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Satsangi J, Nowak J, Kalla R, Colombel JF. Treatment strategies and biomarkers in Crohn's disease: the PROFILE trial. Lancet Gastroenterol Hepatol 2024; 9:591-592. [PMID: 38870964 DOI: 10.1016/s2468-1253(24)00082-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 06/15/2024]
Affiliation(s)
- Jack Satsangi
- Translational Gastroenterology and Liver Unit, Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DU, UK.
| | - Jan Nowak
- Poznan University of Medical Sciences, Poznan, Poland
| | - Rahul Kalla
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
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Chen R, Zhang S. Treatment strategies and biomarkers in Crohn's disease: the PROFILE trial. Lancet Gastroenterol Hepatol 2024; 9:592. [PMID: 38870967 DOI: 10.1016/s2468-1253(24)00077-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 03/04/2024] [Indexed: 06/15/2024]
Affiliation(s)
- Rirong Chen
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510060, China
| | - Shenghong Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510060, China; Guangxi Hospital Division of The First Affiliated Hospital, Sun Yat-sen University, Nanning, China.
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Syed AH, Abujabal HAS, Ahmad S, Malebary SJ, Alromema N. Advances in Inflammatory Bowel Disease Diagnostics: Machine Learning and Genomic Profiling Reveal Key Biomarkers for Early Detection. Diagnostics (Basel) 2024; 14:1182. [PMID: 38893707 PMCID: PMC11172026 DOI: 10.3390/diagnostics14111182] [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: 04/25/2024] [Revised: 05/25/2024] [Accepted: 06/01/2024] [Indexed: 06/21/2024] Open
Abstract
This study, utilizing high-throughput technologies and Machine Learning (ML), has identified gene biomarkers and molecular signatures in Inflammatory Bowel Disease (IBD). We could identify significant upregulated or downregulated genes in IBD patients by comparing gene expression levels in colonic specimens from 172 IBD patients and 22 healthy individuals using the GSE75214 microarray dataset. Our ML techniques and feature selection methods revealed six Differentially Expressed Gene (DEG) biomarkers (VWF, IL1RL1, DENND2B, MMP14, NAAA, and PANK1) with strong diagnostic potential for IBD. The Random Forest (RF) model demonstrated exceptional performance, with accuracy, F1-score, and AUC values exceeding 0.98. Our findings were rigorously validated with independent datasets (GSE36807 and GSE10616), further bolstering their credibility and showing favorable performance metrics (accuracy: 0.841, F1-score: 0.734, AUC: 0.887). Our functional annotation and pathway enrichment analysis provided insights into crucial pathways associated with these dysregulated genes. DENND2B and PANK1 were identified as novel IBD biomarkers, advancing our understanding of the disease. The validation in independent cohorts enhances the reliability of these findings and underscores their potential for early detection and personalized treatment of IBD. Further exploration of these genes is necessary to fully comprehend their roles in IBD pathogenesis and develop improved diagnostic tools and therapies. This study significantly contributes to IBD research with valuable insights, potentially greatly enhancing patient care.
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Affiliation(s)
- Asif Hassan Syed
- Department of Computer Science, Faculty of Computing and Information Technology-Rabigh, King Abdulaziz University, Jeddah 22254, Saudi Arabia;
| | - Hamza Ali S. Abujabal
- Department of Mathematics, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia;
| | - Shakeel Ahmad
- Department of Computer Science, Faculty of Computing and Information Technology-Rabigh, King Abdulaziz University, Jeddah 22254, Saudi Arabia;
| | - Sharaf J. Malebary
- Department of Information Technology, Faculty of Computing and Information Technology-Rabigh, King Abdulaziz University, P.O. Box 344, Rabigh 21911, Saudi Arabia;
| | - Nashwan Alromema
- Department of Computer Science, Faculty of Computing and Information Technology-Rabigh, King Abdulaziz University, P.O. Box 344, Rabigh 21911, Saudi Arabia;
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Allegretti JR, Bordeianou LG, Damas OM, Eisenstein S, Greywoode R, Minar P, Singh S, Harmon S, Lisansky E, Malone-King M, Litwin NS, Weaver A, Heller CA, Moss AC, Adler J. Challenges in IBD Research 2024: Pragmatic Clinical Research. Inflamm Bowel Dis 2024; 30:S55-S66. [PMID: 38778623 DOI: 10.1093/ibd/izae083] [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
Pragmatic clinical research is 1 of the 5 focus areas of the Challenges in IBD Research 2024, a multidisciplinary effort by scientists, clinicians, patients, and funders to identify priorities for patient-centric research. This summary provides a comprehensive overview of current gaps in inflammatory bowel disease (IBD) clinical research and actionable approaches to address them. This review is focused on identifying research that is needed to achieve the best outcomes for patients in clinical practice. Research gaps include understanding the needs of understudied patient groups and addressing barriers to care so all patients receive optimal care, validating and using biomarkers to enable early diagnosis and result in better outcomes for adults and children with IBD, and determining the optimal sequencing of treatments (medical, surgical, adjunct) in children and adults. Inclusive pragmatic research is needed to address these gaps and lead to improvements in patient care and outcomes for all populations of patients with IBD.
