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Syed S, Boland BS, Bourke LT, Chen LA, Churchill L, Dobes A, Greene A, Heller C, Jayson C, Kostiuk B, Moss A, Najdawi F, Plung L, Rioux JD, Rosen MJ, Torres J, Zulqarnain F, Satsangi J. Challenges in IBD Research 2024: Precision Medicine. Inflamm Bowel Dis 2024; 30:S39-S54. [PMID: 38778628 DOI: 10.1093/ibd/izae084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Indexed: 05/25/2024]
Abstract
Precision medicine is part of 5 focus areas of the Challenges in IBD Research 2024 research document, which also includes preclinical human IBD mechanisms, environmental triggers, novel technologies, and pragmatic clinical research. Building on Challenges in IBD Research 2019, the current Challenges aims to provide a comprehensive overview of current gaps in inflammatory bowel diseases (IBDs) research and deliver actionable approaches to address them with a focus on how these gaps can lead to advancements in interception, remission, and restoration for these diseases. The document is the result of multidisciplinary input from scientists, clinicians, patients, and funders, and represents a valuable resource for patient-centric research prioritization. In particular, the precision medicine section is focused on the main research gaps in elucidating how to bring the best care to the individual patient in IBD. Research gaps were identified in biomarker discovery and validation for predicting disease progression and choosing the most appropriate treatment for each patient. Other gaps were identified in making the best use of existing patient biosamples and clinical data, developing new technologies to analyze large datasets, and overcoming regulatory and payer hurdles to enable clinical use of biomarkers. To address these gaps, the Workgroup suggests focusing on thoroughly validating existing candidate biomarkers, using best-in-class data generation and analysis tools, and establishing cross-disciplinary teams to tackle regulatory hurdles as early as possible. Altogether, the precision medicine group recognizes the importance of bringing basic scientific biomarker discovery and translating it into the clinic to help improve the lives of IBD patients.
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Affiliation(s)
- Sana Syed
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
- Patient representative for Crohn's & Colitis Foundation, New York, NY, USA
| | - Brigid S Boland
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lauren T Bourke
- Precision Medicine Drug Development, Early Respiratory and Immunology, AstraZeneca, Boston, MA, USA
| | - Lea Ann Chen
- Division of Gastroenterology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Laurie Churchill
- Leona M. and Harry B. Helmsley Charitable Trust, New York, NY, USA
| | | | - Adam Greene
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | | | | | | | - Alan Moss
- Crohn's & Colitis Foundation, New York, NY, USA
| | | | - Lori Plung
- Patient representative for Crohn's & Colitis Foundation, New York, NY, USA
| | - John D Rioux
- Research Center, Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | - Michael J Rosen
- Division of Pediatric Gastroenterology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Joana Torres
- Division of Gastroenterology, Hospital Beatriz Ângelo, Hospital da Luz, Lisbon, Portugal
- Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Fatima Zulqarnain
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | - Jack Satsangi
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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Winter DA, de Bruyne P, van der Woude J, Rizopoulos D, de Ridder L, Samsom J, Escher JC. Biomarkers predicting the effect of anti-TNF treatment in paediatric and adult inflammatory bowel disease. J Pediatr Gastroenterol Nutr 2024. [PMID: 38698646 DOI: 10.1002/jpn3.12221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 02/08/2024] [Accepted: 02/15/2024] [Indexed: 05/05/2024]
Abstract
OBJECTIVES Paediatric and adult inflammatory bowel disease (pIBD, aIBD) patients may lose response to anti-TNF treatment within the first year. Adult-extrapolated weight-based dosing is incorrect in children, due to age-related pharmacokinetic differences. We investigated biomarkers for initial and maintenance of response to infliximab (IFX) or adalimumab (ADA), comparing pIBD and aIBD patients. METHODS In this prospective, observational study, pIBD (n = 24) and aIBD (n = 21) patients were included when initiating anti-TNF. Escalation from standard dosing and continued anti-TNF at 12 and 18 months were assessed. Biomarkers included clinical laboratory parameters, faecal calprotectin (FCP) and IFX trough levels (TLs). Plasma proteomics was performed in pIBD. RESULTS During our study, treatment escalation (in clinical loss of response) occurred more common in pIBD versus aIBD (p = 0.02). We established that IFX therapy escalation in pIBD patients was not due to low infliximab levels. We identified 9 pro-inflammatory proteins that were elevated in patients losing response. CONCLUSION Anti-TNF exposure-response relationship may be different in pIBD versus aIBD. No biomarkers for maintained response were identified, but 9 inflammatory proteins were of interest as potential predictors for loss of response in pIBD.
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Affiliation(s)
- Dwight A Winter
- Department of Paediatric Gastroenterology, Erasmus MC-Sophia Children's Hospital, Rotterdam, Netherlands
| | - Pauline de Bruyne
- Department of Pediatrics, Ghent University Hospital, Ghent University, Ghent, Belgium
| | | | | | - Lissy de Ridder
- Department of Paediatric Gastroenterology, Erasmus MC-Sophia Children's Hospital, Rotterdam, Netherlands
| | - Janneke Samsom
- Laboratory of Paediatrics, Erasmus MC-Sophia Children's Hospital, Rotterdam, Netherlands
| | - Johanna C Escher
- Department of Paediatric Gastroenterology, Erasmus MC-Sophia Children's Hospital, Rotterdam, Netherlands
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Kouwenberg CV, Kuiper JJW, de Boer JH, Kalinina Ayuso V. Serum Biomarkers of Vascular Involvement in Childhood Uveitis. Transl Vis Sci Technol 2024; 13:9. [PMID: 38573655 PMCID: PMC11005069 DOI: 10.1167/tvst.13.4.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 02/27/2024] [Indexed: 04/05/2024] Open
Abstract
Purpose Nonanterior uveitis frequently involves the retinal vasculature; however, no molecular markers associated with the retinal vascular disease are currently known. In this study, we aimed to identify serum biomarker signatures associated with retinal vascular involvement in noninfectious pediatric uveitis. Methods We performed a 384-plex targeted proteomic analysis of serum samples of 154 noninfectious pediatric uveitis patients diagnosed with nonanterior uveitis (n = 74), idiopathic chronic anterior uveitis (iCAU, n = 36), or juvenile idiopathic arthritis-associated uveitis (JIA-U, n = 44), as well as 22 noninflammatory pediatric controls. Data on retinal vascular involvement (i.e., papillitis, cystoid macular edema, retinal vasculitis, or retinal capillary leakage on optical coherence tomography and/or fluorescein angiography) were used to stratify cases in the nonanterior uveitis group. Results In the analysis of nonanterior uveitis, we identified nine proteins significantly associated with retinal vascular involvement, including F13B, MYOM3, and PTPN9. These proteins were enriched through pathway enrichment analysis for the coagulation cascade. Comparing cases and controls, we identified 63 differentially expressed proteins, notably proteins involved in platelet biology and complement cascades, which could be primarily attributed to differences in serum proteomes between anterior uveitis and nonanterior uveitis groups. Conclusions Serum proteins related to the coagulation and complement cascade are associated with retinal vascular involvement in pediatric uveitis patients. Our results indicate involvement of mediators that could interact with the microcirculation in pediatric uveitis and might serve as potential biomarkers in personalized medicine in the future. Translational Relevance Our targeted proteomics analysis in serum of pediatric uveitis patients indicates involvement of mediators that could interact with the microcirculation in pediatric uveitis and might serve as potential biomarkers in personalized medicine in the future.
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Affiliation(s)
- Carlyn V. Kouwenberg
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jonas J. W. Kuiper
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht, The Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Joke H. de Boer
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Viera Kalinina Ayuso
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht, The Netherlands
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Tang J, Mou M, Zheng X, Yan J, Pan Z, Zhang J, Li B, Yang Q, Wang Y, Zhang Y, Gao J, Li S, Yang H, Zhu F. Strategy for Identifying a Robust Metabolomic Signature Reveals the Altered Lipid Metabolism in Pituitary Adenoma. Anal Chem 2024; 96:4745-4755. [PMID: 38417094 DOI: 10.1021/acs.analchem.3c03796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
Despite the well-established connection between systematic metabolic abnormalities and the pathophysiology of pituitary adenoma (PA), current metabolomic studies have reported an extremely limited number of metabolites associated with PA. Moreover, there was very little consistency in the identified metabolite signatures, resulting in a lack of robust metabolic biomarkers for the diagnosis and treatment of PA. Herein, we performed a global untargeted plasma metabolomic profiling on PA and identified a highly robust metabolomic signature based on a strategy. Specifically, this strategy is unique in (1) integrating repeated random sampling and a consensus evaluation-based feature selection algorithm and (2) evaluating the consistency of metabolomic signatures among different sample groups. This strategy demonstrated superior robustness and stronger discriminative ability compared with that of other feature selection methods including Student's t-test, partial least-squares-discriminant analysis, support vector machine recursive feature elimination, and random forest recursive feature elimination. More importantly, a highly robust metabolomic signature comprising 45 PA-specific differential metabolites was identified. Moreover, metabolite set enrichment analysis of these potential metabolic biomarkers revealed altered lipid metabolism in PA. In conclusion, our findings contribute to a better understanding of the metabolic changes in PA and may have implications for the development of diagnostic and therapeutic approaches targeting lipid metabolism in PA. We believe that the proposed strategy serves as a valuable tool for screening robust, discriminating metabolic features in the field of metabolomics.
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Affiliation(s)
- Jing Tang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- Department of Bioinformatics, Chongqing Medical University, Chongqing 400016, China
| | - Minjie Mou
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xin Zheng
- Multidisciplinary Center for Pituitary Adenoma of Chongqing, Department of Neuosurgery, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Jin Yan
- Multidisciplinary Center for Pituitary Adenoma of Chongqing, Department of Neuosurgery, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Ziqi Pan
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Jinsong Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Bo Li
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Qingxia Yang
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Yunxia Wang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Ying Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Jianqing Gao
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Song Li
- Multidisciplinary Center for Pituitary Adenoma of Chongqing, Department of Neuosurgery, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Hui Yang
- Multidisciplinary Center for Pituitary Adenoma of Chongqing, Department of Neuosurgery, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
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Kumar M, Murugesan S, Ibrahim N, Elawad M, Al Khodor S. Predictive biomarkers for anti-TNF alpha therapy in IBD patients. J Transl Med 2024; 22:284. [PMID: 38493113 PMCID: PMC10943853 DOI: 10.1186/s12967-024-05058-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/04/2024] [Indexed: 03/18/2024] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic gastrointestinal condition characterized by severe gut inflammation, commonly presenting as Crohn's disease, ulcerative colitis or categorized as IBD- unclassified. While various treatments have demonstrated efficacy in adult IBD patients, the advent of anti-TNF therapies has significantly revolutionized treatment outcomes and clinical management. These therapies have played a pivotal role in achieving clinical and endoscopic remission, promoting mucosal healing, averting disease progression, and diminishing the necessity for surgery. Nevertheless, not all patients exhibit positive responses to these therapies, and some may experience a loss of responsiveness over time. This review aims to present a comprehensive examination of predictive biomarkers for monitoring the therapeutic response to anti-TNF therapy in IBD patients. It will explore their limitations and clinical utilities, paving the way for a more personalized and effective therapeutic approach.
