, and mitochondrial dysfunction, as well as intestinal motility and permeability. Additionally, gut dysbiosis further aggravates behavioral impairments in animal models of TBI and spinal cord injury, as well as negatively affects health outcomes in murine stroke models. Recent studies indicate that microbiota transplants and probiotics ameliorate neuroanatomical damage and functional impairments in animal models of stroke and spinal cord injury. In addition, probiotics have been shown to reduce the rate of infection and time spent in intensive care of hospitalized patients suffering from brain trauma. Perturbations in the composition of the gut microbiota and its metabolite profile may also serve as potential diagnostic and theragnostic biomarkers for injury severity and progression. This review aims to address the etiological role of the gut microbiome in the biochemical, neuroanatomical, and behavioral/cognitive consequences of TBI, as well as explore the potential of gut microbiome manipulation in the form of probiotics as an effective therapeutic to ameliorate TBI-induced pathology and symptoms.
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Affiliation(s)
- Matthew W Rice
- Brain Trauma Neuroprotection Branch, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Jignesh D Pandya
- Brain Trauma Neuroprotection Branch, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Deborah A Shear
- Brain Trauma Neuroprotection Branch, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD, United States
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Lu S, Zhu ZG, Lu WC. Inferring novel genes related to colorectal cancer via random walk with restart algorithm. Gene Ther 2019; 26:373-385. [PMID: 31308477 DOI: 10.1038/s41434-019-0090-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 05/20/2019] [Accepted: 06/11/2019] [Indexed: 12/12/2022]
Abstract
Colorectal cancer (CRC) is the third most common type of cancer. In recent decades, genomic analysis has played an increasingly important role in understanding the molecular mechanisms of CRC. However, its pathogenesis has not been fully uncovered. Identification of genes related to CRC as complete as possible is an important way to investigate its pathogenesis. Therefore, we proposed a new computational method for the identification of novel CRC-associated genes. The proposed method is based on existing proven CRC-associated genes, human protein-protein interaction networks, and random walk with restart algorithm. The utility of the method is indicated by comparing it to the methods based on Guilt-by-association or shortest path algorithm. Using the proposed method, we successfully identified 298 novel CRC-associated genes. Previous studies have validated the involvement of the majority of these 298 novel genes in CRC-associated biological processes, thus suggesting the efficacy and accuracy of our method.
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Affiliation(s)
- Sheng Lu
- Department of General Surgery, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute of Digestive Surgery, Shanghai, 200025, China
| | - Zheng-Gang Zhu
- Department of General Surgery, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute of Digestive Surgery, Shanghai, 200025, China
| | - Wen-Cong Lu
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai, 200444, China.
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Kirov S, Sasson A, Zhang C, Chasalow S, Dongre A, Steen H, Stensballe A, Andersen V, Birkelund S, Bennike TB. Degradation of the extracellular matrix is part of the pathology of ulcerative colitis. Mol Omics 2019; 15:67-76. [PMID: 30702115 DOI: 10.1039/c8mo00239h] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The scientific value of re-analyzing existing datasets is often proportional to the complexity of the data. Proteomics data are inherently complex and can be analyzed at many levels, including proteins, peptides, and post-translational modifications to verify and/or develop new hypotheses. In this paper, we present our re-analysis of a previously published study comparing colon biopsy samples from ulcerative colitis (UC) patients to non-affected controls. We used a different statistical approach, employing a linear mixed-effects regression model and analyzed the data both on the protein and peptide level. In addition to confirming and reinforcing the original finding of upregulation of neutrophil extracellular traps (NETs), we report novel findings, including that Extracellular Matrix (ECM) degradation and neutrophil maturation are involved in the pathology of UC. The pharmaceutically most relevant differential protein expressions were confirmed using immunohistochemistry as an orthogonal method. As part of this study, we also compared proteomics data to previously published mRNA expression data. These comparisons indicated compensatory regulation at transcription levels of the ECM proteins we identified and open possible new avenues for drug discovery.
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Affiliation(s)
- Stefan Kirov
- Translational Bioinformatics, Bristol Myers Squib, Pennington, NJ, USA.
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He Y, Mohamedali A, Huang C, Baker MS, Nice EC. Oncoproteomics: Current status and future opportunities. Clin Chim Acta 2019; 495:611-624. [PMID: 31176645 DOI: 10.1016/j.cca.2019.06.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/05/2019] [Accepted: 06/05/2019] [Indexed: 02/07/2023]
Abstract
Oncoproteomics is the systematic study of cancer samples using omics technologies to detect changes implicated in tumorigenesis. Recent progress in oncoproteomics is already opening new avenues for the identification of novel biomarkers for early clinical stage cancer detection, targeted molecular therapies, disease monitoring, and drug development. Such information will lead to new understandings of cancer biology and impact dramatically on the future care of cancer patients. In this review, we will summarize the advantages and limitations of the key technologies used in (onco)proteogenomics, (the Omics Pipeline), explain how they can assist us in understanding the biology behind the overarching "Hallmarks of Cancer", discuss how they can advance the development of precision/personalised medicine and the future directions in the field.
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Affiliation(s)
- Yujia He
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, PR China
| | - Abidali Mohamedali
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, New South Wales 2109, Australia
| | - Canhua Huang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, PR China
| | - Mark S Baker
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, New South Wales 2109, Australia.
| | - Edouard C Nice
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, PR China; Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, New South Wales 2109, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia.