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Affiliation(s)
- Jessica R Allegretti
- Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women's Hospital, Boston, MA, USA
| | - Liliana G Bordeianou
- Department of General and Gastrointestinal Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Oriana M Damas
- Division of Gastroenterology, Department of Medicine, University of Miami Leonard Miller School of Medicine, Miami, FL, USA
| | - Samuel Eisenstein
- Division of Colon and Rectal Surgery, Department of Surgery, University of California San Diego, La Jolla, CA, USA
| | - Ruby Greywoode
- Division of Gastroenterology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Phillip Minar
- Division of Gastroenterology, Hepatology, and Nutrition, Cleveland Clinic, Cleveland, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Siddharth Singh
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sabrina Harmon
- Division of Gastroenterology, Hepatology, and Nutrition, Cleveland Clinic, Cleveland, OH, USA
| | - Eugene Lisansky
- Patient representative for Crohn's & Colitis Foundation, New York, NY, USA
| | - Myisha Malone-King
- Division of Gastroenterology, Hepatology, and Nutrition, Cleveland Clinic, Cleveland, OH, USA
| | | | | | | | - Alan C Moss
- Crohn's & Colitis Foundation, New York, NY, USA
| | - Jeremy Adler
- Susan B. Meister Child Health Evaluation and Research Center and Division of Pediatric Gastroenterology, C.S. Mott Children's Hospital, Michigan Medicine, Ann Arbor, MI, USA
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Clough J, Colwill M, Poullis A, Pollok R, Patel K, Honap S. Biomarkers in inflammatory bowel disease: a practical guide. Therap Adv Gastroenterol 2024; 17:17562848241251600. [PMID: 38737913 PMCID: PMC11085009 DOI: 10.1177/17562848241251600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 04/12/2024] [Indexed: 05/14/2024] Open
Abstract
Inflammatory bowel disease (IBD), comprising ulcerative colitis (UC) and Crohn's disease (CD), is a costly condition in terms of morbidity and healthcare utilization, with an increasing prevalence now approaching 1% in the Western world. Endoscopic assessment of IBD remains the gold standard for diagnosis, evaluation of treatment response and determination of post-operative recurrence, but is expensive and invasive. Biomarkers can facilitate non-invasive disease assessment, with C-reactive protein and faecal calprotectin as the most widely available biomarkers in current clinical practice. This narrative review summarizes the evidence for their use in both UC and CD and offers practical guidance for healthcare providers taking into account the limitations of biomarker interpretation. We present evidence for the future use of novel biomarkers in IBD and discuss how biomarker discovery could deliver the goal of precision medicine in IBD.
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Affiliation(s)
- Jennie Clough
- St George’s University Hospitals NHS Foundation Trust, London, UK
- School of Immunology and Microbial Sciences, King’s College London, London, UK
| | - Michael Colwill
- St George’s University Hospitals NHS Foundation Trust, London, UK
| | - Andrew Poullis
- St George’s University Hospitals NHS Foundation Trust, London, UK
| | - Richard Pollok
- St George’s University Hospital NHS Foundation Trust
- Institute of Infection and Immunity, St George’s University, London, UK
| | - Kamal Patel
- St George’s University Hospitals NHS Foundation Trust, London, UK
| | - Sailish Honap
- St George’s University Hospitals NHS Foundation Trust, London, UK
- School of Immunology and Microbial Sciences, King’s College London, London, UK
- INFINY Institute, Nancy University Hospital, Vandœuvre-lès-Nancy, France
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Noor NM, Lee JC, Bond S, Dowling F, Brezina B, Patel KV, Ahmad T, Banim PJ, Berrill JW, Cooney R, De La Revilla Negro J, de Silva S, Din S, Durai D, Gordon JN, Irving PM, Johnson M, Kent AJ, Kok KB, Moran GW, Mowat C, Patel P, Probert CS, Raine T, Saich R, Seward A, Sharpstone D, Smith MA, Subramanian S, Upponi SS, Wiles A, Williams HRT, van den Brink GR, Vermeire S, Jairath V, D'Haens GR, McKinney EF, Lyons PA, Lindsay JO, Kennedy NA, Smith KGC, Parkes M. A biomarker-stratified comparison of top-down versus accelerated step-up treatment strategies for patients with newly diagnosed Crohn's disease (PROFILE): a multicentre, open-label randomised controlled trial. Lancet Gastroenterol Hepatol 2024; 9:415-427. [PMID: 38402895 PMCID: PMC11001594 DOI: 10.1016/s2468-1253(24)00034-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 02/27/2024]
Abstract
BACKGROUND Management strategies and clinical outcomes vary substantially in patients newly diagnosed with Crohn's disease. We evaluated the use of a putative prognostic biomarker to guide therapy by assessing outcomes in patients randomised to either top-down (ie, early combined immunosuppression with infliximab and immunomodulator) or accelerated step-up (conventional) treatment strategies. METHODS PROFILE (PRedicting Outcomes For Crohn's disease using a moLecular biomarker) was a multicentre, open-label, biomarker-stratified, randomised controlled trial that enrolled adults with newly diagnosed active Crohn's disease (Harvey-Bradshaw Index ≥7, either elevated C-reactive protein or faecal calprotectin or both, and endoscopic evidence of active inflammation). Potential participants had blood drawn to be tested for a prognostic biomarker derived from T-cell transcriptional signatures (PredictSURE-IBD assay). Following testing, patients were randomly assigned, via a secure online platform, to top-down or accelerated step-up treatment stratified by biomarker subgroup (IBDhi or IBDlo), endoscopic inflammation (mild, moderate, or severe), and extent (colonic or other). Blinding to biomarker status was maintained throughout the trial. The primary endpoint was sustained steroid-free and surgery-free remission to week 48. Remission was defined by a composite of symptoms and inflammatory markers at all visits. Flare required active symptoms (HBI ≥5) plus raised inflammatory markers (CRP >upper limit of normal or faecal calprotectin ≥200 μg/g, or both), while remission was the converse-ie, quiescent symptoms (HBI <5) or resolved inflammatory markers (both CRP ≤ the upper limit of normal and calprotectin <200 μg/g) or both. Analyses were done in the full analysis (intention-to-treat) population. The trial has completed and is registered (ISRCTN11808228). FINDINGS Between Dec 29, 2017, and Jan 5, 2022, 386 patients (mean age 33·6 years [SD 13·2]; 179 [46%] female, 207 [54%] male) were randomised: 193 to the top-down group and 193 to the accelerated step-up group. Median time from diagnosis to trial enrolment was 12 days (range 0-191). Primary outcome data were available for 379 participants (189 in the top-down group; 190 in the accelerated step-up group). There was no biomarker-treatment interaction effect (absolute difference 1 percentage points, 95% CI -15 to 15; p=0·944). Sustained steroid-free and surgery-free remission was significantly more frequent in the top-down group than in the accelerated step-up group (149 [79%] of 189 patients vs 29 [15%] of 190 patients, absolute difference 64 percentage points, 95% CI 57 to 72; p<0·0001). There were fewer adverse events (including disease flares) and serious adverse events in the top-down group than in the accelerated step-up group (adverse events: 168 vs 315; serious adverse events: 15 vs 42), with fewer complications requiring abdominal surgery (one vs ten) and no difference in serious infections (three vs eight). INTERPRETATION Top-down treatment with combination infliximab plus immunomodulator achieved substantially better outcomes at 1 year than accelerated step-up treatment. The biomarker did not show clinical utility. Top-down treatment should be considered standard of care for patients with newly diagnosed active Crohn's disease. FUNDING Wellcome and PredictImmune Ltd.