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Affiliation(s)
- Manoj Kumar
- Research Department, Sidra Medicine, Doha, Qatar
| | | | - Nazira Ibrahim
- Division of Gastroenterology, Hepatology and Nutrition, Sidra Medicine, Doha, Qatar
| | - Mamoun Elawad
- Division of Gastroenterology, Hepatology and Nutrition, Sidra Medicine, Doha, Qatar
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Arosa L, Camba-Gómez M, Lorenzo-Martín LF, Clavaín L, López M, Conde-Aranda J. RNA Expression of MMP12 Is Strongly Associated with Inflammatory Bowel Disease and Is Regulated by Metabolic Pathways in RAW 264.7 Macrophages. Int J Mol Sci 2024; 25:3167. [PMID: 38542140 PMCID: PMC10970096 DOI: 10.3390/ijms25063167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 04/04/2024] Open
Abstract
Macrophage metalloelastase or matrix metalloproteinase-12 (MMP12) is a macrophage-specific proteolytic enzyme involved in the physiopathology of many inflammatory diseases, including inflammatory bowel disease. Although previously published data suggested that the modulation of MMP12 in macrophages could be a determinant for the development of intestinal inflammation, scarce information is available on the mechanisms underlying the regulation of MMP12 expression in those phagocytes. Therefore, in this study, we aimed to delineate the association of MMP12 with inflammatory bowel disease and the molecular events leading to the transcriptional control of this metalloproteinase. For that, we used publicly available transcriptional data. Also, we worked with the RAW 264.7 macrophage cell line for functional experiments. Our results showed a strong association of MMP12 expression with the severity of inflammatory bowel disease and the response to relevant biological therapies. In vitro assays revealed that the inhibition of mechanistic target of rapamycin complex 1 (mTORC1) and the stimulation of the AMP-activated protein kinase (AMPK) signaling pathway potentiated the expression of Mmp12. Additionally, AMPK and mTOR required a functional downstream glycolytic pathway to fully engage with Mmp12 expression. Finally, the pharmacological inhibition of MMP12 abolished the expression of the proinflammatory cytokine Interleukin-6 (Il6) in macrophages. Overall, our findings provide a better understanding of the mechanistic regulation of MMP12 in macrophages and its relationship with inflammation.
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Affiliation(s)
- Laura Arosa
- Molecular and Cellular Gastroenterology Group, Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (L.A.); (M.C.-G.)
| | - Miguel Camba-Gómez
- Molecular and Cellular Gastroenterology Group, Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (L.A.); (M.C.-G.)
| | | | - Laura Clavaín
- EGO Genomics, Scientific Park of the University of Salamanca, Adaja Street 4, Building M2, 37185 Villamayor, Spain;
| | - Miguel López
- NeurObesity Group, Department of Physiology, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain;
- CIBER Fisiopatologia de la Obesidad y Nutrición (CIBERobn), 15706 Santiago de Compostela, Spain
| | - Javier Conde-Aranda
- Molecular and Cellular Gastroenterology Group, Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (L.A.); (M.C.-G.)
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Lucaciu LA, Seicean R, Uifălean A, Iacobescu M, Iuga CA, Seicean A. Unveiling Distinct Proteomic Signatures in Complicated Crohn's Disease That Could Predict the Disease Course. Int J Mol Sci 2023; 24:16966. [PMID: 38069288 PMCID: PMC10707401 DOI: 10.3390/ijms242316966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Crohn's disease (CD) is characterized by a chronic, progressive inflammation of the gastrointestinal tract often leading to complications, such as strictures and fistulae. Currently, there are no validated tools anticipating short- and long-term outcomes at an early stage. This investigation aims to elucidate variations in protein abundance across distinct CD phenotypes with the objective of uncovering potential biomarkers implicated in disease advancement. Serum samples collected from 30 CD patients and 15 healthy age-matched controls (HC) were subjected to depletion of highly abundant proteins and to a label-free mass spectrometry analysis. Twenty-four proteins were shown to be significantly different when comparing CD with HC. Of these, WD repeat-containing protein 31 (WDR31), and proteins involved in the acute inflammatory response, leucine-rich alpha-2-glycoprotein (LRG1) and serum amyloid A1 (SAA1), were more abundant in the aggressive subgroup. Against standard biomarkers, a positive correlation between SAA1 and WDR31 and C-reactive protein (CRP) was found. In this study, a unique serum biomarker panel for aggressive CD was identified, which could aid in predicting the disease course.
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Affiliation(s)
- Laura A. Lucaciu
- Department of Gastroenterology and Hepatology, “Iuliu Haţieganu” University of Medicine and Pharmacy, Croitorilor 19-21, 400162 Cluj-Napoca, Romania; (L.A.L.); (A.S.)
| | - Radu Seicean
- Department of General Surgery, First Surgical Clinic, “Iuliu Haţieganu” University of Medicine and Pharmacy, Clinicilor 3-5, 400006 Cluj-Napoca, Romania;
| | - Alina Uifălean
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, “Iuliu Haţieganu” University of Medicine and Pharmacy, Louis Pasteur 6, 400349 Cluj-Napoca, Romania; (A.U.); (C.A.I.)
| | - Maria Iacobescu
- Department of Proteomics and Metabolomics, MEDFUTURE-Research Centre for Advanced Medicine, “Iuliu Haţieganu” University of Medicine and Pharmacy, Louis Pasteur 4, 400349 Cluj-Napoca, Romania
| | - Cristina A. Iuga
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, “Iuliu Haţieganu” University of Medicine and Pharmacy, Louis Pasteur 6, 400349 Cluj-Napoca, Romania; (A.U.); (C.A.I.)
- Department of Proteomics and Metabolomics, MEDFUTURE-Research Centre for Advanced Medicine, “Iuliu Haţieganu” University of Medicine and Pharmacy, Louis Pasteur 4, 400349 Cluj-Napoca, Romania
| | - Andrada Seicean
- Department of Gastroenterology and Hepatology, “Iuliu Haţieganu” University of Medicine and Pharmacy, Croitorilor 19-21, 400162 Cluj-Napoca, Romania; (L.A.L.); (A.S.)
- “Prof. Dr. Octavian Fodor” Regional Institute of Gastroenterology and Hepatology, Croitorilor Street No. 19-21, 400162 Cluj-Napoca, Romania
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Kamal S, Parkash N, Beattie W, Christensen B, Segal JP. Are We Ready to Reclassify Crohn's Disease Using Molecular Classification? J Clin Med 2023; 12:5786. [PMID: 37762727 PMCID: PMC10532006 DOI: 10.3390/jcm12185786] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/21/2023] [Accepted: 09/02/2023] [Indexed: 09/29/2023] Open
Abstract
Crohn's disease (CD) is a type of inflammatory bowel disease. The number of IBD cases worldwide was estimated to be 4.9 million in 2019. CD exhibits heterogeneity in clinical presentation, anatomical involvement, disease behaviour, clinical course and response to treatment. The classical description of CD involves transmural inflammation with skip lesions anywhere along the entire gastrointestinal tract. The complexity and heterogeneity of Crohn's disease is not currently reflected in the conventional classification system. Though the knowledge of Crohn's pathophysiology remains far from understood, the established complex interplay of the omics-genomics, transcriptomics, proteomics, epigenomics, metagenomics, metabolomics, lipidomics and immunophenomics-provides numerous targets for potential molecular markers of disease. Advancing technology has enabled identification of small molecules within these omics, which can be extrapolated to differentiate types of Crohn's disease. The multi-omic future of Crohn's disease is promising, with potential for advancements in understanding of its pathogenesis and implementation of personalised medicine.
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Affiliation(s)
- Shahed Kamal
- Department of Gastroenterology, Northern Hospital, Epping, Melbourne VIC 3076, Australia
| | - Nikita Parkash
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, Melbourne VIC 3052, Australia
| | - William Beattie
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, Melbourne VIC 3052, Australia
| | - Britt Christensen
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, Melbourne VIC 3052, Australia
- Department of Gastroenterology, The University of Melbourne, Parkville, Melbourne VIC 3010, Australia
| | - Jonathan P. Segal
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, Melbourne VIC 3052, Australia
- Department of Gastroenterology, The University of Melbourne, Parkville, Melbourne VIC 3010, Australia
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Jiang S, Wang T, Zhang KH. Data-driven decision-making for precision diagnosis of digestive diseases. Biomed Eng Online 2023; 22:87. [PMID: 37658345 PMCID: PMC10472739 DOI: 10.1186/s12938-023-01148-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 08/15/2023] [Indexed: 09/03/2023] Open
Abstract
Modern omics technologies can generate massive amounts of biomedical data, providing unprecedented opportunities for individualized precision medicine. However, traditional statistical methods cannot effectively process and utilize such big data. To meet this new challenge, machine learning algorithms have been developed and applied rapidly in recent years, which are capable of reducing dimensionality, extracting features, organizing data and forming automatable data-driven clinical decision systems. Data-driven clinical decision-making have promising applications in precision medicine and has been studied in digestive diseases, including early diagnosis and screening, molecular typing, staging and stratification of digestive malignancies, as well as precise diagnosis of Crohn's disease, auxiliary diagnosis of imaging and endoscopy, differential diagnosis of cystic lesions, etiology discrimination of acute abdominal pain, stratification of upper gastrointestinal bleeding (UGIB), and real-time diagnosis of esophageal motility function, showing good application prospects. Herein, we reviewed the recent progress of data-driven clinical decision making in precision diagnosis of digestive diseases and discussed the limitations of data-driven decision making after a brief introduction of methods for data-driven decision making.
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Affiliation(s)
- Song Jiang
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, No. 17, Yongwai Zheng Street, Nanchang, 330006 China
- Jiangxi Institute of Gastroenterology and Hepatology, Nanchang, 330006 China
| | - Ting Wang
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, No. 17, Yongwai Zheng Street, Nanchang, 330006 China
- Jiangxi Institute of Gastroenterology and Hepatology, Nanchang, 330006 China
| | - Kun-He Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, No. 17, Yongwai Zheng Street, Nanchang, 330006 China
- Jiangxi Institute of Gastroenterology and Hepatology, Nanchang, 330006 China
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10
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Nowak JK, Kalla R, Satsangi J. Current and emerging biomarkers for ulcerative colitis. Expert Rev Mol Diagn 2023; 23:1107-1119. [PMID: 37933807 DOI: 10.1080/14737159.2023.2279611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 11/01/2023] [Indexed: 11/08/2023]
Abstract
INTRODUCTION Ulcerative colitis (UC) is a chronic illness requiring lifelong management that could be enhanced by personalizing care using biomarkers. AREAS COVERED The main biomarker discovery modalities are reviewed, highlighting recent results across the spectrum of applications, including diagnostics (serum anti-αvβ6 antibodies achieving an area under the curve [AUC] = 0.99; serum oncostatin M AUC = 0.94), disease activity assessment (fecal calprotectin and serum trefoil factor 3: AUC > 0.90), prognostication of the need for treatment escalation (whole blood transcriptomic panels and CLEC5A/CDH2 ratio: AUC > 0.90), prediction of treatment response, and early identification of patients with subclinical disease. The use of established biomarkers is discussed, along with new evidence regarding autoantibodies, proteins, proteomic panels, transcriptomic signatures, deoxyribonucleic acid methylation patterns, and UC-specific glycomic and metabolic disturbances. EXPERT OPINION Novel biomarkers will pave the way for optimized UC care. However, validation, simplification, and direct clinical translation of complex models may prove challenging. Currently, few candidates exist to assess key characteristics, such as UC susceptibility, histological disease activity, drug response, and long-term disease behavior. Further research will likely not only reveal new tools to tackle these issues but also contribute to understanding UC pathogenesis mechanisms.