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Qin W, Li L, Wang T, Huang H, Gao Y. Urine Proteome Changes in a TNBS‐Induced Colitis Rat Model. Proteomics Clin Appl 2019; 13:e1800100. [DOI: 10.1002/prca.201800100] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 05/06/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Weiwei Qin
- Department of Biochemistry and Molecular BiologyGene Engineering Drug and Biotechnology Beijing Key LaboratoryBeijing Normal University Beijing 100875 China
- Department of AnesthesiologyQingdao Municipal Hospital Qingdao 266073 China
| | - Lujun Li
- Department of Biochemistry and Molecular BiologyGene Engineering Drug and Biotechnology Beijing Key LaboratoryBeijing Normal University Beijing 100875 China
| | - Ting Wang
- Department of Biochemistry and Molecular BiologyGene Engineering Drug and Biotechnology Beijing Key LaboratoryBeijing Normal University Beijing 100875 China
| | - He Huang
- Department of Biochemistry and Molecular BiologyGene Engineering Drug and Biotechnology Beijing Key LaboratoryBeijing Normal University Beijing 100875 China
| | - Youhe Gao
- Department of Biochemistry and Molecular BiologyGene Engineering Drug and Biotechnology Beijing Key LaboratoryBeijing Normal University Beijing 100875 China
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Furtado M, Van Lieshout RJ, Van Ameringen M, Green SM, Frey BN. Biological and psychosocial predictors of anxiety worsening in the postpartum period: A longitudinal study. J Affect Disord 2019; 250:218-225. [PMID: 30870771 DOI: 10.1016/j.jad.2019.02.064] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/21/2019] [Accepted: 02/25/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND As many as 20% of women will experience an anxiety disorder during the perinatal period. Women with pre-existing anxiety disorders are at increased risk of worsening during this time, yet little is known about its predictors. STUDY AIM To investigate the psychosocial and biological risk factors for anxiety worsening in the postpartum in women with pre-existing anxiety disorders. METHODS Thirty-five (n = 35) pregnant women with pre-existing DSM-5 anxiety disorders were enrolled in this prospective study investigating the psychosocial (e.g., childhood trauma, intolerance of uncertainty, depression) and biological risk factors (e.g. C-reactive protein, interleukin-6, tumor necrosis factor-α) for anxiety worsening in the postpartum period. Anxiety worsening was defined as an increase of ≥50% or greater on Hamilton Anxiety Rating Scale scores from the third trimester of pregnancy (32.94 ± 3.35 weeks) to six weeks postpartum. RESULTS Intolerance of uncertainty, depressive symptom severity, and obsessive-compulsive disorder symptoms present in pregnancy were significant predictors of anxiety worsening in the postpartum. LIMITATIONS Sample heterogeneity and limited sample size may affect study generalizability. CONCLUSIONS To our knowledge, this is the first longitudinal study to investigate psychosocial and biological risk factors for anxiety worsening in the postpartum in women with pre-existing anxiety disorders. Continued research investigating these risk factors is needed to elucidate whether they differ from women experiencing new-onset anxiety disorders in the perinatal period, and those in non-puerperal groups. Identifying these risk factors can guide the development of screening measures for early and accurate symptom detection. This can lead to the implementation of appropriate interventions aimed at decreasing the risk of perinatal anxiety worsening.
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Affiliation(s)
- Melissa Furtado
- Neuroscience Graduate Program, McMaster University, Ontario, Canada; Women's Health Concerns Clinic, St. Joseph's Healthcare Hamilton, Ontario, Canada
| | - Ryan J Van Lieshout
- Neuroscience Graduate Program, McMaster University, Ontario, Canada; Women's Health Concerns Clinic, St. Joseph's Healthcare Hamilton, Ontario, Canada; Department of Psychiatry and Behavioural Neurosciences, McMaster University, Ontario, Canada
| | - Michael Van Ameringen
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Ontario, Canada
| | - Sheryl M Green
- Women's Health Concerns Clinic, St. Joseph's Healthcare Hamilton, Ontario, Canada; Department of Psychiatry and Behavioural Neurosciences, McMaster University, Ontario, Canada
| | - Benicio N Frey
- Neuroscience Graduate Program, McMaster University, Ontario, Canada; Women's Health Concerns Clinic, St. Joseph's Healthcare Hamilton, Ontario, Canada; Department of Psychiatry and Behavioural Neurosciences, McMaster University, Ontario, Canada; Mood Disorders Program, St. Joseph's Healthcare Hamilton, Ontario, Canada.