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Affiliation(s)
- Nurulamin M Noor
- Department of Gastroenterology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - James C Lee
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London, UK; Department of Gastroenterology, UCL Institute of Liver and Digestive Diseases, Royal Free Hospital, London, UK
| | - Simon Bond
- Cambridge Clinical Trials Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Medical Research Council Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Francis Dowling
- Cambridge Clinical Trials Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Biljana Brezina
- Department of Gastroenterology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Kamal V Patel
- Department of Gastroenterology, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Tariq Ahmad
- Department of Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK; Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Paul J Banim
- Department of Gastroenterology, James Paget University Hospital, Great Yarmouth, UK
| | - James W Berrill
- Department of Gastroenterology, Royal Glamorgan Hospital, Llantrisant, UK
| | - Rachel Cooney
- GI Unit, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Juan De La Revilla Negro
- Department of Gastroenterology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Shanika de Silva
- Department of Gastroenterology, The Dudley Group NHS Foundation Trust, Dudley, UK
| | - Shahida Din
- Edinburgh IBD Unit, Western General Hospital, Edinburgh, UK
| | - Dharmaraj Durai
- Department of Gastroenterology, Cardiff and Vale University Health Board, University Hospital of Wales, Cardiff, UK
| | - John N Gordon
- Department of Gastroenterology, Royal Hampshire County Hospital, Winchester, UK
| | - Peter M Irving
- Department of Gastroenterology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Matthew Johnson
- Gastroenterology Department, Luton and Dunstable University Hospital, Luton, UK
| | - Alexandra J Kent
- Department of Gastroenterology, King's College Hospital NHS Foundation Trust, London, UK
| | - Klaartje B Kok
- Department of Gastroenterology, Royal London Hospital, Barts Health NHS Trust, London, UK
| | - Gordon W Moran
- National Institute of Health Research Nottingham Biomedical Research Centre, University of Nottingham and Nottingham University Hospitals, Nottingham, UK
| | - Craig Mowat
- Department of Gastroenterology, Ninewells Hospital, Dundee, Scotland, UK
| | - Pritash Patel
- Department of Gastroenterology, Epsom and St Helier University Hospitals, Carshalton, UK
| | - Chris S Probert
- Department of Gastroenterology, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK; Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Tim Raine
- Department of Gastroenterology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Rebecca Saich
- Department of Gastroenterology, Basingstoke and North Hampshire Hospital, Basingstoke, UK
| | - Abigail Seward
- Department of Gastroenterology, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Dan Sharpstone
- Department of Gastroenterology, West Suffolk NHS Foundation Trust, Bury St Edmunds, UK
| | - Melissa A Smith
- Department of Gastroenterology, University Hospitals Sussex NHS Foundation Trust, Brighton, UK
| | - Sreedhar Subramanian
- Department of Gastroenterology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Sara S Upponi
- Department of Radiology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Alan Wiles
- Department of Gastroenterology, The Queen Elizabeth Hospital King's Lynn NHS Trust, King's Lynn, UK
| | - Horace R T Williams
- Department of Gastroenterology, Imperial College Healthcare NHS Trust, St Mary's Hospital, London, UK
| | | | - Séverine Vermeire
- Department of Gastroenterology and Hepatology, Department of Chronic Diseases and Metabolism, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Vipul Jairath
- Division of Gastroenterology, Department of Medicine, Western University, London, Ontario, Canada
| | - Geert R D'Haens
- Department of Gastroenterology, Amsterdam University Medical Center, Amsterdam, Netherlands
| | - Eoin F McKinney
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK; PredictImmune Ltd, Babraham Research Campus, Cambridge, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Paul A Lyons
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK; PredictImmune Ltd, Babraham Research Campus, Cambridge, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - James O Lindsay
- Department of Gastroenterology, Royal London Hospital, Barts Health NHS Trust, London, UK
| | - Nicholas A Kennedy
- Department of Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK; Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Kenneth G C Smith
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK; PredictImmune Ltd, Babraham Research Campus, Cambridge, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Miles Parkes
- Department of Gastroenterology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK.
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Zhang R, Trotter PB, McCaffrey J, Fitzroy R, Trivioli G, Stewart BJ, Ferdinand JR, Loudon KW, Riding A, West J, Ferro A, Clatworthy MR. Assessment of biological organ age using molecular pathology in pre-transplant kidney biopsies. Kidney Int 2024:S0085-2538(24)00311-9. [PMID: 38692408 DOI: 10.1016/j.kint.2024.03.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 01/21/2024] [Accepted: 03/18/2024] [Indexed: 05/03/2024]
Abstract
Organ shortage is a major challenge in kidney transplantation but the use of older donors, often with co-morbidities, is hampered by inconsistent outcomes. Methods of accurately stratifying marginal donor organs by clinical and histological assessment are lacking. To better understand organ variability, we profiled the transcriptomes of 271 kidneys from deceased donors at retrieval. Following correction for biopsy composition, we assessed molecular pathways that associated with delayed, and sub-optimal one-year graft function. Analysis of cortical biopsies identified an adaptive immune gene-rich module that significantly associated with increasing age and worse outcomes. Cellular deconvolution using human kidney reference single cell transcriptomes confirmed an increase in kidney-specific B and T cell signatures, as well as kidney macrophage, myofibroblast and fibroblast gene sets in this module. Surprisingly, innate immune pathway and neutrophil gene signature enrichment was associated with better outcomes. Thus, our work uncovers cellular molecular features of pathological organ ageing, identifiable at kidney retrieval, with translational potential.