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Affiliation(s)
- Jan K Nowak
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Rahul Kalla
- Medical Research Council Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Jack Satsangi
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, Oxford, UK
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Yu J, Boland L, Catt M, Puk L, Wong N, Krockenberger M, Bennett P, Ruaux C, Wasinger VC. Serum proteome profiles in cats with chronic enteropathies. J Vet Intern Med 2023; 37:1358-1367. [PMID: 37279179 PMCID: PMC10365053 DOI: 10.1111/jvim.16743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 05/07/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND Serum protein biomarkers are used to diagnose, monitor treatment response, and to differentiate various forms of chronic enteropathies (CE) in humans. The utility of liquid biopsy proteomic approaches has not been examined in cats. HYPOTHESIS/OBJECTIVES To explore the serum proteome in cats to identify markers differentiating healthy cats from cats with CE. ANIMALS Ten cats with CE with signs of gastrointestinal disease of at least 3 weeks duration, and biopsy-confirmed diagnoses, with or without treatment and 19 healthy cats were included. METHODS Cross-sectional, multicenter, exploratory study with cases recruited from 3 veterinary hospitals between May 2019 and November 2020. Serum samples were analyzed and evaluated using mass spectrometry-based proteomic techniques. RESULTS Twenty-six proteins were significantly (P < .02, ≥5-fold change in abundance) differentially expressed between cats with CE and controls. Thrombospondin-1 (THBS1) was identified with >50-fold increase in abundance in cats with CE (P < 0.001) compared to healthy cats. CONCLUSIONS AND CLINICAL IMPORTANCE Damage to the gut lining released marker proteins of chronic inflammation that were detectable in serum samples of cats. This early-stage exploratory study strongly supports THBS1 as a candidate biomarker for chronic inflammatory enteropathy in cats.
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Affiliation(s)
- Jane Yu
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Lara Boland
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Melissa Catt
- Paddington Cat Hospital, Paddington, New South Wales, Australia
| | - Leah Puk
- Paddington Cat Hospital, Paddington, New South Wales, Australia
| | - Nadia Wong
- McIvor Road Veterinary Centre, Bendigo, Victoria, Australia
| | - Mark Krockenberger
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Peter Bennett
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Craig Ruaux
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Valerie C Wasinger
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales, Australia
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12
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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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13
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Yu J, Ruaux C, Griebsch C, Boland L, Wong N, Bennett P, Wasinger VC. Serum proteome of dogs with chronic enteropathy. J Vet Intern Med 2023; 37:925-935. [PMID: 37186013 DOI: 10.1111/jvim.16682] [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: 09/28/2022] [Accepted: 02/24/2023] [Indexed: 05/17/2023] Open
Abstract
BACKGROUND Chronic enteropathy (CE) is common in dogs and can occur with multiple etiologies including food-responsive enteropathy (FRE) and idiopathic inflammatory bowel disease (IBD). HYPOTHESIS/OBJECTIVE To study the protein profile and pathway differences among dogs with FRE, IBD, and healthy controls using serum proteome analysis. ANIMALS Nine CE dogs with signs of gastrointestinal disease and histologically confirmed chronic inflammatory enteropathy and 16 healthy controls. METHODS A cross-sectional study with cases recruited from 2 veterinary hospitals between May 2019 and November 2020 was performed. Serum samples were analyzed using mass spectrometry-based proteomic techniques. RESULTS Proteomic profiles showed marked variation in relative protein abundances. Forty-five proteins were significantly (P ≤ .01) differentially expressed among the dogs with CE and controls with ≥2-fold change in abundance. The fold change of dogs with IBD normalized to controls was more pronounced for the majority of proteins than that seen in the dogs with FRE normalized to control dogs. Proteins involving reactive oxygen species, cytokine activation, acute phase response signaling, and lipid metabolism were altered in dogs with CE. CONCLUSIONS AND CLINICAL IMPORTANCE Cytokine alterations, acute phase response signaling, and lipid metabolism are likely involved in pathogenesis of CE. Although there are insufficient current data to justify the use of proteomic biomarkers for assessment of CE in dogs, our study identifies potential candidates.
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Affiliation(s)
- Jane Yu
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Craig Ruaux
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Christine Griebsch
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Lara Boland
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Nadia Wong
- McIvor Road Veterinary Centre, Bendigo, Victoria, Australia
| | - Peter Bennett
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Valerie C Wasinger
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales, Australia
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14
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Livanos AE, Dunn A, Fischer J, Ungaro RC, Turpin W, Lee SH, Rui S, Del Valle DM, Jougon JJ, Martinez-Delgado G, Riddle MS, Murray JA, Laird RM, Torres J, Agrawal M, Magee JS, Dervieux T, Gnjatic S, Sheppard D, Sands BE, Porter CK, Croitoru K, Petralia F, Colombel JF, Mehandru S. Anti-Integrin αvβ6 Autoantibodies Are a Novel Biomarker That Antedate Ulcerative Colitis. Gastroenterology 2023; 164:619-629. [PMID: 36634824 DOI: 10.1053/j.gastro.2022.12.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/14/2023]
Abstract
BACKGROUND & AIMS Better biomarkers for prediction of ulcerative colitis (UC) development and prognostication are needed. Anti-integrin αvβ6 (anti-αvβ6) autoantibodies have been described in patients with UC. We tested for the presence of anti-αvβ6 antibodies in the preclinical phase of UC and studied their association with disease-related outcomes after diagnosis. METHODS Anti-αvβ6 autoantibodies were measured in 4 longitudinal serum samples collected from 82 subjects who later developed UC and 82 matched controls from a Department of Defense preclinical cohort (PREDICTS [Proteomic Evaluation and Discovery in an IBD Cohort of Tri-service Subjects]). In a distinct, external validation cohort (Crohn's and Colitis Canada Genetic Environmental Microbial project cohort), we tested 12 pre-UC subjects and 49 matched controls. Furthermore, anti-αvβ6 autoantibodies were measured in 2 incident UC cohorts (COMPASS [Comprehensive Care for the Recently Diagnosed IBD Patients], n = 55 and OSCCAR [Ocean State Crohn's and Colitis Area Registry], n = 104) and associations between anti-αvβ6 autoantibodies and UC-related outcomes were defined using Cox proportional hazards model. RESULTS Anti-αvβ6 autoantibodies were significantly higher among individuals who developed UC compared with controls up to 10 years before diagnosis in PREDICTS. The anti-αvβ6 autoantibody seropositivity was 12.2% 10 years before diagnosis and increased to 52.4% at the time of diagnosis in subjects who developed UC compared with 2.7% in controls across the 4 time points. Anti-αvβ6 autoantibodies predicted UC development with an area under the curve of at least 0.8 up to 10 years before diagnosis. The presence of anti-αvβ6 autoantibodies in preclinical UC samples was validated in the GEM cohort. Finally, high anti-αvβ6 autoantibodies was associated with a composite of adverse UC outcomes, including hospitalization, disease extension, colectomy, systemic steroid use, and/or escalation to biologic therapy in recently diagnosed UC. CONCLUSIONS Anti-integrin αvβ6 autoantibodies precede the clinical diagnosis of UC by up to 10 years and are associated with adverse UC-related outcomes.
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Affiliation(s)
- Alexandra E Livanos
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Alexandra Dunn
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jeremy Fischer
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ryan C Ungaro
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Williams Turpin
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada; Division of Gastroenterology and Hepatology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Sun-Ho Lee
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada; Division of Gastroenterology and Hepatology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Shumin Rui
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Diane Marie Del Valle
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Human Immune Monitoring Center, Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Julia J Jougon
- Hepato-Gastroenterology Department, Claude Huriez Hospital, University of Lille, Lille, France
| | | | - Mark S Riddle
- University of Nevada, Reno School of Medicine, Reno, Nevada; Veterans Affairs Sierra Nevada Health Care System, Reno, Nevada
| | - Joseph A Murray
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Renee M Laird
- Enteric Diseases Department, Naval Medical Research Center, Silver Spring, Maryland; Henry M. Jackson Foundation for Military Medicine, Bethesda, Maryland
| | - Joana Torres
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Gastroenterology Division, Hospital Beatriz Ângelo, Loures, Portugal; Gastroenterology Division, Hospital da Luz, Lisbon, Portugal; Faculdade de Medicina, Universidade de Lisboa, Portugal
| | - Manasi Agrawal
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jared S Magee
- Gastroenterology, Walter Reed National Military Medical Center, Bethesda, Maryland
| | | | - Sacha Gnjatic
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Human Immune Monitoring Center, Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Dean Sheppard
- Division of Pulmonary, Critical Care, Allergy and Sleep, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Bruce E Sands
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Chad K Porter
- Enteric Diseases Department, Naval Medical Research Center, Silver Spring, Maryland
| | - Kenneth Croitoru
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada; Division of Gastroenterology and Hepatology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | | | - Jean-Frederic Colombel
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Saurabh Mehandru
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York.
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15
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Kalla R, Adams AT, Nowak JK, Bergemalm D, Vatn S, Ventham NT, Kennedy NA, Ricanek P, Lindstrom J, Söderholm J, Pierik M, D’Amato M, Gomollón F, Olbjørn C, Richmond R, Relton C, Jahnsen J, Vatn MH, Halfvarson J, Satsangi J. Analysis of Systemic Epigenetic Alterations in Inflammatory Bowel Disease: Defining Geographical, Genetic and Immune-Inflammatory influences on the Circulating Methylome. J Crohns Colitis 2023; 17:170-184. [PMID: 36029471 PMCID: PMC10024547 DOI: 10.1093/ecco-jcc/jjac127] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND Epigenetic alterations may provide valuable insights into gene-environment interactions in the pathogenesis of inflammatory bowel disease [IBD]. METHODS Genome-wide methylation was measured from peripheral blood using the Illumina 450k platform in a case-control study in an inception cohort (295 controls, 154 Crohn's disease [CD], 161 ulcerative colitis [UC], 28 IBD unclassified [IBD-U)] with covariates of age, sex and cell counts, deconvoluted by the Houseman method. Genotyping was performed using Illumina HumanOmniExpressExome-8 BeadChips and gene expression using the Ion AmpliSeq Human Gene Expression Core Panel. Treatment escalation was characterized by the need for biological agents or surgery after initial disease remission. RESULTS A total of 137 differentially methylated positions [DMPs] were identified in IBD, including VMP1/MIR21 [p = 9.11 × 10-15] and RPS6KA2 [6.43 × 10-13], with consistency seen across Scandinavia and the UK. Dysregulated loci demonstrate strong genetic influence, notably VMP1 [p = 1.53 × 10-15]. Age acceleration is seen in IBD [coefficient 0.94, p < 2.2 × 10-16]. Several immuno-active genes demonstrated highly significant correlations between methylation and gene expression in IBD, in particular OSM: IBD r = -0.32, p = 3.64 × 10-7 vs non-IBD r = -0.14, p = 0.77]. Multi-omic integration of the methylome, genome and transcriptome also implicated specific pathways that associate with immune activation, response and regulation at disease inception. At follow-up, a signature of three DMPs [TAP1, TESPA1, RPTOR] were associated with treatment escalation to biological agents or surgery (hazard ratio of 5.19 [CI: 2.14-12.56], logrank p = 9.70 × 10-4). CONCLUSION These data demonstrate consistent epigenetic alterations at diagnosis in European patients with IBD, providing insights into the pathogenetic importance and translational potential of epigenetic mapping in complex disease.