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Pavlidis S, Monast C, Loza MJ, Branigan P, Chung KF, Adcock IM, Guo Y, Rowe A, Baribaud F. I_MDS: an inflammatory bowel disease molecular activity score to classify patients with differing disease-driving pathways and therapeutic response to anti-TNF treatment. PLoS Comput Biol 2019; 15:e1006951. [PMID: 31039157 PMCID: PMC6510457 DOI: 10.1371/journal.pcbi.1006951] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 05/10/2019] [Accepted: 03/13/2019] [Indexed: 02/06/2023] Open
Abstract
Crohn’s disease and ulcerative colitis are driven by both common and distinct underlying mechanisms of pathobiology. Both diseases, exhibit heterogeneity underscored by the variable clinical responses to therapeutic interventions. We aimed to identify disease-driving pathways and classify individuals into subpopulations that differ in their pathobiology and response to treatment. We applied hierarchical clustering of enrichment scores derived from gene set variation analysis of signatures representative of various immunological processes and activated cell types, to a colonic biopsy dataset that included healthy volunteers, Crohn’s disease and ulcerative colitis patients. Patient stratification at baseline or after anti-TNF treatment in clinical responders and non-responders was queried. Signatures with significantly different enrichment scores were identified using a general linear model. Comparisons to healthy controls were made at baseline in all participants and then separately in responders and non-responders. Fifty-nine percent of the signatures were commonly enriched in both conditions at baseline, supporting the notion of a disease continuum within ulcerative colitis and Crohn’s disease. Signatures included T cells, macrophages, neutrophil activation and poly:IC signatures, representing acute inflammation and a complex mix of potential disease-driving biology. Collectively, identification of significantly enriched signatures allowed establishment of an inflammatory bowel disease molecular activity score which uses biopsy transcriptomics as a surrogate marker to accurately track disease severity. This score separated diseased from healthy samples, enabled discrimination of clinical responders and non-responders at baseline with 100% specificity and 78.8% sensitivity, and was validated in an independent data set that showed comparable classification. Comparing responders and non-responders separately at baseline to controls, 43% and 70% of signatures were enriched, respectively, suggesting greater molecular dysregulation in TNF non-responders at baseline. This methodological approach could facilitate better targeted design of clinical studies to test therapeutics, concentrating on patient subsets sharing similar underlying pathobiology, therefore increasing the likelihood of clinical response. Patients exhibiting similar phenotypical characteristics, diagnosed with the same disease, exhibit variable response to therapeutics. This is a major health care issue, due to the increased patient suffering and the socioeconomical burden that occurs. Crohn’s disease and ulcerative colitis constitute good examples of inflammatory conditions, with sufferers responding differentially to existent therapeutics. Here, we identified disease-driving pathways and classified individuals into subpopulations that differ in their pathobiology and response to treatment. We utilized gene set variation analysis and transcriptomic data from inflammatory bowel disease sufferers to stratify patients at baseline or after anti-TNF treatment in clinical responders and non-responders. We explored gene signatures obtained from the literature, relevant to immune processes, which were significantly enriched in disease compared to healthy controls, as well as before and after treatment. Using these signatures, we established an inflammatory bowel disease molecular activity score, which allowed us to separate clinical responders and non-responders at baseline with high specificity and sensitivity. We validated the proposed approach in an independent data set, demonstrating comparable classification. This methodological approach may lead to better targeted design of clinical studies, allowing the selection of patient sharing similar underlying pathobiology, thus increasing the likelihood of clinical response to treatment.
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Affiliation(s)
- Stelios Pavlidis
- Janssen Research & Development Ltd, High Wycombe, United Kingdom
- National Heart and Lung Institute, Imperial College & Biomedical Research Unit, Royal Brompton & Harefield NHS Trust, London, United Kingdom
- Data Science Institute, Imperial College London, London, United Kingdom
| | - Calixte Monast
- Janssen Research & Development LLC, United States of America
| | - Matthew J. Loza
- Janssen Research & Development LLC, United States of America
| | | | - Kiang F. Chung
- National Heart and Lung Institute, Imperial College & Biomedical Research Unit, Royal Brompton & Harefield NHS Trust, London, United Kingdom
| | - Ian M. Adcock
- National Heart and Lung Institute, Imperial College & Biomedical Research Unit, Royal Brompton & Harefield NHS Trust, London, United Kingdom
| | - Yike Guo
- Data Science Institute, Imperial College London, London, United Kingdom
| | - Anthony Rowe
- Janssen Research & Development LLC, United States of America
| | - Frédéric Baribaud
- Janssen Research & Development LLC, United States of America
- * E-mail:
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38
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Gisbert JP, Chaparro M. Clinical Usefulness of Proteomics in Inflammatory Bowel Disease: A Comprehensive Review. J Crohns Colitis 2019; 13:374-384. [PMID: 30307487 DOI: 10.1093/ecco-jcc/jjy158] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The protein domain is probably the most ubiquitously affected in disease, response and recovery, and therefore proteomics holds special promise for biomarker discovery in general, and particularly in inflammatory bowel disease [IBD], i.e. ulcerative colitis and Crohn's disease. Tremendous progress has been made over the past decade in the development and refinement of proteomics technologies. These advances provide opportunities for a long-anticipated personalized medicine approach to the treatment of IBD. The present review examines the current state of IBD proteomics research and its usefulness in clinical practice. We performed a systematic bibliographic search to identify studies investigating the use of proteomics in patients with IBD, and we then summarized the current 'state of the art' in the applications of proteomic technologies in the study of IBD. In particular, in the present review we provide: [1] a brief introduction to proteomics in health and disease; [2] a review of the different stages from biomarker discovery to clinical application; and [3] a comprehensive review of the clinical usefulness and application of proteomics in IBD, including: [a] screening to differentiate IBD from healthy controls; [b] differentiating Crohn's disease from ulcerative colitis; [c] prediction of the behaviour or the IBD course; [d] prediction of IBD response to biological treatment; and [e] monitoring response to treatment. We also review the importance of the type of sample-blood vs intestinal tissue-for the study of proteomics in IBD patients. Finally, we emphasize the current limitations of proteomic studies in IBD.