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Affiliation(s)
- Roy Zhang
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Patrick B Trotter
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - James McCaffrey
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK; Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Rory Fitzroy
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Giorgio Trivioli
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Benjamin J Stewart
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK; Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - John R Ferdinand
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Kevin W Loudon
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Alexandra Riding
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Jonathan West
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Ashley Ferro
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Menna R Clatworthy
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK; Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK.
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Kruis W, Bokemeyer B, Jessen P, Hoesl M, Mroß M, Morgenstern J, Reimers B, Müller-Grage N, Leifeld L. Prospective Evaluation of the Prediction Score for a Mild Course of Crohn's Disease (PreMiCC) in Newly Diagnosed Patients With Crohn's Disease: The PROGNOS Study. Inflamm Bowel Dis 2024:izae086. [PMID: 38648264 DOI: 10.1093/ibd/izae086] [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: 10/22/2023] [Indexed: 04/25/2024]
Abstract
BACKGROUND AND AIMS The course of Crohn's disease (CD) is highly variable. The Prospektive Evaluation eines Score zur Vorhersage eines milden Verlaufsbei neu diagnostizierten Morbus Crohn-Patienten in gastroenterologischen Fachpraxen (PROGNOS) study aimed to determine the frequency of a mild disease course and validate a proposed prediction score. METHODS The PROGNOS study is a prospective study of CD patients who were newly diagnosed and, except for 1 course of 5-aminosalicylic acid or steroids for ≤10 days, therapy-naïve. Among other predefined inclusion criteria, the initial diagnosis had to be made ≤6 weeks before enrollment. All inception cohort patients were diagnosed and screened consecutively in participating gastroenterology practices in Germany specialized in inflammatory bowel disease. All screened CD patients were scored and, if possible, included in the study for up to 5 years (NCT02193048). RESULTS A total of 201 CD patients were included in the study (43.3% male; mean age 33 years, mean follow-up 38 months). Altogether, 29.5% of the patients had a mild course at 36 months. Among those with a score ≤2, therapy escalation at 36 months was necessary for only 24.2%, whereas in the group with a score >2, therapy escalation was necessary for 70.2% of patients. In the Kaplan-Meier curve showing time to therapy escalation in the 2 groups, there was a pronounced and statistically significant divergence of the curves starting at 3 months and extending to 48 months (P < .001). CONCLUSIONS In this prospective study, about 30% of incident CD patients had a mild disease course. Our suggested PreMiCC (prediction score for a mild course of Crohn's disease) successfully predicted this.
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Affiliation(s)
- Wolfgang Kruis
- Internal Medicine, Protestant Hospital, Cologne, Germany
| | - Bernd Bokemeyer
- Department of Internal Medicine, Interdisciplinary Crohn Colitis Centre, Minden, Germany
- Clinic of General Internal Medicine I, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Petra Jessen
- Gastroenterology Practice, Kiel-Altenholz, Germany
| | - Mark Hoesl
- Gastroenterology Practice Clinic, Nuremberg, Germany
| | | | | | - Birgitta Reimers
- Department of Internal Medicine, Ferring Arzneimittel GmbH, Kiel, Germany
| | - Nike Müller-Grage
- Department of Internal Medicine, Ferring Arzneimittel GmbH, Kiel, Germany
| | - Ludger Leifeld
- Department of Internal Medicine, St. Bernward Hospital, Hildesheim, Germany
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9
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Storan D, McDermott E, Moloney J, Keenan L, Stack R, Sheridan J, Doherty G, Cullen G, McHugh L, Mulcahy HE. Inflammatory Bowel Disease Disability Index is a valid and reliable measure of disability in an English-speaking hospital practice and predicts long-term requirement for treatment escalation. Frontline Gastroenterol 2024; 15:130-136. [PMID: 38486665 PMCID: PMC10935531 DOI: 10.1136/flgastro-2023-102428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 10/24/2023] [Indexed: 03/17/2024] Open
Abstract
Objective The Inflammatory Bowel Disease Disability Index (IBD-DI) was developed according to WHO standards and has been validated in population-based cohorts. However, there are limited data on its relationship to various psychosocial and economic variables or its relevance to hospital clinical practice. The study aims were to determine the validity and reliability of the IBD-DI in an English-speaking hospital out-patient population and to evaluate its association with short and long-term disease activity. Design/Methods 329 subjects were enrolled in a cross-sectional and longitudinal study assessing the IBD-DI and a range of quality of life, work impairment, depression, anxiety, body image, interpersonal, self-esteem, disease activity, symptom scoring scales in addition to long-term outcome. Results The IBD-DI had adequate structure, was internally consistent and demonstrated convergent and predictive validity and was reliable in test-retest study. Disability was related to female sex (p=0.002), antidepressant use (p<0.001), steroid use (p<0.001) and disease activity (p<0.001). Higher IBD-DI scores were associated with long-term disease activity and need for treatment escalation in univariate (p<0.001) and multivariate (p=0.002) analyses. Conclusion The IBD-DI is a valid and reliable measure of disability in English-speaking hospital populations and predicts long-term requirement for treatment escalation.