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Affiliation(s)
- Rahul Kalla
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- MRC Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Alex T Adams
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Jan K Nowak
- Department of Paediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Daniel Bergemalm
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Simen Vatn
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
| | - Nicholas T Ventham
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Nicholas A Kennedy
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Exeter IBD and Pharmacogenetics group, University of Exeter, Exeter, UK
| | - Petr Ricanek
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - Jonas Lindstrom
- Health Services Research Unit, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - Johan Söderholm
- Department of Surgery and Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Marie Pierik
- Maastricht University Medical Centre (MUMC), Department of Gastroenterology and Hepatology, Maastricht, Netherlands
| | - Mauro D’Amato
- CIC bioGUNE – BRTA, Derio, SpainIKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | | | - Christine Olbjørn
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - Rebecca Richmond
- Medical Research Council Integrative Epidemiology Unit (MRC IEU), School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Caroline Relton
- Medical Research Council Integrative Epidemiology Unit (MRC IEU), School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Jørgen Jahnsen
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - Morten H Vatn
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Jack Satsangi
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, UK
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16
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Leibovitzh H, Lee SH, Raygoza Garay JA, Espin-Garcia O, Xue M, Neustaeter A, Goethel A, Huynh HQ, Griffiths AM, Turner D, Madsen KL, Moayyedi P, Steinhart AH, Silverberg MS, Deslandres C, Bitton A, Mack DR, Jacobson K, Cino M, Aumais G, Bernstein CN, Panaccione R, Weiss B, Halfvarson J, Xu W, Turpin W, Croitoru K. Immune response and barrier dysfunction-related proteomic signatures in preclinical phase of Crohn's disease highlight earliest events of pathogenesis. Gut 2023:gutjnl-2022-328421. [PMID: 36788016 DOI: 10.1136/gutjnl-2022-328421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 01/25/2023] [Indexed: 02/16/2023]
Abstract
OBJECTIVE The measure of serum proteome in the preclinical state of Crohn's disease (CD) may provide insight into biological pathways involved in CD pathogenesis. We aimed to assess associations of serum proteins with future CD onset and with other biomarkers predicting CD risk in a healthy at-risk cohort. DESIGN In a nested case-control study within the Crohn's and Colitis Canada Genetics Environment Microbial Project (CCC-GEM) cohort, which prospectively follows healthy first-degree relatives (FDRs), subjects who developed CD (n=71) were matched with four FDRs remaining healthy (n=284). Using samples at recruitment, serum protein profiles using the Olink Proximity Extension Assay platform was assessed for association with future development of CD and with other baseline biomarkers as follows: serum antimicrobial antibodies (AS: positive antibody sum) (Prometheus); faecal calprotectin (FCP); gut barrier function using the fractional excretion of lactulose-to-mannitol ratio (LMR) assay. RESULTS We identified 25 of 446 serum proteins significantly associated with future development of CD. C-X-C motif chemokine 9 (CXCL9) had the highest OR with future risk of CD (OR=2.07 per SD, 95% CI 1.58 to 2.73, q=7.9e-5), whereas matrix extracellular phosphoglycoprotein had the lowest OR (OR 0.44, 95% CI 0.29 to 0.66, q=0.02). Notably, CXCL9 was the only analyte significantly associated with all other CD-risk biomarkers with consistent direction of effect (FCP: OR=2.21; LMR: OR=1.67; AS: OR=1.59) (q<0.05 for all). CONCLUSION We identified serum proteomic signatures associated with future CD development, reflecting potential early biological processes of immune and barrier dysfunction.
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Affiliation(s)
- Haim Leibovitzh
- Zane Cohen Centre for Digestive Diseases, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.,Division of Gastroenterology & Hepatology, University of Toronto Temerty Faculty of Medicine, Toronto, Ontario, Canada
| | - Sun-Ho Lee
- Zane Cohen Centre for Digestive Diseases, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.,Division of Gastroenterology & Hepatology, University of Toronto Temerty Faculty of Medicine, Toronto, Ontario, Canada
| | - Juan Antonio Raygoza Garay
- Zane Cohen Centre for Digestive Diseases, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.,Division of Gastroenterology & Hepatology, University of Toronto Temerty Faculty of Medicine, Toronto, Ontario, Canada
| | - Osvaldo Espin-Garcia
- Division of Biostatistics, University of Toronto Dalla Lana School of Public Health, Toronto, Ontario, Canada
| | - Mingyue Xue
- Zane Cohen Centre for Digestive Diseases, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Anna Neustaeter
- Zane Cohen Centre for Digestive Diseases, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Ashleigh Goethel
- Zane Cohen Centre for Digestive Diseases, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Hien Q Huynh
- Division of Gastroenterology and Nutrition, Department of Pediatrics, University of Alberta Faculty of Medicine & Dentistry, Edmonton, Alberta, Canada
| | - Anne M Griffiths
- IBD Center, Department of Paediatrics, Faculty of Medicine, University of Toronto, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Dan Turner
- The Juliet Keidan Institute of Pediatric Gastroenterology and Nutrition, The Hebrew University of Jerusalem, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Karen L Madsen
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Paul Moayyedi
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - A Hillary Steinhart
- Zane Cohen Centre for Digestive Diseases, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.,Division of Gastroenterology & Hepatology, University of Toronto Temerty Faculty of Medicine, Toronto, Ontario, Canada
| | - Mark S Silverberg
- Zane Cohen Centre for Digestive Diseases, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.,Division of Gastroenterology & Hepatology, University of Toronto Temerty Faculty of Medicine, Toronto, Ontario, Canada
| | - Colette Deslandres
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, University of Montreal, Saint Justine Hospital, Montreal, Quebec, Canada
| | - Alain Bitton
- Division of Gastroenterology and Hepatology, McGill University Health Centre, Montreal, Quebec, Canada
| | - David R Mack
- Division of Gastroenterology, Hepatology & Nutrition, University of Ottawa, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Kevan Jacobson
- Canadian Gastro-Intestinal Epidemiology Consortium, British Columbia Children's Hospital Research Institute, University of British Columbia, British Columbia Children's Hospital, Vancouver, British Columbia, Canada
| | - Maria Cino
- Department of Medicine, Division of Gastroenterology, University of Toronto, Toronto, Ontario, Canada
| | - Guy Aumais
- Department of Medicine, Montreal University, Hôpital Maisonneuve-Rosemont, Montreal, Quebec, Canada
| | - Charles N Bernstein
- University of Manitoba Inflammatory Bowel Disease Clinical and Research Centre and Department of Internal Medicine, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Remo Panaccione
- Inflammatory Bowel Disease Clinic, Division of Gastroenterology and Hepatology of Gastroenterology, University of Calgary, Calgary, Alberta, Canada
| | - Batia Weiss
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Sheba Medical Center, Tel-Hashomer, Sackler Faculty of Medicine, Tel-Aviv University, The Edmond and Lily Safra Children's Hospital, Tel Aviv, Israel
| | - Jonas Halfvarson
- School of Medical Sciences. Department of Gastroenterology, Örebro University, Orebro, Sweden
| | - Wei Xu
- Division of Biostatistics, University of Toronto Dalla Lana School of Public Health, Toronto, Ontario, Canada
| | - Williams Turpin
- Zane Cohen Centre for Digestive Diseases, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.,Division of Gastroenterology & Hepatology, University of Toronto Temerty Faculty of Medicine, Toronto, Ontario, Canada
| | - Kenneth Croitoru
- Zane Cohen Centre for Digestive Diseases, Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada .,Division of Gastroenterology & Hepatology, University of Toronto Temerty Faculty of Medicine, Toronto, Ontario, Canada
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17
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Yan P, Sun Y, Luo J, Liu X, Wu J, Miao Y. Integrating the serum proteomic and fecal metaproteomic to analyze the impacts of overweight/obesity on IBD: a pilot investigation. Clin Proteomics 2023; 20:6. [PMID: 36759757 PMCID: PMC9909917 DOI: 10.1186/s12014-023-09396-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 02/02/2023] [Indexed: 02/11/2023] Open
Abstract
BACKGROUND Inflammatory bowel disease (IBD) encompasses a group of chronic relapsing disorders which include ulcerative colitis (UC) and Crohn's disease (CD). The incidences of IBD and overweight/obesity are increasing in parallel. Here, we investigated alterations in proteomic in serum and metaproteomic in feces of IBD patients with overweight/obesity and aimed to explore the effect of overweight/ obesity on IBD and the underlying mechanism. METHODS This prospective observational study (n = 64) comprised 26 health control subjects (HC, 13 with overweight/obesity) and 38 IBD patients (19 with overweight/obesity) at a tertiary hospital. Overweight/obesity was evaluated by body mass index (BMI) and defined as a BMI greater than 24 kg/m2. The comprehensive serum proteomic and fecal metaproteomic analyses were conducted by ultra-performance liquid chromatography-Orbitrap Exploris 480 mass spectrometry. RESULTS UC and CD presented similar serum molecular profiles but distinct gut microbiota. UC and CD serum exhibited higher levels of cytoskeleton organization- associated and inflammatory response-related proteins than the HC serum. Compared the serum proteome of UC and CD without overweight/obesity, inflammatory response-associated proteins were dramatically decreased in UC and CD with overweight/obesity. Fecal metaproteome identified 66 species in the feces. Among them, Parasutterella excrementihominis was increased in CD compared with that in HC. UC group had a significant enrichment of Moniliophthora roreri, but had dramatically decreased abundances of Alistipes indistinctus, Clostridium methylpentosum, Bacteroides vulgatus, and Schizochytrium aggregatum. In addition, overweight/obesity could improve the microbial diversity of UC. Specifically, the UC patients with overweight/obesity had increased abundance of some probiotics in contrast to those without overweight/obesity, including Parabacteroides distasonis, Alistipes indistincus, and Ruminococcus bromii. CONCLUSION This study provided high-quality multi-omics data of IBD serum and fecal samples, which enabled deciphering the molecular bases of clinical phenotypes of IBD, revealing the impacts of microbiota on IBD, and emphasizing the important role of overweight/obesity in IBD.