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Affiliation(s)
- Javier P Gisbert
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
| | - María Chaparro
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
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iTRAQ-based pharmacoproteomics reveals potential targets of berberine, a promising therapy for ulcerative colitis. Eur J Pharmacol 2019; 850:167-179. [PMID: 30771347 DOI: 10.1016/j.ejphar.2019.02.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/13/2019] [Accepted: 02/13/2019] [Indexed: 12/18/2022]
Abstract
Previous studies by us and others have indicated that berberine is a promising therapy for ulcerative colitis (UC). However, the mechanisms of UC and the therapeutic targets of berberine are poorly understood. iTRAQ-based proteomics was utilized to characterize the proteins and pathways associated with the development of colitis and its improvement after berberine treatment. By using a modified dextran sodium sulfate (DSS) colitis as the UC model, confirmed that berberine significantly attenuated clinical symptoms and colon shorting of the colitis mice. Proteomics identified 140 and 391 proteins that were differentially expressed in the colons of DSS- or DSS plus berberine-treated mice, respectively. Subsequent verification of 15 selected differentially expressed proteins (DEPs) by multiple reaction monitoring confirmed the reliability of the iTRAQ data. Further comparisons and bioinformatics analysis demonstrated that among the identified DEPs, 26, including Hist2h2be, Tubb3, and five immunoglobulins, were oppositely regulated by DSS and DSS plus berberine treatments. In addition, five commonly dysregulated pathways, including natural killer cell-mediated cytotoxicity and RRAR signaling were identified. Network analysis revealed that proteins involved in 7 and 11 pathways in DSS and DSS plus berberine treated mice, respectively, engaged in protein-protein interactions. Our study provides the first pharmacoproteomics profiling of colitis and its recovery after berberine treatment. The proteins, pathways and networks identified provide novel insights into the pathogenesis of colitis and the action mechanism of berberine, demonstrating their values for validation in human UC which could serve as targets for the development of novel therapies for UC.
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40
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Proteomic analysis of lipopolysaccharide activated human monocytes. Mol Immunol 2018; 103:257-269. [PMID: 30326359 DOI: 10.1016/j.molimm.2018.09.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 08/20/2018] [Accepted: 09/25/2018] [Indexed: 12/21/2022]
Abstract
Monocytes are key mediators of innate immunity and comprise an important cellular defence against invading pathogens. However, exaggerated or dysregulated monocyte activation can lead to severe immune-mediated pathology such as sepsis or chronic inflammatory diseases. Thus, detailed insight into the molecular mechanisms of monocyte activation is essential to understand monocyte-driven inflammatory pathologies. We therefore investigated the global protein changes in human monocytes during lipopolysaccharide (LPS) activation to mimic bacterial activation. Purified human monocytes were stimulated with LPS for 17 h and analyzed by state-of-the-art liquid chromatography tandem mass spectrometry (LC-MS/MS). The label-free quantitative proteome analysis identified 2746 quantifiable proteins of which 101 had a statistically significantly different abundance between LPS-stimulated cells and unstimulated controls. Additionally, 143 proteins were exclusively identified in either LPS stimulated cells or unstimulated controls. Functional annotation clustering demonstrated that LPS, most significantly, regulates proteasomal- and lysosomal proteins but in opposite directions. Thus, seven proteasome subunits were upregulated by LPS while 11 lysosomal proteins were downregulated. Both systems are critically involved in processing of proteins for antigen-presentation and together with LPS-induced regulation of CD74 and tapasin, our data suggest that LPS can skew monocytic antigen-presentation towards MHC class I rather than MHC class II. In summary, this study provides a sensitive high throughput protein analysis of LPS-induced monocyte activation and identifies several LPS-regulated proteins not previously described in the literature which can be used as a source for future studies.
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Titz B, Gadaleta RM, Lo Sasso G, Elamin A, Ekroos K, Ivanov NV, Peitsch MC, Hoeng J. Proteomics and Lipidomics in Inflammatory Bowel Disease Research: From Mechanistic Insights to Biomarker Identification. Int J Mol Sci 2018; 19:ijms19092775. [PMID: 30223557 PMCID: PMC6163330 DOI: 10.3390/ijms19092775] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 09/11/2018] [Accepted: 09/12/2018] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease (IBD) represents a group of progressive disorders characterized by recurrent chronic inflammation of the gut. Ulcerative colitis and Crohn's disease are the major manifestations of IBD. While our understanding of IBD has progressed in recent years, its etiology is far from being fully understood, resulting in suboptimal treatment options. Complementing other biological endpoints, bioanalytical "omics" methods that quantify many biomolecules simultaneously have great potential in the dissection of the complex pathogenesis of IBD. In this review, we focus on the rapidly evolving proteomics and lipidomics technologies and their broad applicability to IBD studies; these range from investigations of immune-regulatory mechanisms and biomarker discovery to studies dissecting host⁻microbiome interactions and the role of intestinal epithelial cells. Future studies can leverage recent advances, including improved analytical methodologies, additional relevant sample types, and integrative multi-omics analyses. Proteomics and lipidomics could effectively accelerate the development of novel targeted treatments and the discovery of complementary biomarkers, enabling continuous monitoring of the treatment response of individual patients; this may allow further refinement of treatment and, ultimately, facilitate a personalized medicine approach to IBD.
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Affiliation(s)
- Bjoern Titz
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Raffaella M Gadaleta
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Giuseppe Lo Sasso
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Ashraf Elamin
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Kim Ekroos
- Lipidomics Consulting Ltd., Irisviksvägen 31D, 02230 Esbo, Finland.