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Affiliation(s)
- Darragh Storan
- Department of Gastroenterology, Saint Vincent's University Hospital, Dublin, Ireland
| | - Edel McDermott
- Department of Gastroenterology, Saint Vincent's University Hospital, Dublin, Ireland
| | - Jenny Moloney
- Department of Gastroenterology, St Luke’s Hospital, Kilkenny, Ireland
| | - Lisa Keenan
- School of Psychology, University College Dublin, Dublin, Ireland
| | - Roisin Stack
- Department of Gastroenterology, Saint Vincent's University Hospital, Dublin, Ireland
- Department of Gastroenterology, St Luke’s Hospital, Kilkenny, Ireland
| | - Juliette Sheridan
- Department of Gastroenterology, Saint Vincent's University Hospital, Dublin, Ireland
| | - Glen Doherty
- Department of Gastroenterology, Saint Vincent's University Hospital, Dublin, Ireland
| | - Garret Cullen
- Department of Gastroenterology, Saint Vincent's University Hospital, Dublin, Ireland
| | - Louise McHugh
- School of Psychology, University College Dublin, Dublin, Ireland
| | - Hugh E Mulcahy
- Department of Gastroenterology, Saint Vincent's University Hospital, Dublin, Ireland
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10
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Wacker EM, Uellendahl-Werth F, Bej S, Wolkenhauer O, Vesterhus M, Lieb W, Franke A, Karlsen TH, Folseraas T, Ellinghaus D. Whole blood RNA sequencing identifies transcriptional differences between primary sclerosing cholangitis and ulcerative colitis. JHEP Rep 2024; 6:100988. [PMID: 38304234 PMCID: PMC10832281 DOI: 10.1016/j.jhepr.2023.100988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 11/10/2023] [Accepted: 12/06/2023] [Indexed: 02/03/2024] Open
Abstract
Background & Aims Genetic and microbiome studies across patients with primary sclerosing cholangitis (PSC) and ulcerative colitis (UC) have indicated that UC in PSC is a separate disease entity to primary UC, but expression studies for PSC are lacking. Methods We conducted whole blood RNA sequencing experiments for 495 patients with UC, 220 patients with PSC (including 177 with UC), and 320 healthy controls from Germany and Norway. Differential expression analyses, gene ontology and coexpression analyses and random forest machine learning were performed to identify genes, ontologies and transcriptional features that discriminate diagnoses. Results The blood transcriptome in UC and PSC is dominated by neutrophil activation genes (e.g. S100A12). In UC, but not in PSC (neither PSC alone nor patients with an additional diagnosis of UC [PSC/UC]), ribosomal, mitochondrial, and energy metabolism genes are upregulated in conjunction with antibody transcript expression (MZB1, IGJ). In PSC, there is an increase in modules related to apoptosis and expression of genes of interferon-I-related ontologies. Random forest analysis could poorly discriminate PSC alone from PSC/UC (AUROC 0.56), but could discriminate PSC, UC, and controls with high accuracy (AUROC UC vs. controls 0.95, PSC vs. controls 0.88, UC vs. PSC 0.986). The main coexpression modules relevant for distinguishing PSC, UC, and controls are enriched in neutrophil degranulation and antibody production genes. Conclusions Supported by machine learning results, PSC and UC appear to be separate entities on a molecular level, while PSC/UC and PSC are indistinguishable. Impact and implications Clinical and genetic studies suggest that the colitis-like symptoms in primary sclerosing cholangitis (PSC) represent a different disease entity from primary ulcerative colitis (UC). The present study supports this assumption with transcriptomic data from whole blood and describes notable differences in gene expression between primary UC and PSC, providing insights into the still unclear pathophysiology of both diseases. These findings are of interest to scientists seeking to decipher the molecular pathophysiology of both diseases and provide evidence that a redefinition of the PSC-UC phenotype should be considered. The study practically supports future molecular research by providing a large transcriptomic whole blood reference cohort.
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Affiliation(s)
- Eike Matthias Wacker
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | | | - Saptarshi Bej
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
- Indian Institute of Science Education and Research, Thiruvananthapuram, India
| | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
- Leibniz-Institute for Food Systems Biology at the Technical University Munich, Munich, Germany
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
| | - Mette Vesterhus
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway
- Department of Medicine, Haraldsplass Deaconess Hospital, Bergen, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Wolfgang Lieb
- Institute of Epidemiology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Tom Hemming Karlsen
- Research Institute for Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway
| | - Trine Folseraas
- Research Institute for Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
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11
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Ananthakrishnan AN. Precision medicine in inflammatory bowel diseases. Intest Res 2024; 22:8-14. [PMID: 37939722 PMCID: PMC10850693 DOI: 10.5217/ir.2023.00087] [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: 07/26/2023] [Revised: 09/16/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023] Open
Abstract
Inflammatory bowel diseases comprising Crohn's disease and ulcerative colitis have emerged as global diseases. Multiple distinct therapeutic mechanisms have allowed us to increase our rates of achieving remission and reducing permanent disease-related morbidity. However, there is limited data to inform relative positioning of different therapies. This review will summarize existing literature on use of clinical decision models to inform relative efficacy of one therapeutic mechanism compared to the other given individual patient characteristics. It will also demonstrate the value of serologic, transcriptomic (from biopsies), and microbiome-based biomarkers in identifying which therapy is most likely to work for a given patient. We will review the existing gaps in the literature in this field and suggest a path forward for future studies to better inform patient care, incorporating the principles of precision medicine in the management of inflammatory bowel disease.