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Affiliation(s)
- Ping Yan
- grid.285847.40000 0000 9588 0960Kunming Medical University, Kunming, China ,grid.440682.c0000 0001 1866 919XDepartment of Gastroenterology, First Affiliated Hospital of Dali University, Dali, China ,Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, China
| | - Yang Sun
- grid.414902.a0000 0004 1771 3912Department of Gastroenterology, First Affiliated Hospital of Kunming Medical University, Kunming, China ,Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, China
| | - Juan Luo
- grid.414902.a0000 0004 1771 3912Department of Gastroenterology, First Affiliated Hospital of Kunming Medical University, Kunming, China ,Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, China
| | - Xiaolin Liu
- grid.414902.a0000 0004 1771 3912Department of Gastroenterology, First Affiliated Hospital of Kunming Medical University, Kunming, China ,Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, China
| | - Jing Wu
- grid.414902.a0000 0004 1771 3912Department of Gastroenterology, First Affiliated Hospital of Kunming Medical University, Kunming, China ,Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, China
| | - Yinglei Miao
- Department of Gastroenterology, First Affiliated Hospital of Kunming Medical University, Kunming, China. .,Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, China.
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18
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Chen J, Zhou Y, Sun Y, Yuan S, Kalla R, Sun J, Zhao J, Wang L, Chen X, Zhou X, Dai S, Zhang Y, Ho GT, Xia D, Cao Q, Liu Z, Larsson SC, Wang X, Ding K, Halfvarson J, Li X, Theodoratou E, Satsangi J. Bi-directional Mendelian randomization analysis provides evidence for the causal involvement of dysregulation of CXCL9, CCL11 and CASP8 in the pathogenesis of ulcerative colitis. J Crohns Colitis 2022; 17:777-785. [PMID: 36576886 PMCID: PMC10155748 DOI: 10.1093/ecco-jcc/jjac191] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Indexed: 12/29/2022]
Abstract
BACKGROUND AND AIMS Systemic inflammation is well-recognized to be associated with ulcerative colitis (UC), but whether these effects are causal or consequential remains unclear. We aimed to define potential causal relationship of cytokine dysregulation with different tiers of evidence. METHODS We firstly synthesized serum proteomic profiling data from two multi-centered observational studies, in which a panel of systemic inflammatory proteins was analyzed to examine their associations with UC risk. To further dissect observed associations, we then performed a bidirectional two-sample Mendelian randomization (TSMR) analysis from both forward and reverse directions using five genome-wide association study (GWAS) summary level data for serum proteomic profiles and the largest GWAS of 28,738 European-ancestry individuals for UC risk. RESULTS Pooled analysis of serum proteomic data identified 14 proteins to be associated with the risk of UC. Forward MR analysis using only cis-acting protein quantitative trait loci (cis-pQTLs) or trans-pQTLs further validated causal associations of two chemokines and the increased risk of UC: C-X-C motif chemokine ligand 9 (CXCL9) (OR, 1.45, 95% CI, 1.08-1.95, P=.012) and C-C motif chemokine ligand 11 (CCL11) (OR, 1.14, 95%CI: 1.09-1.18, P=3.89×10 -10). Using both cis- and trans-acting pQTLs, an association of caspase-8 (CASP8) (OR, 1.04, 95% CI, 1.03-1.05, P= 7.63×10 -19) was additionally identified. Reverse MR did not find any influence of genetic predisposition to UC on any of these three inflammation proteins. CONCLUSIONS Pre-existing elevated levels of CXCL9, CCL11 and CASP8 may play a role in the pathogenesis of UC.
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Affiliation(s)
- Jie Chen
- Department of Big Data in Health Science, School of Public Health and The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Centre for Global Health, Zhejiang University School of Medicine, Hangzhou, China
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yajing Zhou
- Department of Big Data in Health Science, School of Public Health and The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yuhao Sun
- Centre for Global Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Shuai Yuan
- Department of Big Data in Health Science, School of Public Health and The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Unit of Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Rahul Kalla
- Edinburgh IBD Science Unit, Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - Jing Sun
- Department of Big Data in Health Science, School of Public Health and The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jianhui Zhao
- Department of Big Data in Health Science, School of Public Health and The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lijuan Wang
- Department of Big Data in Health Science, School of Public Health and The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xuejie Chen
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Xuan Zhou
- Department of Big Data in Health Science, School of Public Health and The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Siqi Dai
- Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, China
| | - Yu Zhang
- Department of Gastroenterology, Sir Run Run Shaw Hospital, College of Medicine Zhejiang University, Hangzhou, China
| | - Gwo-Tzer Ho
- Edinburgh IBD Science Unit, Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - Dajing Xia
- Department of Toxicology of School of Public Health, & Center of Immunology & Infection, Zhejiang University School of Medicine, Hangzhou, China
| | - Qian Cao
- Department of Gastroenterology, Sir Run Run Shaw Hospital, College of Medicine Zhejiang University, Hangzhou, China
| | - Zhanju Liu
- Center for IBD Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Susanna C Larsson
- Unit of Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Unit of Medical Epidemiology, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Xiaoyan Wang
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Kefeng Ding
- Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, China
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Xue Li
- Department of Big Data in Health Science, School of Public Health and The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Evropi Theodoratou
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Jack Satsangi
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, UK
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19
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Sezgin E, Terlemez G, Bozkurt B, Bengi G, Akpinar H, Büyüktorun İ. Quantitative real-time PCR analysis of bacterial biomarkers enable fast and accurate monitoring in inflammatory bowel disease. PeerJ 2022; 10:e14217. [PMID: 36275453 PMCID: PMC9586115 DOI: 10.7717/peerj.14217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/20/2022] [Indexed: 01/24/2023] Open
Abstract
Inflammatory bowel diseases (IBD) affect millions of people worldwide with increasing incidence. Ulcerative colitis (UC) and Crohn's disease (CD) are the two most common IBDs. There is no definite cure for IBD, and response to treatment greatly vary among patients. Therefore, there is urgent need for biomarkers to monitor therapy efficacy, and disease prognosis. We aimed to test whether qPCR analysis of common candidate bacteria identified from a patient's individual fecal microbiome can be used as a fast and reliable personalized microbial biomarker for efficient monitoring of disease course in IBD. Next generation sequencing (NGS) of 16S rRNA gene region identified species level microbiota profiles for a subset of UC, CD, and control samples. Common high abundance bacterial species observed in all three groups, and reported to be associated with IBD are chosen as candidate marker species. These species, and total bacteria amount are quantified in all samples with qPCR. Relative abundance of anti-inflammatory, beneficial Faecalibacterium prausnitzii, Akkermansia muciniphila, and Streptococcus thermophilus was significantly lower in IBD compared to control samples. Moreover, the relative abundance of the examined common species was correlated with the severity of IBD disease. The variance in qPCR data was much lower compared to NGS data, and showed much higher statistical power for clinical utility. The qPCR analysis of target common bacterial species can be a powerful, cost and time efficient approach for monitoring disease status and identify better personalized treatment options for IBD patients.
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Affiliation(s)
- Efe Sezgin
- Izmir Institute of Technology, Izmir, Turkey
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20
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Spencer EA, Agrawal M, Jess T. Prognostication in inflammatory bowel disease. Front Med (Lausanne) 2022; 9:1025375. [PMID: 36275829 PMCID: PMC9582521 DOI: 10.3389/fmed.2022.1025375] [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: 08/22/2022] [Accepted: 09/14/2022] [Indexed: 11/13/2022] Open
Abstract
Personalized care in inflammatory bowel diseases (IBD) hinges on parsing the heterogeneity of IBD patients through prognostication of their disease course and therapeutic response to allow for tailor-made treatment and monitoring strategies to optimize care. Herein we review the currently available predictors of outcomes in IBD and those on the both near and far horizons. We additionally discuss the importance of worldwide collaborative efforts and tools to support clinical use of these prognostication tools.
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Affiliation(s)
- Elizabeth A. Spencer
- Division of Pediatric Gastroenterology and Nutrition, Icahn School of Medicine, Mount Sinai Hospital, New York, NY, United States,*Correspondence: Elizabeth A. Spencer
| | - Manasi Agrawal
- Division of Gastroenterology, Icahn School of Medicine, Mount Sinai Hospital, New York, NY, United States,Center for Molecular Prediction of Inflammatory Bowel Disease, PREDICT, Aalborg University, Aalborg, Denmark
| | - Tine Jess
- Center for Molecular Prediction of Inflammatory Bowel Disease, PREDICT, Aalborg University, Aalborg, Denmark,Department of Gastroenterology and Hepatology, Aalborg University Hospital, Aalborg, Denmark
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21
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Ura B, Capaci V, Aloisio M, Di Lorenzo G, Romano F, Ricci G, Monasta L. A Targeted Proteomics Approach for Screening Serum Biomarkers Observed in the Early Stage of Type I Endometrial Cancer. Biomedicines 2022; 10:biomedicines10081857. [PMID: 36009404 PMCID: PMC9405144 DOI: 10.3390/biomedicines10081857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/22/2022] [Accepted: 07/28/2022] [Indexed: 11/16/2022] Open
Abstract
Endometrial cancer (EC) is the most common gynecologic malignancy, and it arises in the inner part of the uterus. Identification of serum biomarkers is essential for diagnosing the disease at an early stage. In this study, we selected 44 healthy controls and 44 type I EC at tumor stage 1, and we used the Immuno-oncology panel and the Target 96 Oncology III panel to simultaneously detect the levels of 92 cancer-related proteins in serum, using a proximity extension assay. By applying this methodology, we identified 20 proteins, associated with the outcome at binary logistic regression, with a p-value below 0.01 for the first panel and 24 proteins with a p-value below 0.02 for the second one. The final multivariate logistic regression model, combining proteins from the two panels, generated a model with a sensitivity of 97.67% and a specificity of 83.72%. These results support the use of the proposed algorithm after a validation phase.
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Affiliation(s)
- Blendi Ura
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 34137 Trieste, Italy; (V.C.); (M.A.); (G.D.L.); (F.R.); (G.R.); (L.M.)
- Correspondence:
| | - Valeria Capaci
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 34137 Trieste, Italy; (V.C.); (M.A.); (G.D.L.); (F.R.); (G.R.); (L.M.)
| | - Michelangelo Aloisio
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 34137 Trieste, Italy; (V.C.); (M.A.); (G.D.L.); (F.R.); (G.R.); (L.M.)
| | - Giovanni Di Lorenzo
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 34137 Trieste, Italy; (V.C.); (M.A.); (G.D.L.); (F.R.); (G.R.); (L.M.)
| | - Federico Romano
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 34137 Trieste, Italy; (V.C.); (M.A.); (G.D.L.); (F.R.); (G.R.); (L.M.)
| | - Giuseppe Ricci
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 34137 Trieste, Italy; (V.C.); (M.A.); (G.D.L.); (F.R.); (G.R.); (L.M.)
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34129 Trieste, Italy
| | - Lorenzo Monasta
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 34137 Trieste, Italy; (V.C.); (M.A.); (G.D.L.); (F.R.); (G.R.); (L.M.)