| | - Nikolai V Ivanov
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Manuel C Peitsch
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
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Clerc F, Novokmet M, Dotz V, Reiding KR, de Haan N, Kammeijer GSM, Dalebout H, Bladergroen MR, Vukovic F, Rapp E, Targan SR, Barron G, Manetti N, Latiano A, McGovern DPB, Annese V, Lauc G, Wuhrer M. Plasma N-Glycan Signatures Are Associated With Features of Inflammatory Bowel Diseases. Gastroenterology 2018; 155:829-843. [PMID: 29792883 DOI: 10.1053/j.gastro.2018.05.030] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 04/07/2018] [Accepted: 05/15/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND & AIMS Biomarkers are needed for early detection of Crohn's disease (CD) and ulcerative colitis (UC) or to predict patient outcomes. Glycosylation is a common and complex posttranslational modification of proteins that affects their structure and activity. We compared plasma N-glycosylation profiles between patients with CD or UC and healthy individuals (controls). METHODS We analyzed the total plasma N-glycomes of 2635 patients with inflammatory bowel diseases and 996 controls by mass spectrometry with a linkage-specific sialic acid derivatization technique. Plasma samples were acquired from 2 hospitals in Italy (discovery cohort, 1989 patients with inflammatory bowel disease [IBD] and 570 controls) and 1 medical center in the United States (validation cohort, 646 cases of IBD and 426 controls). Sixty-three glycoforms met our criteria for relative quantification and were extracted from the raw data with the software MassyTools. Common features shared by the glycan compositions were combined in 78 derived traits, including the number of antennae of complex-type glycans and levels of fucosylation, bisection, galactosylation, and sialylation. Associations of plasma N-glycomes with age, sex, CD, UC, and IBD-related parameters such as disease location, surgery and medication, level of C-reactive protein, and sedimentation rate were tested by linear and logistic regression. RESULTS Plasma samples from patients with IBD had a higher abundance of large-size glycans compared with controls, a decreased relative abundance of hybrid and high-mannose structures, lower fucosylation, lower galactosylation, and higher sialylation (α2,3- and α2,6-linked). We could discriminate plasma from patients with CD from that of patients with UC based on higher bisection, lower galactosylation, and higher sialylation (α2,3-linked). Glycosylation patterns were associated with disease location and progression, the need for a more potent medication, and surgery. These results were replicated in a large independent cohort. CONCLUSIONS We performed high-throughput analysis to compare total plasma N-glycomes of individuals with vs without IBD and to identify patterns associated with disease features and the need for treatment. These profiles might be used in diagnosis and for predicting patients' responses to treatment.
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Affiliation(s)
- Florent Clerc
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | | | - Viktoria Dotz
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Karli R Reiding
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Noortje de Haan
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Guinevere S M Kammeijer
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Hans Dalebout
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Marco R Bladergroen
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Frano Vukovic
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany; glyXera GmbH, Magdeburg, Germany
| | | | - Stephan R Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Gildardo Barron
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Natalia Manetti
- Unit of Gastroenterology SOD2 (Strutture Organizzative Dipartimentali), Azienda Ospedaliero Universitaria (AOU) Careggi, Florence, Italy
| | - Anna Latiano
- Unit of Gastroenterology, IRCCS-CSS (Istituto di Ricovero e Cura a Carattere Scientifico-Casa Sollievo della Sofferenza) Hospital, San Giovanni Rotondo, Italy
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Vito Annese
- Unit of Gastroenterology SOD2 (Strutture Organizzative Dipartimentali), Azienda Ospedaliero Universitaria (AOU) Careggi, Florence, Italy; Unit of Gastroenterology, IRCCS-CSS (Istituto di Ricovero e Cura a Carattere Scientifico-Casa Sollievo della Sofferenza) Hospital, San Giovanni Rotondo, Italy
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Leiden, The Netherlands.
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Diagnostic Markers for Nonspecific Inflammatory Bowel Diseases. DISEASE MARKERS 2018; 2018:7451946. [PMID: 29991970 PMCID: PMC6016179 DOI: 10.1155/2018/7451946] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 04/18/2018] [Accepted: 05/16/2018] [Indexed: 12/13/2022]
Abstract
The nonspecific inflammatory bowel diseases (IBD) represent a heterogeneous group of chronic inflammatory disorders of the gastrointestinal tract, and Leśniowski-Crohn's disease (CD) and ulcerative colitis (UC) are among the two major clinical forms. Despite the great progress in understanding the pathogenesis of these diseases, their etiology remains unclear. Genetic, immune, and environmental factors are thought to play a key role. The correct diagnosis of nonspecific inflammatory bowel diseases as well as the determination of disease activity, risk stratification, and prediction of response to therapy still relies on a multidisciplinary approach based on clinical, laboratory, endoscopic, and histologic examination. However, considerable effort has been devoted to the development of an accurate panel of noninvasive biomarkers that have increased diagnostic sensitivity and specificity. Laboratory biomarkers useful in differentiating IBD with functional disorders and in evaluating disease activity, prognosis, and treatment selection for IBD are presented in this study.
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Bennike TB, Bellin MD, Xuan Y, Stensballe A, Møller FT, Beilman GJ, Levy O, Cruz-Monserrate Z, Andersen V, Steen J, Conwell DL, Steen H. A Cost-Effective High-Throughput Plasma and Serum Proteomics Workflow Enables Mapping of the Molecular Impact of Total Pancreatectomy with Islet Autotransplantation. J Proteome Res 2018; 17:1983-1992. [PMID: 29641209 DOI: 10.1021/acs.jproteome.8b00111] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Blood is an ideal body fluid for the discovery or monitoring of diagnostic and prognostic protein biomarkers. However, discovering robust biomarkers requires the analysis of large numbers of samples to appropriately represent interindividual variability. To address this analytical challenge, we established a high-throughput and cost-effective proteomics workflow for accurate and comprehensive proteomics at an analytical depth applicable for clinical studies. For validation, we processed 1 μL each from 62 plasma samples in 96-well plates and analyzed the product by quantitative data-independent acquisition liquid chromatography/mass spectrometry; the data were queried using feature quantification with Spectronaut. To show the applicability of our workflow to serum, we analyzed a unique set of samples from 48 chronic pancreatitis patients, pre and post total pancreatectomy with islet autotransplantation (TPIAT) surgery. We identified 16 serum proteins with statistically significant abundance alterations, which represent a molecular signature distinct from that of chronic pancreatitis. In summary, we established a cost-efficient high-throughput workflow for comprehensive proteomics using PVDF-membrane-based digestion that is robust, automatable, and applicable to small plasma and serum volumes, e.g., finger stick. Application of this plasma/serum proteomics workflow resulted in the first mapping of the molecular implications of TPIAT on the serum proteome.