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Affiliation(s)
- Ashwin N. Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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12
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Wang XY, Zhang D. Identifying Key Genes to the Early Diagnosis of Inflammatory Bowel Disease by Integrating Analysis at the Blood and Tissue Levels. Gastroenterology Res 2023; 16:318-333. [PMID: 38186585 PMCID: PMC10769606 DOI: 10.14740/gr1683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 12/09/2023] [Indexed: 01/09/2024] Open
Abstract
Background Inflammatory bowel disease (IBD) encompasses Crohn's disease (CD) and ulcerative colitis (UC), is challenging to diagnose, and frequently relapses, significantly affecting patients' quality of life. Despite extensive efforts, the pathogenesis of IBD remains unclear. Methods In this study, we integrated bioinformatics analysis and animal disease model to investigate IBD from two dimensions to identify potential diagnostic biomarkers and explore the pathogenesis of distinct conditions at tissue-specific levels. Results Firstly, we identified dysferlin (DYSF) and C-X-C motif chemokine ligand 2 (CXCL2) as crucial biomarkers for IBD, with 11 and 13 putative biomarkers for CD and UC, respectively, identified by peripheral blood testing only. CXCL8 and S100 calcium-binding protein A8 (S100A8) were determined to be critical hub genes and validated by real-time polymerase chain reaction (RT-PCR). Secondly, in CD, the differentially expressed genes (DEGs) were mainly associated with immunity based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, while the metabolism of multiple substances and substance transport activity were dominant in UC. Thirdly, essential genes in the pathological progression of CD and UC were identified through protein-protein interaction networks and molecular complex detection (MCODE) analysis. Finally, pathological examination and quantitative analysis of IBD models confirmed the above results. Conclusions Our findings could contribute to understanding the molecular mechanism of IBD, hold clinical significance for early diagnosis and prevention, and provide effective targets for treating IBD.
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Affiliation(s)
- Xin Yu Wang
- Key Laboratory of Medical Electrophysiology, Ministry of Education & Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou 646000, China
| | - Dan Zhang
- Key Laboratory of Medical Electrophysiology, Ministry of Education & Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou 646000, China
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13
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Rimmer P, Iqbal T. Prognostic modelling in IBD. Best Pract Res Clin Gastroenterol 2023; 67:101877. [PMID: 38103929 DOI: 10.1016/j.bpg.2023.101877] [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: 11/16/2023] [Accepted: 11/24/2023] [Indexed: 12/19/2023]
Abstract
In the ideal world prognostication or predicting disease course in any chronic condition would allow the clinician to anticipate disease behaviour, providing crucial information for the patient and data regarding best use of resources. Prognostication also allows an understanding of likely response to treatment and the risk of adverse effects of a treatment leading to withdrawal in any individual patient. Therefore, the ability to predict outcomes from the onset of disease is the key step to developing precision personalised medicine, which is the design of medical care to optimise efficiency or therapeutic benefit based on careful profiling of patients. An important corollary is to prevent unnecessary healthcare costs. This paper outlines currently available predictors of disease outcome in IBD and looks to the future which will involve the use of artificial intelligence to interrogate big data derived from various important 'omes' to tease out a more holistic approach to IBD.
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Affiliation(s)
- Peter Rimmer
- Queen Elizabeth Hospital Birmingham, B15 2TH, UK; University of Birmingham, College of Medical and Dental Science, UK.
| | - Tariq Iqbal
- Queen Elizabeth Hospital Birmingham, B15 2TH, UK; University of Birmingham, College of Medical and Dental Science, UK.
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14
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Shen X, Mo S, Zeng X, Wang Y, Lin L, Weng M, Sugasawa T, Wang L, Gu W, Nakajima T. Identification of antigen-presentation related B cells as a key player in Crohn's disease using single-cell dissecting, hdWGCNA, and deep learning. Clin Exp Med 2023; 23:5255-5267. [PMID: 37550553 DOI: 10.1007/s10238-023-01145-7] [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: 04/23/2023] [Accepted: 07/12/2023] [Indexed: 08/09/2023]
Abstract
Crohn's disease (CD) arises from intricate intercellular interactions within the intestinal lamina propria. Our objective was to use single-cell RNA sequencing to investigate CD pathogenesis and explore its clinical significance. We identified a distinct subset of B cells, highly infiltrated in the CD lamina propria, that expressed genes related to antigen presentation. Using high-dimensional weighted gene co-expression network analysis and nine machine learning techniques, we demonstrated that the antigen-presenting CD-specific B cell signature effectively differentiated diseased mucosa from normal mucosa (Independent external testing AUC = 0.963). Additionally, using MCPcounter and non-negative matrix factorization, we established a relationship between the antigen-presenting CD-specific B cell signature and immune cell infiltration and patient heterogeneity. Finally, we developed a gene-immune convolutional neural network deep learning model that accurately diagnosed CD mucosa in diverse cohorts (Independent external testing AUC = 0.963). Our research has revealed a population of B cells with a potential promoting role in CD pathogenesis and represents a fundamental step in the development of future clinical diagnostic tools for the disease.
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Affiliation(s)
- Xin Shen
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Shaocong Mo
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, 200040, China.
| | - Xinlei Zeng
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Yulin Wang
- Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Lingxi Lin
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Meilin Weng
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Takehito Sugasawa
- Laboratory of Clinical Examination and Sports Medicine, Department of Clinical Medicine, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8577, Japan
| | - Lei Wang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Wenchao Gu
- Department of Diagnostic and Interventional Radiology, University of Tsukuba, Ibaraki, 305-8577, Japan.
- Department of Diagnostic Radiology and Nuclear Medicine, Gunma University Graduate School of Medicine, Maebashi, 371-8511, Japan.