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22
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Mendelian randomization study for the roles of IL-18 and IL-1 receptor antagonist in the development of inflammatory bowel disease. Int Immunopharmacol 2022; 110:109020. [PMID: 35843146 DOI: 10.1016/j.intimp.2022.109020] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/17/2022] [Accepted: 06/30/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND AND AIMS IL-1 and IL-18 play important roles in intestine barrier integrity maintenance and inflammatory response. However, their net effects on the risk of IBD are still inconclusive. Here, we used Mendelian randomization (MR) approaches to investigate the causal associations of IL-18 and IL-1Ra (receptor antagonist) on the risks of IBD and subtypes. METHODS For IL-18, both three-sample and two-sample MR approaches were used for the causal inferences. In three-sample MR, three single nucleotide polymorphisms (SNPs) and the effect values were extracted from two quantitative trait loci (pQTL) datasets with non-overlapping populations. In two-sample MR, we extracted genetic instruments information from the same larger pQTL dataset. For IL-1Ra, we applied the two-sample MR method with summary-statistics from the larger pQTL dataset. Summary-level results of three large IBD/CD/UC genome-wide association studies in European ancestry were employed. Inverse-variance weighted method, various sensitivity analyses and meta-analysis were performed to give causal estimates, detect heterogeneity and correct for outliers. RESULTS We observed consistent positive causal effects of IL-18 on all three major outcomes using three-sample MR, with meta-analyses odds ratios (ORs) equal to 1.240 (IBD), 1.199 (CD) and 1.274 (UC) respectively. The two-sample MR demonstrated similar results. Moreover, genetically predicted IL-1Ra is inversely associated with the risk of IBD/UC/CD with ORs equal to 0.915 (IBD), 0.902 (CD) and 0.899 (UC) respectively in meta-analyses. CONCLUSIONS This study suggested genetically predicted IL-18 and IL-1Ra level are causally associated with an increased and decreased risk of IBD and subtypes.
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23
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Elhag DA, Kumar M, Saadaoui M, Akobeng AK, Al-Mudahka F, Elawad M, Al Khodor S. Inflammatory Bowel Disease Treatments and Predictive Biomarkers of Therapeutic Response. Int J Mol Sci 2022; 23:ijms23136966. [PMID: 35805965 PMCID: PMC9266456 DOI: 10.3390/ijms23136966] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/05/2022] [Accepted: 06/06/2022] [Indexed: 02/08/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic immune-mediated inflammation of the gastrointestinal tract with a highly heterogeneous presentation. It has a relapsing and remitting clinical course that necessitates lifelong monitoring and treatment. Although the availability of a variety of effective therapeutic options including immunomodulators and biologics (such as TNF, CAM inhibitors) has led to a paradigm shift in the treatment outcomes and clinical management of IBD patients, some patients still either fail to respond or lose their responsiveness to therapy over time. Therefore, according to the recent Selecting Therapeutic Targets in Inflammatory Bowel Disease (STRIDE-II) recommendations, continuous disease monitoring from symptomatic relief to endoscopic healing along with short- and long-term therapeutic responses are critical for providing IBD patients with a tailored therapy algorithm. Moreover, considering the high unmet need for novel therapeutic approaches for IBD patients, various new modulators of cytokine signaling events (for example, JAK/TYK inhibitors), inhibitors of cytokines (for example IL-12/IL-23, IL-22, IL-36, and IL-6 inhibitors), anti-adhesion and migration strategies (for example, β7 integrin, sphingosine 1-phosphate receptors, and stem cells), as well as microbial-based therapeutics to decolonize the bed buds (for example, fecal microbiota transplantation and bacterial inhibitors) are currently being evaluated in different phases of controlled clinical trials. This review aims to offer a comprehensive overview of available treatment options and emerging therapeutic approaches for IBD patients. Furthermore, predictive biomarkers for monitoring the therapeutic response to different IBD therapies are also discussed.
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Affiliation(s)
- Duaa Ahmed Elhag
- Research Department, Sidra Medicine, Doha 26999, Qatar; (D.A.E.); (M.K.); (M.S.)
| | - Manoj Kumar
- Research Department, Sidra Medicine, Doha 26999, Qatar; (D.A.E.); (M.K.); (M.S.)
| | - Marwa Saadaoui
- Research Department, Sidra Medicine, Doha 26999, Qatar; (D.A.E.); (M.K.); (M.S.)
| | - Anthony K. Akobeng
- Division of Gastroenterology, Hepatology and Nutrition, Sidra Medicine, Doha 26999, Qatar; (A.K.A.); (F.A.-M.); (M.E.)
| | - Fatma Al-Mudahka
- Division of Gastroenterology, Hepatology and Nutrition, Sidra Medicine, Doha 26999, Qatar; (A.K.A.); (F.A.-M.); (M.E.)
| | - Mamoun Elawad
- Division of Gastroenterology, Hepatology and Nutrition, Sidra Medicine, Doha 26999, Qatar; (A.K.A.); (F.A.-M.); (M.E.)
| | - Souhaila Al Khodor
- Research Department, Sidra Medicine, Doha 26999, Qatar; (D.A.E.); (M.K.); (M.S.)
- Correspondence:
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24
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Li Y, Yang X, Yuan JN, Lin R, Tian YY, Li YX, Zhang Y, Wang XF, Xie YH, Wang SW, Zheng XH. Ilex rotunda Thunb Protects Against Dextran Sulfate Sodium-Induced Ulcerative Colitis in Mice by Restoring the Intestinal Mucosal Barrier and Modulating the Oncostatin M/Oncostatin M Receptor Pathway. Front Pharmacol 2022; 13:819826. [PMID: 35645824 PMCID: PMC9140055 DOI: 10.3389/fphar.2022.819826] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 04/26/2022] [Indexed: 11/13/2022] Open
Abstract
Ilex rotunda Thunb (IR) is a traditional Chinese medicine used for the clinical treatment of gastric ulcers and duodenal ulcers; however, the effect of IR on ulcerative colitis (UC) and its underlying mechanism remains unclear. This study investigated the therapeutic effect of IR on UC mice induced by dextran sulfate sodium (DSS) as well as the potential underlying mechanism. The main components of IR were analyzed by ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry. Then we established a model of UC mice by administering 2.0% DSS for 7 days followed by 2 weeks of tap water for three cycles and administered IR. On day 56, the disease activity index (DAI), colon length, pathological changes, and inflammatory response of the colon tissue of mice were assessed. The oxidative stress and apoptosis of colon tissue were detected, and the integrity of the intestinal mucosal barrier was evaluated to assess the effect of IR. Furthermore, the relationship between oncostatin M (OSM) and its receptor (OSMR) in addition to the IR treatment of UC were evaluated using a mouse model and Caco2 cell model. The results showed that IR significantly alleviated the symptoms of UC including rescuing the shortened colon length; reducing DAI scores, serum myeloperoxidase and lipopolysaccharide levels, pathological damage, inflammatory cell infiltration and mRNA levels of interleukin one beta, tumor necrosis factor alpha, and interleukin six in colon tissue; alleviating oxidative stress and apoptosis by decreasing kelch-like ECH-associated protein 1 expression and increasing nuclear factor-erythroid factor 2-related factor 2 and heme oxygenase-1 protein expression; and promoting the regeneration of epithelial cells. IR also promoted the restoration of the intestinal mucosal barrier and modulated the OSM/OSMR pathway to alleviate UC. It was found that IR exerted therapeutic effects on UC by restoring the intestinal mucosal barrier and regulating the OSM/OSMR pathway.
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Affiliation(s)
- Yao Li
- The College of Life Sciences, Northwest University, Xi’an, China
| | - Xu Yang
- The College of Life Sciences, Northwest University, Xi’an, China
| | - Jia-ni Yuan
- Air Force Hospital of Western Theater Command, Chengdu, China
| | - Rui Lin
- Department of Pharmacy, Xijing Hospital, Xi’an, China
| | - Yun-yuan Tian
- Department of Chinese Materia Medica and Natural Medicines, Air Force Medical University, Xi’an, China
| | - Yu-xin Li
- The College of Life Sciences, Northwest University, Xi’an, China
| | - Yan Zhang
- The College of Life Sciences, Northwest University, Xi’an, China
| | - Xu-fang Wang
- The College of Life Sciences, Northwest University, Xi’an, China
| | - Yan-hua Xie
- The College of Life Sciences, Northwest University, Xi’an, China
| | - Si-wang Wang
- The College of Life Sciences, Northwest University, Xi’an, China
| | - Xiao-hui Zheng
- The College of Life Sciences, Northwest University, Xi’an, China
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25
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Scott JI, Mendive-Tapia L, Gordon D, Barth ND, Thompson EJ, Cheng Z, Taggart D, Kitamura T, Bravo-Blas A, Roberts EW, Juarez-Jimenez J, Michel J, Piet B, de Vries IJ, Verdoes M, Dawson J, Carragher NO, Connor RAO, Akram AR, Frame M, Serrels A, Vendrell M. A fluorogenic probe for granzyme B enables in-biopsy evaluation and screening of response to anticancer immunotherapies. Nat Commun 2022; 13:2366. [PMID: 35501326 PMCID: PMC9061857 DOI: 10.1038/s41467-022-29691-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 03/29/2022] [Indexed: 02/06/2023] Open
Abstract
Immunotherapy promotes the attack of cancer cells by the immune system; however, it is difficult to detect early responses before changes in tumor size occur. Here, we report the rational design of a fluorogenic peptide able to detect picomolar concentrations of active granzyme B as a biomarker of immune-mediated anticancer action. Through a series of chemical iterations and molecular dynamics simulations, we synthesize a library of FRET peptides and identify probe H5 with an optimal fit into granzyme B. We demonstrate that probe H5 enables the real-time detection of T cell-mediated anticancer activity in mouse tumors and in tumors from lung cancer patients. Furthermore, we show image-based phenotypic screens, which reveal that the AKT kinase inhibitor AZD5363 shows immune-mediated anticancer activity. The reactivity of probe H5 may enable the monitoring of early responses to anticancer treatments using tissue biopsies.
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Affiliation(s)
- Jamie I Scott
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
| | - Lorena Mendive-Tapia
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
| | - Doireann Gordon
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
| | - Nicole D Barth
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
| | - Emily J Thompson
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
| | - Zhiming Cheng
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
| | - David Taggart
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
| | - Takanori Kitamura
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
| | | | | | - Jordi Juarez-Jimenez
- EaStChem School of Chemistry, Joseph Black Building, The University of Edinburgh, Edinburgh, UK
| | - Julien Michel
- EaStChem School of Chemistry, Joseph Black Building, The University of Edinburgh, Edinburgh, UK
| | - Berber Piet
- Department of Pulmonary Diseases, Radboud University Medical Centre, Nijmegen, Netherlands
| | - I Jolanda de Vries
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Martijn Verdoes
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, Netherlands
| | - John Dawson
- Cancer Research UK Edinburgh Centre, The University of Edinburgh, Edinburgh, UK
| | - Neil O Carragher
- Cancer Research UK Edinburgh Centre, The University of Edinburgh, Edinburgh, UK
| | - Richard A O' Connor
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
| | - Ahsan R Akram
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
| | - Margaret Frame
- Cancer Research UK Edinburgh Centre, The University of Edinburgh, Edinburgh, UK
| | - Alan Serrels
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
| | - Marc Vendrell
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK.
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Plevris N, Lees CW. Disease Monitoring in Inflammatory Bowel Disease: Evolving Principles and Possibilities. Gastroenterology 2022; 162:1456-1475.e1. [PMID: 35101422 DOI: 10.1053/j.gastro.2022.01.024] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/07/2022] [Accepted: 01/18/2022] [Indexed: 02/07/2023]
Abstract
Inflammatory bowel disease is a progressive and debilitating condition. Early and effective treatment using a treat-to-target approach is key to improving patient outcomes. Therefore, proactive monitoring is essential to ensure that treatment strategies are working and targets are being met. In this review we discuss the current monitoring tools available to us and how they can be used. We also discuss the importance of monitoring during key phases of the disease and propose an optimum treat-to-target monitoring strategy for Crohn's disease and ulcerative colitis. Regarding the advent of new technology, we discuss how this may improve our monitoring capabilities and how we envisage future monitoring strategies of inflammatory bowel diseases.