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Affiliation(s)
- Tue Bjerg Bennike
- Department of Pathology , Harvard Medical School , Boston , Massachusetts , United States.,Department of Pathology , Boston Children's Hospital , Boston , Massachusetts , United States.,Precision Vaccines Program , Boston Children's Hospital , Boston , Massachusetts , United States.,Department of Health Science and Technology , Aalborg University , Aalborg , Denmark
| | - Melena D Bellin
- Department of Surgery , University of Minnesota Medical Center , Minneapolis , Minnesota , United States.,Department of Pediatrics , University of Minnesota Medical Center , Minneapolis , Minnesota , United States
| | - Yue Xuan
- Thermo Fisher Scientific , Bremen , Germany
| | - Allan Stensballe
- Department of Health Science and Technology , Aalborg University , Aalborg , Denmark
| | | | - Gregory J Beilman
- Department of Surgery , University of Minnesota Medical Center , Minneapolis , Minnesota , United States
| | - Ofer Levy
- Precision Vaccines Program , Boston Children's Hospital , Boston , Massachusetts , United States.,Division of Infectious Diseases, Department of Medicine , Boston Children's Hospital , Boston , Massachusetts , United States
| | - Zobeida Cruz-Monserrate
- Division of Gastroenterology, Hepatology and Nutrition , The Ohio State University Wexner Medical Center , Columbus , Ohio United States
| | - Vibeke Andersen
- Focused Research Unit for Molecular Diagnostic and Clinical Research (MOK), IRS-Center Sonderjylland , Hospital of Southern Jutland , Aabenraa , Denmark.,Institute of Molecular Medicine , University of Southern Denmark , Odense , Denmark
| | - Judith Steen
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology , Harvard Medical School , Boston , Massachusetts , United States
| | - Darwin L Conwell
- Division of Gastroenterology, Hepatology and Nutrition , The Ohio State University Wexner Medical Center , Columbus , Ohio United States
| | - Hanno Steen
- Department of Pathology , Harvard Medical School , Boston , Massachusetts , United States.,Department of Pathology , Boston Children's Hospital , Boston , Massachusetts , United States.,Precision Vaccines Program , Boston Children's Hospital , Boston , Massachusetts , United States
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Šimurina M, de Haan N, Vučković F, Kennedy NA, Štambuk J, Falck D, Trbojević-Akmačić I, Clerc F, Razdorov G, Khon A, Latiano A, D'Incà R, Danese S, Targan S, Landers C, Dubinsky M, McGovern DPB, Annese V, Wuhrer M, Lauc G. Glycosylation of Immunoglobulin G Associates With Clinical Features of Inflammatory Bowel Diseases. Gastroenterology 2018; 154:1320-1333.e10. [PMID: 29309774 PMCID: PMC5880750 DOI: 10.1053/j.gastro.2018.01.002] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 12/15/2017] [Accepted: 01/02/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS Causes of inflammatory bowel diseases are not well understood and the most prominent forms, Crohn's disease (CD) and ulcerative colitis (UC), are sometimes hard to distinguish. Glycosylation of IgG has been associated with CD and UC. IgG Fc-glycosylation affects IgG effector functions. We evaluated changes in IgG Fc-glycosylation associated with UC and CD, as well as with disease characteristics in different patient groups. METHODS We analyzed 3441 plasma samples obtained from 2 independent cohorts of patients with CD (874 patients from Italy and 391 from the United States) or UC (1056 from Italy and 253 from the US and healthy individuals [controls]; 427 in Italy and 440 from the United States). IgG Fc-glycosylation (tryptic glycopeptides) was analyzed by liquid chromatography coupled to mass spectrometry. We analyzed associations between disease status (UC vs controls, CD vs controls, and UC vs CD) and glycopeptide traits, and associations between clinical characteristics and glycopeptide traits, using a logistic regression model with age and sex included as covariates. RESULTS Patients with CD or UC had lower levels of IgG galactosylation than controls. For example, the odds ratio (OR) for IgG1 galactosylation in patients with CD was 0.59 (95% confidence interval [CI], 0.51-0.69) and for patients with UC was 0.81 (95% CI, 0.71-0.92). Fucosylation of IgG was increased in patients with CD vs controls (for IgG1: OR, 1.27; 95% CI, 1.12-1.44), but decreased in patients with UC vs controls (for IgG23: OR, 0.72; 95% CI, 0.63-0.82). Decreased galactosylation associated with more severe CD or UC, including the need for surgery in patients with UC vs controls (for IgG1: OR, 0.69; 95% CI, 0.54-0.89) and in patients with CD vs controls (for IgG23: OR, 0.78; 95% CI, 0.66-0.91). CONCLUSIONS In a retrospective analysis of plasma samples from patients with CD or UC, we associated levels of IgG Fc-glycosylation with disease (compared to controls) and its clinical features. These findings could increase our understanding of mechanisms of CD and UC pathogenesis and be used to develop diagnostics or guide treatment.