| | - Takahito Nakajima
- Department of Diagnostic and Interventional Radiology, University of Tsukuba, Ibaraki, 305-8577, Japan
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15
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Sun Z, Braga-Neto MB, Xiong Y, Bhagwate AV, Gibbons HR, Sagstetter MR, Hamdan FH, Baheti S, Friton J, Nair A, Ye Z, Faubion WA. Hypomethylation and Overexpression of Th17-Associated Genes is a Hallmark of Intestinal CD4+ Lymphocytes in Crohn's Disease. J Crohns Colitis 2023; 17:1847-1857. [PMID: 37280154 PMCID: PMC10673812 DOI: 10.1093/ecco-jcc/jjad093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/14/2023] [Accepted: 06/06/2023] [Indexed: 06/08/2023]
Abstract
BACKGROUND The development of Crohn's disease [CD] involves immune cell signalling pathways regulated by epigenetic modifications. Aberrant DNA methylation has been identified in peripheral blood and bulk intestinal tissue from CD patients. However, the DNA methylome of disease-associated intestinal CD4+ lymphocytes has not been evaluated. MATERIALS AND METHODS Genome-wide DNA methylation sequencing was performed from terminal ileum CD4+ cells from 21 CD patients and 12 age- and sex-matched controls. Data were analysed for differentially methylated CpGs [DMCs] and methylated regions [DMRs]. Integration was performed with RNA-sequencing data to evaluate the functional impact of DNA methylation changes on gene expression. DMRs were overlapped with regions of differentially open chromatin [by ATAC-seq] and CCCTC-binding factor [CTCF] binding sites [by ChIP-seq] between peripherally derived Th17 and Treg cells. RESULTS CD4+ cells in CD patients had significantly increased DNA methylation compared to those from the controls. A total of 119 051 DMCs and 8113 DMRs were detected. While hypermethylated genes were mostly related to cell metabolism and homeostasis, hypomethylated genes were significantly enriched within the Th17 signalling pathway. The differentially enriched ATAC regions in Th17 cells [compared to Tregs] were hypomethylated in CD patients, suggesting heightened Th17 activity. There was significant overlap between hypomethylated DNA regions and CTCF-associated binding sites. CONCLUSIONS The methylome of CD patients shows an overall dominant hypermethylation yet hypomethylation is more concentrated in proinflammatory pathways, including Th17 differentiation. Hypomethylation of Th17-related genes associated with areas of open chromatin and CTCF binding sites constitutes a hallmark of CD-associated intestinal CD4+ cells.
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Affiliation(s)
- Zhifu Sun
- Division of Computational Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Manuel B Braga-Neto
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Yuning Xiong
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Adytia V Bhagwate
- Division of Computational Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Hunter R Gibbons
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Mary R Sagstetter
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Feda H Hamdan
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Saurabh Baheti
- Division of Computational Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jessica Friton
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Asha Nair
- Division of Computational Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhenqing Ye
- Greehey Children’s Cancer Research Institute, UT Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - William A Faubion
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
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16
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Sarter H, Savoye G, Marot G, Ley D, Turck D, Hugot JP, Vasseur F, Duhamel A, Wils P, Princen F, Colombel JF, Gower-Rousseau C, Fumery M. A Novel 8-Predictors Signature to Predict Complicated Disease Course in Pediatric-onset Crohn's Disease: A Population-based Study. Inflamm Bowel Dis 2023; 29:1793-1804. [PMID: 37266570 DOI: 10.1093/ibd/izad090] [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: 08/28/2022] [Indexed: 06/03/2023]
Abstract
BACKGROUND The identification of patients at high risk of a disabling disease course would be invaluable in guiding initial therapy in Crohn's disease (CD). Our objective was to evaluate a combination of clinical, serological, and genetic factors to predict complicated disease course in pediatric-onset CD. METHODS Data for pediatric-onset CD patients, diagnosed before 17 years of age between 1988 and 2004 and followed more than 5 years, were extracted from the population-based EPIMAD registry. The main outcome was defined by the occurrence of complicated behavior (stricturing or penetrating) and/or intestinal resection within the 5 years following diagnosis. Lasso logistic regression models were used to build a predictive model based on clinical data at diagnosis, serological data (ASCA, pANCA, anti-OmpC, anti-Cbir1, anti-Fla2, anti-Flax), and 369 candidate single nucleotide polymorphisms. RESULTS In total, 156 children with an inflammatory (B1) disease at diagnosis were included. Among them, 35% (n = 54) progressed to a complicated behavior or an intestinal resection within the 5 years following diagnosis. The best predictive model (PREDICT-EPIMAD) included the location at diagnosis, pANCA, and 6 single nucleotide polymorphisms. This model showed good discrimination and good calibration, with an area under the curve of 0.80 after correction for optimism bias (sensitivity, 79%, specificity, 74%, positive predictive value, 61%, negative predictive value, 87%). Decision curve analysis confirmed the clinical utility of the model. CONCLUSIONS A combination of clinical, serotypic, and genotypic variables can predict disease progression in this population-based pediatric-onset CD cohort. Independent validation is needed before it can be used in clinical practice.