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Affiliation(s)
- Nikolas Plevris
- The Edinburgh IBD Unit, Western General Hospital, Edinburgh, Scotland, United Kingdom; Centre for Genomics and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital Campus, Edinburgh, Scotland, United Kingdom
| | - Charlie W Lees
- The Edinburgh IBD Unit, Western General Hospital, Edinburgh, Scotland, United Kingdom; Centre for Genomics and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital Campus, Edinburgh, Scotland, United Kingdom.
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MEFV and NLRP3 Inflammasome Expression Is Attributed to Immature Macrophages and Correlates with Serum Inflammatory Proteins in Crohn´s Disease Patients. Inflammation 2022; 45:1631-1650. [PMID: 35190924 PMCID: PMC8860375 DOI: 10.1007/s10753-022-01647-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 12/27/2022]
Abstract
Inflammasomes are intracellular protein complexes whose activation results in proinflammatory cytokines. Inflammasomes are implicated in Crohn´s disease (CD) pathogenesis, yet the contribution of inflammasomes in intestinal epithelial cells (IECs) versus lamina propria (LP) macrophages is poorly understood. Whether inflammasome expression in intestinal tissue reflects the serum inflammatory protein profile of patients is also not known. We aimed to determine the intestinal cell types where inflammasome expression is increased in CD and if they correlate with the serum protein profile. RT-PCR and NanoString nCounter technology were used to characterize inflammasome gene expression in CD patients and controls. The mucosa, LP and IEC cell fractions and FACS-sorted cells were analyzed. Proximity extension assay with a 92-protein panel was used to determine the serum inflammatory protein profile. Compositional analysis was used to correlate ileum inflammasome gene expression with intestinal mononuclear phagocyte populations. We show that NLRP3 and MEFV inflammasome sensors and downstream effector expression including IL-1β are increased in inflamed mucosa of IBD patients and correlate with disease activity. Inflammasome gene expression increased with the abundance of immature intestinal macrophages, and increased IL-1β released by CD LP cells correlated with immature macrophage frequency. Inflammasome gene expression was also increased in circulating monocytes, the precursors of immature intestinal macrophages. Finally, the serum inflammatory profile of CD patients correlates with ileal expression of genes related to NLRP3 and MEFV inflammasomes. Overall, we show that MEFV and NLRP3 inflammasome expression in CD intestine is attributed to the accumulation of immature macrophages and correlates with serum inflammatory proteins.
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28
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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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29
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Barron-Millar B, Ogle L, Mells G, Flack S, Badrock J, Sandford R, Kirby J, Palmer J, Jopson L, Brain J, Smith GR, Rushton S, Hegade VS, Jones R, Rushbrook S, Thorburn D, Ryder S, Hirschfield G, Dyson JK, Jones DEJ. The Serum Proteome and Ursodeoxycholic Acid Response in Primary Biliary Cholangitis. Hepatology 2021; 74:3269-3283. [PMID: 34129689 DOI: 10.1002/hep.32011] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 05/20/2021] [Accepted: 05/22/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND AND AIMS Stratified therapy has entered clinical practice in primary biliary cholangitis (PBC), with routine use of second-line therapy in nonresponders to first-line therapy with ursodeoxycholic acid (UDCA). The mechanism for nonresponse to UDCA remains, however, unclear and we lack mechanistic serum markers. The UK-PBC study was established to explore the biological basis of UDCA nonresponse in PBC and identify markers to enhance treatment. APPROACH AND RESULTS Discovery serum proteomics (Olink) with targeted multiplex validation were carried out in 526 subjects from the UK-PBC cohort and 97 healthy controls. In the discovery phase, untreated PBC patients (n = 68) exhibited an inflammatory proteome that is typically reduced in scale, but not resolved, with UDCA therapy (n = 416 treated patients). Nineteen proteins remained at a significant expression level (defined using stringent criteria) in UDCA-treated patients, six of them representing a tightly linked profile of chemokines (including CCL20, known to be released by biliary epithelial cells (BECs) undergoing senescence in PBC). All showed significant differential expression between UDCA responders and nonresponders in both the discovery and validation cohorts. A linear discriminant analysis, using serum levels of C-X-C motif chemokine ligand 11 and C-C motif chemokine ligand 20 as markers of responder status, indicated a high level of discrimination with an AUC of 0.91 (CI, 0.83-0.91). CONCLUSIONS UDCA under-response in PBC is characterized by elevation of serum chemokines potentially related to cellular senescence and was previously shown to be released by BECs in PBC, suggesting a potential role in the pathogenesis of high-risk disease. These also have potential for development as biomarkers for identification of high-risk disease, and their clinical utility as biomarkers should be evaluated further in prospective studies.
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Affiliation(s)
- Ben Barron-Millar
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Laura Ogle
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - George Mells
- Department of Human Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Steven Flack
- Department of Human Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Jonathan Badrock
- Department of Human Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Richard Sandford
- Department of Human Genetics, University of Cambridge, Cambridge, United Kingdom
| | - John Kirby
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Jeremy Palmer
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Laura Jopson
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - John Brain
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Graham R Smith
- Bioinformatics Support Unit (BSU), Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Steve Rushton
- School of Natural and Environmental Science, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | | | - Rebecca Jones
- Liver Unit, St James' Hospital, Leeds, United Kingdom
| | - Simon Rushbrook
- Norfolk and Norwich University Hospital, Norwich, United Kingdom
| | | | - Steve Ryder
- Queen's Medical Centre, Nottingham, United Kingdom
| | - Gideon Hirschfield
- Queen Elizabeth Hospital, Birmingham, United Kingdom
- Toronto Centre for Liver Disease, University of Toronto, Toronto, ON, Canada
| | - Jessica K Dyson
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, United Kingdom
- Freeman Hospital, Newcastle-upon-Tyne, United Kingdom
| | - David E J Jones
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, United Kingdom
- Freeman Hospital, Newcastle-upon-Tyne, United Kingdom
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30
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Arnone D, Vallier M, Hergalant S, Chabot C, Ndiaye NC, Moulin D, Aignatoaei AM, Alberto JM, Louis H, Boulard O, Mayeur C, Dreumont N, Peuker K, Strigli A, Zeissig S, Hansmannel F, Chamaillard M, Kökten T, Peyrin-Biroulet L. Long-Term Overconsumption of Fat and Sugar Causes a Partially Reversible Pre-inflammatory Bowel Disease State. Front Nutr 2021; 8:758518. [PMID: 34869528 PMCID: PMC8637418 DOI: 10.3389/fnut.2021.758518] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 10/22/2021] [Indexed: 12/13/2022] Open
Abstract
Nutrition appears to be an important environmental factor involved in the onset of inflammatory bowel diseases (IBD) through yet poorly understood biological mechanisms. Most studies focused on fat content in high caloric diets, while refined sugars represent up to 40% of caloric intake within industrialized countries and contribute to the growing epidemics of inflammatory diseases. Herein we aim to better understand the impact of a high-fat-high-sucrose diet on intestinal homeostasis in healthy conditions and the subsequent colitis risk. We investigated the early events and the potential reversibility of high caloric diet-induced damage in mice before experimental colitis. C57BL/6 mice were fed with a high-fat or high-fat high-sucrose or control diet before experimental colitis. In healthy mice, a high-fat high-sucrose diet induces a pre-IBD state characterized by gut microbiota dysbiosis with a total depletion of bacteria belonging to Barnesiella that is associated with subclinical endoscopic lesions. An overall down-regulation of the colonic transcriptome converged with broadly decreased immune cell populations in the mesenteric lymph nodes leading to the inability to respond to tissue injury. Such in-vivo effects on microbiome and transcriptome were partially restored when returning to normal chow. Long-term consumption of diet enriched in sucrose and fat predisposes mice to colitis. This enhanced risk is preceded by gut microbiota dysbiosis and transcriptional reprogramming of colonic genes related to IBD. Importantly, diet-induced transcriptome and microbiome disturbances are partially reversible after switching back to normal chow with persistent sequelae that may contribute to IBD predisposition in the general population.
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Affiliation(s)
- Djésia Arnone
- Inserm U1256, Nutrition Genetics and Exposition NGERE, Université de Lorraine, Nancy, France
| | - Marie Vallier
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University and Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Sébastien Hergalant
- Inserm U1256, Nutrition Genetics and Exposition NGERE, Université de Lorraine, Nancy, France
| | - Caroline Chabot
- CHRU-Nancy, Pediatric Hepato-Gastroenterology and Nutrition Unit, Department of Child Medicine and Clinical Genetics, Inserm U1256, Université de Lorraine, Nancy, France
| | - Ndeye Coumba Ndiaye
- Inserm U1256, Nutrition Genetics and Exposition NGERE, Université de Lorraine, Nancy, France
| | - David Moulin
- IMoPA, UMR7365 CNRS-Université de Lorraine, CHRU de Nancy, Contrat d'interface, Nancy, France
| | | | - Jean-Marc Alberto
- Inserm U1256, Nutrition Genetics and Exposition NGERE, Université de Lorraine, Nancy, France
| | - Huguette Louis
- Department Inserm UMRS_1116 DCAC, Université de Lorraine, Nancy, France
- Cytometry Core Facility, UMS2008 IBSLor (CNRS-Université de Lorraine-INSERM), Campus Brabois-Santé, Nancy, France
| | - Olivier Boulard
- Laboratory of Cell Physiology, INSERM U1003, University of Lille, Lille, France
| | - Camille Mayeur
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Natacha Dreumont
- Inserm U1256, Nutrition Genetics and Exposition NGERE, Université de Lorraine, Nancy, France
| | - Kenneth Peuker
- Center for Regenerative Therapies, Technische Universität (TU) Dresden, Dresden, Germany
- Department of Medicine I, University Medical Center Dresden, Technische Universität (TU) Dresden, Dresden, Germany
| | - Anne Strigli
- Center for Regenerative Therapies, Technische Universität (TU) Dresden, Dresden, Germany
- Department of Medicine I, University Medical Center Dresden, Technische Universität (TU) Dresden, Dresden, Germany
| | - Sebastian Zeissig
- Center for Regenerative Therapies, Technische Universität (TU) Dresden, Dresden, Germany
- Department of Medicine I, University Medical Center Dresden, Technische Universität (TU) Dresden, Dresden, Germany
| | - Franck Hansmannel
- Inserm U1256, Nutrition Genetics and Exposition NGERE, Université de Lorraine, Nancy, France
| | | | - Tunay Kökten
- Inserm U1256, Nutrition Genetics and Exposition NGERE, Université de Lorraine, Nancy, France
| | - Laurent Peyrin-Biroulet
- Inserm U1256, Nutrition Genetics and Exposition NGERE, Université de Lorraine, Nancy, France
- Department of Gastroenterology, CHRU-Nancy, Université de Lorraine, Nancy, France
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31
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Bergemalm D, Andersson E, Hultdin J, Eriksson C, Rush ST, Kalla R, Adams AT, Keita ÅV, D'Amato M, Gomollon F, Jahnsen J, Ricanek P, Satsangi J, Repsilber D, Karling P, Halfvarson J. Systemic Inflammation in Preclinical Ulcerative Colitis. Gastroenterology 2021; 161:1526-1539.e9. [PMID: 34298022 DOI: 10.1053/j.gastro.2021.07.026] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 07/12/2021] [Accepted: 07/12/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Preclinical ulcerative colitis is poorly defined. We aimed to characterize the preclinical systemic inflammation in ulcerative colitis, using a comprehensive set of proteins. METHODS We obtained plasma samples biobanked from individuals who developed ulcerative colitis later in life (n = 72) and matched healthy controls (n = 140) within a population-based screening cohort. We measured 92 proteins related to inflammation using a proximity extension assay. The biologic relevance of these findings was validated in an inception cohort of patients with ulcerative colitis (n = 101) and healthy controls (n = 50). To examine the influence of genetic and environmental factors on these markers, a cohort of healthy twin siblings of patients with ulcerative colitis (n = 41) and matched healthy controls (n = 37) were explored. RESULTS Six proteins (MMP10, CXCL9, CCL11, SLAMF1, CXCL11 and MCP-1) were up-regulated (P < .05) in preclinical ulcerative colitis compared with controls based on both univariate and multivariable models. Ingenuity Pathway Analyses identified several potential key regulators, including interleukin-1β, tumor necrosis factor, interferon-gamma, oncostatin M, nuclear factor-κB, interleukin-6, and interleukin-4. For validation, we built a multivariable model to predict disease in the inception cohort. The model discriminated treatment-naïve patients with ulcerative colitis from controls with leave-one-out cross-validation (area under the curve = 0.92). Consistently, MMP10, CXCL9, CXCL11, and MCP-1, but not CCL11 and SLAMF1, were significantly up-regulated among the healthy twin siblings, even though their relative abundances seemed higher in incident ulcerative colitis. CONCLUSIONS A set of inflammatory proteins are up-regulated several years before a diagnosis of ulcerative colitis. These proteins were highly predictive of an ulcerative colitis diagnosis, and some seemed to be up-regulated already at exposure to genetic and environmental risk factors.