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Affiliation(s)
- Mirna Šimurina
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Noortje de Haan
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Frano Vučković
- Genos Glycoscience Research Laboratory, BIOCentar, Zagreb, Croatia
| | | | - Jerko Štambuk
- Genos Glycoscience Research Laboratory, BIOCentar, Zagreb, Croatia
| | - David Falck
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Florent Clerc
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Genadij Razdorov
- Genos Glycoscience Research Laboratory, BIOCentar, Zagreb, Croatia
| | - Anna Khon
- Division of Gastroenterology, S. Camillo-Forlanini Hospital, Circonvallazione Gianicolense, Rome, Italy
| | - Anna Latiano
- Division of Gastroenterology, Casa Sollievo della Sofferenza Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, San Giovanni Rotondo, Italy
| | - Renata D'Incà
- Division of Gastroenterology, University Hospital, Padua, Italy
| | - Silvio Danese
- Humanitas University, Inflammatory Bowel Disease Center, Department of Gastroenterology, Humanitas Clinical and Research Hospital, Milan, Italy
| | - Stephan Targan
- F. Widjaja Foundation, Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Carol Landers
- F. Widjaja Foundation, Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Marla Dubinsky
- F. Widjaja Foundation, Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Dermot P B McGovern
- F. Widjaja Foundation, Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Vito Annese
- Division of Gastroenterology, University Hospital Azienda Ospedaliero-Universitaria Careggi, Florence, Italy; Valiant Clinic, Dubai, United Arab Emirates
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Gordan Lauc
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia; Genos Glycoscience Research Laboratory, BIOCentar, Zagreb, Croatia.
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Schniers A, Anderssen E, Fenton CG, Goll R, Pasing Y, Paulssen RH, Florholmen J, Hansen T. The Proteome of Ulcerative Colitis in Colon Biopsies from Adults - Optimized Sample Preparation and Comparison with Healthy Controls. Proteomics Clin Appl 2017; 11. [PMID: 28856821 DOI: 10.1002/prca.201700053] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 08/03/2017] [Indexed: 12/17/2022]
Abstract
PURPOSE The purpose of the study was to optimize the sample preparation and to further use an improved sample preparation to identify proteome differences between inflamed ulcerative colitis tissue from untreated adults and healthy controls. EXPERIMENTAL DESIGN To optimize the sample preparation, we studied the effect of adding different detergents to a urea containing lysis buffer for a Lys-C/trypsin tandem digestion. With the optimized method, we prepared clinical samples from six ulcerative colitis patients and six healthy controls and analysed them by LC-MS/MS. We examined the acquired data to identify differences between the states. RESULTS We improved the protein extraction and protein identification number by utilizing a urea and sodium deoxycholate containing buffer. Comparing ulcerative colitis and healthy tissue, we found 168 of 2366 identified proteins differently abundant. Inflammatory proteins are higher abundant in ulcerative colitis, proteins related to anion-transport and mucus production are lower abundant. A high proportion of S100 proteins is differently abundant, notably with both up-regulated and down-regulated proteins. CONCLUSION AND CLINICAL RELEVANCE The optimized sample preparation method will improve future proteomic studies on colon mucosa. The observed protein abundance changes and their enrichment in various groups improve our understanding of ulcerative colitis on protein level.
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Affiliation(s)
- Armin Schniers
- Natural Products and Medicinal Chemistry Research Group, Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Endre Anderssen
- Department of Clinical Medicine, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Christopher Graham Fenton
- Department of Clinical Medicine, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Rasmus Goll
- Department of Medical Gastroenterology, University Hospital of North Norway, Tromsø, Norway
| | - Yvonne Pasing
- Department of Clinical Medicine, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway.,Division of Internal Medicine, University Hospital of North Norway, Tromsø, Norway
| | - Ruth Hracky Paulssen
- Department of Clinical Medicine, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Jon Florholmen
- Department of Medical Gastroenterology, University Hospital of North Norway, Tromsø, Norway
| | - Terkel Hansen
- Natural Products and Medicinal Chemistry Research Group, Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
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Bennike TB, Carlsen TG, Ellingsen T, Bonderup OK, Glerup H, Bøgsted M, Christiansen G, Birkelund S, Andersen V, Stensballe A. Proteomics dataset: The colon mucosa from inflammatory bowel disease patients, gastrointestinal asymptomic rheumatoid arthritis patients, and controls. Data Brief 2017; 15:511-516. [PMID: 29085871 PMCID: PMC5650644 DOI: 10.1016/j.dib.2017.09.059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/07/2017] [Accepted: 09/26/2017] [Indexed: 12/23/2022] Open
Abstract
The datasets presented in this article are related to the research articles entitled “Neutrophil Extracellular Traps in Ulcerative Colitis: A Proteome Analysis of Intestinal Biopsies” (Bennike et al., 2015 [1]), and “Proteome Analysis of Rheumatoid Arthritis Gut Mucosa” (Bennike et al., 2017 [2]). The colon mucosa represents the main interacting surface of the gut microbiota and the immune system. Studies have found an altered composition of the gut microbiota in rheumatoid arthritis patients (Zhang et al., 2015; Vaahtovuo et al., 2008; Hazenberg et al., 1992) [5], [6], [7] and inflammatory bowel disease patients (Morgan et al., 2012; Abraham and Medzhitov, 2011; Bennike, 2014) [8], [9], [10]. Therefore, we characterized the proteome of colon mucosa biopsies from 10 inflammatory bowel disease ulcerative colitis (UC) patients, 11 gastrointestinal healthy rheumatoid arthritis (RA) patients, and 10 controls. We conducted the sample preparation and liquid chromatography mass spectrometry (LC-MS/MS) analysis of all samples in one batch, enabling label-free comparison between all biopsies. The datasets are made publicly available to enable critical or extended analyses. The proteomics data and search results, have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD001608 for ulcerative colitis and control samples, and PXD003082 for rheumatoid arthritis samples.