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Affiliation(s)
- Daniel Bergemalm
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
| | - Erik Andersson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Johan Hultdin
- Department of Medical Biosciences, Division of Clinical Chemistry, Umeå University, Umeå, Sweden
| | - Carl Eriksson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Stephen T Rush
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Rahul Kalla
- Medical Research Council Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Alex T Adams
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Åsa V Keita
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Mauro D'Amato
- CIC bioGUNE Basque Research and Technology Alliance and Basque Science Foundation, Bilbao, Spain; Division of Clinical Epidemiology, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Fernando Gomollon
- Hospital Clinico Universitario Lozano Blesa, IIS Aragón, Zaragoza, Spain
| | - Jørgen Jahnsen
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | - Petr Ricanek
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
| | - Jack Satsangi
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom; Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Dirk Repsilber
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Pontus Karling
- Department of Public Health and Clinical Medicine, Division of Medicine, Umeå University, Umeå, Sweden
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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32
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Wik L, Nordberg N, Broberg J, Björkesten J, Assarsson E, Henriksson S, Grundberg I, Pettersson E, Westerberg C, Liljeroth E, Falck A, Lundberg M. Proximity Extension Assay in Combination with Next-Generation Sequencing for High-throughput Proteome-wide Analysis. Mol Cell Proteomics 2021; 20:100168. [PMID: 34715355 PMCID: PMC8633680 DOI: 10.1016/j.mcpro.2021.100168] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 10/14/2021] [Accepted: 10/21/2021] [Indexed: 01/21/2023] Open
Abstract
Understanding the dynamics of the human proteome is crucial for developing biomarkers to be used as measurable indicators for disease severity and progression, patient stratification, and drug development. The Proximity Extension Assay (PEA) is a technology that translates protein information into actionable knowledge by linking protein-specific antibodies to DNA-encoded tags. In this report we demonstrate how we have combined the unique PEA technology with an innovative and automated sample preparation and high-throughput sequencing readout enabling parallel measurement of nearly 1500 proteins in 96 samples generating close to 150,000 data points per run. This advancement will have a major impact on the discovery of new biomarkers for disease prediction and prognosis and contribute to the development of the rapidly evolving fields of wellness monitoring and precision medicine.
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33
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Correa Rojo A, Heylen D, Aerts J, Thas O, Hooyberghs J, Ertaylan G, Valkenborg D. Towards Building a Quantitative Proteomics Toolbox in Precision Medicine: A Mini-Review. Front Physiol 2021; 12:723510. [PMID: 34512391 PMCID: PMC8427610 DOI: 10.3389/fphys.2021.723510] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/05/2021] [Indexed: 12/26/2022] Open
Abstract
Precision medicine as a framework for disease diagnosis, treatment, and prevention at the molecular level has entered clinical practice. From the start, genetics has been an indispensable tool to understand and stratify the biology of chronic and complex diseases in precision medicine. However, with the advances in biomedical and omics technologies, quantitative proteomics is emerging as a powerful technology complementing genetics. Quantitative proteomics provide insight about the dynamic behaviour of proteins as they represent intermediate phenotypes. They provide direct biological insights into physiological patterns, while genetics accounting for baseline characteristics. Additionally, it opens a wide range of applications in clinical diagnostics, treatment stratification, and drug discovery. In this mini-review, we discuss the current status of quantitative proteomics in precision medicine including the available technologies and common methods to analyze quantitative proteomics data. Furthermore, we highlight the current challenges to put quantitative proteomics into clinical settings and provide a perspective to integrate proteomics data with genomics data for future applications in precision medicine.
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Affiliation(s)
- Alejandro Correa Rojo
- Data Science Institute, Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Hasselt University, Diepenbeek, Belgium.,Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Dries Heylen
- Data Science Institute, Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Hasselt University, Diepenbeek, Belgium.,Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Jan Aerts
- Data Science Institute, Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Hasselt University, Diepenbeek, Belgium
| | - Olivier Thas
- Data Science Institute, Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Hasselt University, Diepenbeek, Belgium.,Department of Applied Mathematics, Computer Science and Statistics, Faculty of Sciences, Ghent University, Ghent, Belgium.,National Institute for Applied Statistics Research Australia (NIASRA), Wollongong, NSW, Australia
| | - Jef Hooyberghs
- Flemish Institute for Technological Research (VITO), Mol, Belgium.,Theoretical Physics, Data Science Institute, Hasselt University, Diepenbeek, Belgium
| | - Gökhan Ertaylan
- Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Dirk Valkenborg
- Data Science Institute, Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Hasselt University, Diepenbeek, Belgium
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34
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Giachero F, Jenke A, Zilbauer M. Improving prediction of disease outcome for inflammatory bowel disease: progress through systems medicine. Expert Rev Clin Immunol 2021; 17:871-881. [PMID: 34142929 PMCID: PMC8903817 DOI: 10.1080/1744666x.2021.1945442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/08/2021] [Indexed: 11/30/2022]
Abstract
Introduction: Inflammatory bowel diseases (IBDs) are lifelong conditions causing relapsing inflammation of the intestine. In the absence of a cure, clinical management of IBDs is extremely challenging since they present with a wide range of phenotypes and disease behaviors. Hence, there is an urgent need for markers that could guide physicians in making the right choice of the rapidly growing treatment options toward a personalized care that could improve the overall outcome.Areas covered: In this review, the authors summarize existing biomarkers in IBD, discuss the challenges with the development of prognostic biomarkers and propose alternative options such as focusing on the prediction of the response to individual treatments, i.e. predictive biomarkers. The problems related to developing disease prognostic and predictive biomarkers in the field of IBDs are discussed including the difficulties in dealing with phenotypic heterogeneity particularly when performing studies in a real-life setting. The authors reviewed literature from PubMed.Expert opinion: Systems biology provides potential solutions to this problem by offering an unbiased, holistic approach to adjusting for variation in larger datasets thereby increasing the chances of identifying true associations between molecular profiles and clinical phenotypes.
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Affiliation(s)
- Federica Giachero
- Witten/Herdecke University, Faculty of Health, Department of Medicine, Clinical Molecular Genetics and Epigenetics, Centre for Biomedical Education & Research (ZBAF), Germany
| | - Andreas Jenke
- Witten/Herdecke University, Faculty of Health, Department of Medicine, Clinical Molecular Genetics and Epigenetics, Centre for Biomedical Education & Research (ZBAF), Germany
- Children´s Hospital Kassel, Department of Neonatology and Paediatric Gastroenterology, Klinikum Kassel, Mönchenbergstr, Kassel, Germany
| | - Matthias Zilbauer
- Witten/Herdecke University, Faculty of Health, Department of Medicine, Clinical Molecular Genetics and Epigenetics, Centre for Biomedical Education & Research (ZBAF), Germany
- Department of Paediatrics, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge, University Hospitals, Addenbrooke’s, Cambridge, UK
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Atreya R, Neurath MF. Can Serum Proteomic Profiling Annunciate Individual Disease Progression in Newly Diagnosed Inflammatory Bowel Disease Patients? J Crohns Colitis 2021; 15:697-698. [PMID: 33677523 DOI: 10.1093/ecco-jcc/jjab009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Raja Atreya
- Department of Medicine 1, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.,Deutsches Zentrum Immuntherapie [DZI], Erlangen, Germany
| | - Markus F Neurath
- Department of Medicine 1, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.,Deutsches Zentrum Immuntherapie [DZI], Erlangen, Germany
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Serum biomarkers confirming stable remission in inflammatory bowel disease. Sci Rep 2021; 11:6690. [PMID: 33758351 PMCID: PMC7988138 DOI: 10.1038/s41598-021-86251-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 03/11/2021] [Indexed: 12/15/2022] Open
Abstract
Crohn's disease (CD) and ulcerative colitis (UC) have a chronic-remittent course. Optimal management of inflammatory bowel diseases (IBD) relies on early intervention, treat-to-target strategies and a tight disease control. However, it is challenging to assess the risk of relapses in individual patients. We investigated blood-based biomarkers for the confirmation of disease remission in patients with IBD. We retrospectively analyzed samples of 40 IBD patients (30 UC, 10 CD) enrolled in a tight-control follow-up study. Half of the patients had a flare during follow up. Serum was analyzed for S100A12 as well as S100A8/A9 and for 50 further biomarkers in a bead-based multiplex assay. The concentrations of 9 cytokines/chemokines and S100A8/A9 significantly differed in IBD patients with unstable remission (before flares) when compared to IBD patients with stable remission. Although the number of patients was small, ROC curve analyses revealed a number of biomarkers (IL-1β, IL-1RA, IL-8, IL13, IL-15, IL-21, IL-25, IFN-β, CXCL9, CXCL10, CXCL11, Galectin-1, G-CSF and S100A8/A9) that were elevated in patients with later occurring relapses. While earlier studies on peripheral biomarkers in IBD are limited to only few analytes, our study using a broad screening approach identified serum biomarkers with the potential to indicate unstable disease control in IBD, which may help to steer individual therapies to maintain remission.
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