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Affiliation(s)
- Tue Bjerg Bennike
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | | | - Torkell Ellingsen
- Department of Rheumatology, Odense University Hospital, Odense, Denmark
| | - Ole Kristian Bonderup
- Diagnostic Center, Section of Gastroenterology, Regional Hospital Silkeborg, Silkeborg, Denmark.,University Research Clinic for Innovative Patient Pathways, Aarhus University, Aarhus, Denmark
| | - Henning Glerup
- Diagnostic Center, Section of Gastroenterology, Regional Hospital Silkeborg, Silkeborg, Denmark
| | - Martin Bøgsted
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | | | - Svend Birkelund
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Vibeke Andersen
- Institute of Regional Health Research-Center Soenderjylland, University of Southern Denmark, Odense, Denmark.,Department of Internal Medicine, Regional Hospital Viborg, Viborg, Denmark
| | - Allan Stensballe
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
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48
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Palmieri O, Mazza T, Castellana S, Panza A, Latiano T, Corritore G, Andriulli A, Latiano A. Inflammatory Bowel Disease Meets Systems Biology: A Multi-Omics Challenge and Frontier. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2017; 20:692-698. [PMID: 27930092 DOI: 10.1089/omi.2016.0147] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The inflammatory bowel disease (IBD) is a systemic disease that is characterized by the inflammation of the gastrointestinal tract. It includes ulcerative colitis and the Crohn's disease. Presently, IBD is one of the most investigated common complex human disorders, although its causes remain unclear. Multi-omics mechanisms involving genomic, transcriptomic, proteomic, and epigenomic variations, not to forget the miRNome, together with environmental contributions, result in an impairment of the immune system in persons with IBD. Such interactions at multiple levels of biology and in concert with the environment constitute the actual engine of this complex disease, demanding a multifactorial and multi-omics perspective to better understand the root causes of IBD. This expert analysis reviews and examines the latest literature and underscores, from the perspective of systems biology, the value of multi-omics technologies as opportunities to unravel the "IBD integrome." We anticipate that multi-omics research will accelerate the new discoveries and insights on IBD in the near future. It shall also pave the way for early diagnosis and help clinicians and families with IBD to forecast and make informed decisions about the prognosis and, possibly, personalized therapeutics in the future.
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Affiliation(s)
- Orazio Palmieri
- 1 Division of Gastroenterology, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Tommaso Mazza
- 2 Laboratory of Bioinformatics, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Stefano Castellana
- 2 Laboratory of Bioinformatics, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Anna Panza
- 1 Division of Gastroenterology, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Tiziana Latiano
- 1 Division of Gastroenterology, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Giuseppe Corritore
- 1 Division of Gastroenterology, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Angelo Andriulli
- 1 Division of Gastroenterology, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Anna Latiano
- 1 Division of Gastroenterology, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
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49
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Recent Advances in the Etiopathogenesis of Inflammatory Bowel Disease: The Role of Omics. Mol Diagn Ther 2017; 22:11-23. [DOI: 10.1007/s40291-017-0298-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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50
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Mourad FH, Yau Y, Wasinger VC, Leong RW. Proteomics in Inflammatory Bowel Disease: Approach Using Animal Models. Dig Dis Sci 2017; 62:2266-2276. [PMID: 28717845 DOI: 10.1007/s10620-017-4673-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 07/04/2017] [Indexed: 12/14/2022]
Abstract
Recently, proteomics studies have provided important information on the role of proteins in health and disease. In the domain of inflammatory bowel disease, proteomics has shed important light on the pathogenesis and pathophysiology of inflammation and has contributed to the discovery of some putative clinical biomarkers of disease activity. By being able to obtain a large number of specimens from multiple sites and control for confounding environmental, genetic, and metabolic factors, proteomics studies using animal models of colitis offered an alternative approach to human studies. Our aim is to review the information and lessons acquired so far from the use of proteomics in animal models of colitis. These studies helped understand the importance of different proteins at different stages of the disease and unraveled the different pathways that are activated or inhibited during the inflammatory process. Expressed proteins related to inflammation, cellular structure, endoplasmic reticulum stress, and energy depletion advanced the knowledge about the reaction of intestinal cells to inflammation and repair. The role of mesenteric lymphocytes, exosomes, and the intestinal mucosal barrier was emphasized in the inflammatory process. In addition, studies in animal models revealed mechanisms of the beneficial effects of some therapeutic interventions and foods or food components on intestinal inflammation by monitoring changes in protein expression and paved the way for some new possible inflammatory pathways to target in the future. Advances in proteomics technology will further clarify the interaction between intestinal microbiota and IBD pathogenesis and investigate the gene-environmental axis of IBD etiology.
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Affiliation(s)
- Fadi H Mourad
- Department of Internal Medicine, Faculty of Medicine, American University of Beirut, P.O. Box 113-6044, Hamra, Beirut, 110 32090, Lebanon. .,Gastroenterology and Liver Services, Concord Repatriation General Hospital, Hospital Road, Concord, NSW, 2137, Australia.
| | - Yunki Yau
- Gastroenterology and Liver Services, Concord Repatriation General Hospital, Hospital Road, Concord, NSW, 2137, Australia
| | - Valerie C Wasinger
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, The University of NSW Australia, Kensington, NSW, 2052, Australia
| | - Rupert W Leong
- Gastroenterology and Liver Services, Concord Repatriation General Hospital, Hospital Road, Concord, NSW, 2137, Australia
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