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Affiliation(s)
- Hélène Sarter
- Lille Hospital and University, Public Health, Epidemiology and Economic Health, EPIMAD registry, Regional house of clinical research, F-59000 Lille, France
- University of Lille, Inserm, CHU Lille, U1286, INFINITE, Institute for Translational Research in Inflammation, F-59000 Lille, France
| | - Guillaume Savoye
- Rouen Hospital and University, Gastroenterology Unit, EPIMAD registry, Rouen, France
| | - Guillemette Marot
- University of Lille, CHU Lille, ULR 2694-METRICS: Evaluation des Technologies de Santé et des Pratiques Médicales, F-59000 Lille, France
- Inria Lille Nord Europe, Modal, Lille, France
| | - Delphine Ley
- University of Lille, Inserm, CHU Lille, U1286, INFINITE, Institute for Translational Research in Inflammation, F-59000 Lille, France
- Lille University Jeanne de Flandre Children's Hospital and Faculty of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Lille, France
| | - Dominique Turck
- University of Lille, Inserm, CHU Lille, U1286, INFINITE, Institute for Translational Research in Inflammation, F-59000 Lille, France
- Lille University Jeanne de Flandre Children's Hospital and Faculty of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Lille, France
| | - Jean-Pierre Hugot
- Centre de Recherche sur l'Inflammation, UMR1149 INSERM et Université de Paris, France
- Department of Pediatric Gastroenterology, Hôpital Robert Debré, Assistance Publique Hôpitaux de Paris (AP-HP), Paris, France
| | - Francis Vasseur
- University of Lille, CHU Lille, ULR 2694-METRICS: Evaluation des Technologies de Santé et des Pratiques Médicales, F-59000 Lille, France
| | - Alain Duhamel
- University of Lille, CHU Lille, ULR 2694-METRICS: Evaluation des Technologies de Santé et des Pratiques Médicales, F-59000 Lille, France
| | - Pauline Wils
- University of Lille, Inserm, CHU Lille, U1286, INFINITE, Institute for Translational Research in Inflammation, F-59000 Lille, France
- Gastroenterology Unit, Lille Hospital and University, Lille, France
| | | | | | - Corinne Gower-Rousseau
- Lille Hospital and University, Public Health, Epidemiology and Economic Health, EPIMAD registry, Regional house of clinical research, F-59000 Lille, France
- University of Lille, Inserm, CHU Lille, U1286, INFINITE, Institute for Translational Research in Inflammation, F-59000 Lille, France
- Research and Public Health Unit, Reims University & Hospital, Robert-Debré Hospital, Reims, France
| | - Mathurin Fumery
- Amiens Hospital and University, Gastroenterology Unit, EPIMAD Registry, and PeriTox, UMR I-01, Amiens, France
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17
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Caliendo G, D'Elia G, Makker J, Passariello L, Albanese L, Molinari AM, Vietri MT. Biological, genetic and epigenetic markers in ulcerative colitis. Adv Med Sci 2023; 68:386-395. [PMID: 37813048 DOI: 10.1016/j.advms.2023.09.010] [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: 11/17/2022] [Revised: 04/15/2023] [Accepted: 09/18/2023] [Indexed: 10/11/2023]
Abstract
In this review, we have summarized the existing knowledge of ulcerative colitis (UC) markers based on current literature, specifically, the roles of potential new biomarkers, such as circulating, fecal, genetic, and epigenetic alterations, in UC onset, disease activity, and in therapy response. UC is a complex multifactorial inflammatory disease. There are many invasive and non-invasive diagnostic methods in UC, including several laboratory markers which are employed in diagnosis and disease assessment; however, colonoscopy remains the most widely used method. Common laboratory abnormalities currently used in the clinical practice include inflammation-induced alterations, serum autoantibodies, and antibodies against bacterial antigens. Other new serum and fecal biomarkers are supportive in diagnosis and monitoring disease activity and therapy response; and potential salivary markers are currently being evaluated as well. Several UC-related genetic and epigenetic alterations are implied in its pathogenesis and therapeutic response. Moreover, the use of artificial intelligence in the integration of laboratory biomarkers and big data could potentially be useful in clinical translation and precision medicine in UC management.
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Affiliation(s)
- Gemma Caliendo
- Unity of Clinical and Molecular Pathology, AOU University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Giovanna D'Elia
- Unity of Clinical and Molecular Pathology, AOU University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Jasmine Makker
- Department of GKT School of Medical Education, King's College London, London, UK
| | - Luana Passariello
- Unity of Clinical and Molecular Pathology, AOU University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Luisa Albanese
- Unity of Clinical and Molecular Pathology, AOU University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Anna Maria Molinari
- Unity of Clinical and Molecular Pathology, AOU University of Campania "Luigi Vanvitelli", Naples, Italy; Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Maria Teresa Vietri
- Unity of Clinical and Molecular Pathology, AOU University of Campania "Luigi Vanvitelli", Naples, Italy; Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy.
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18
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Spencer EA. Choosing the Right Therapy at the Right Time for Pediatric Inflammatory Bowel Disease: Does Sequence Matter. Gastroenterol Clin North Am 2023; 52:517-534. [PMID: 37543397 DOI: 10.1016/j.gtc.2023.05.006] [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] [Indexed: 08/07/2023]
Abstract
Despite the enlarging therapeutic armamentarium, IBD is still plagued by a therapeutic ceiling. Precision medicine, with the selection of the "rights," may present a solution, and this review will discuss the critical process of pairing the right patient with right therapy at the right time. Firstly, the review will discuss the shift to and evidence behind early effective therapy. Then, it delves into promising future strategies of patient profiling to identify a patients' biological pathway(s) and prognosis. Finally, the review lays out practical considerations that drive treatment selection, particularly the impact of the therapeutic sequence.
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Affiliation(s)
- Elizabeth A Spencer
- Division of Pediatric Gastroenterology & Nutrition, Department of Pediatrics, Icahn School of Medicine, Mount Sinai, 17 East 102nd Street, 5th Floor, New York, NY 10029, USA.
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19
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Scheurlen KM, Parks MA, Macleod A, Galandiuk S. Unmet Challenges in Patients with Crohn's Disease. J Clin Med 2023; 12:5595. [PMID: 37685662 PMCID: PMC10488639 DOI: 10.3390/jcm12175595] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/08/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Patients with Crohn's disease can present with a variety of clinical manifestations; treatment strategies should focus on long-term remission and improvement of quality of life. There is no standardized process of diagnosing, predicting prognosis, and treating the disease. This narrative review was based on a literature search using PubMed, Embase, and Science Direct. Data on unmet challenges in patients with Crohn's disease were extracted from identified manuscripts. The aim was to discuss present research on standardized processes in the management of patients with Crohn's disease and to identify the unmet needs in clinical evaluation and treatment approaches. There is no consensus on standardized diagnostic, treatment, and surveillance algorithms, particularly in assessing complications of Crohn's, such as stricturing disease, intestinal cancer risk, and cutaneous manifestations. Complications and treatment failure rates of conventional, interventional, and surgical therapy place emphasis on the need for standardized treatment algorithms, particularly in the case of acute complications of the disease. Research on standardized clinical approaches, reliable biomarkers for disease diagnosis and therapy monitoring, and new treatment agents is necessary to improve therapy and reduce complications in patients with Crohn's disease.
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Affiliation(s)
- Katharina M Scheurlen
- Price Institute of Surgical Research, Hiram C. Polk Jr. MD Department of Surgery, University of Louisville, Louisville, KY 40202, USA; (K.M.S.); (M.A.P.); (A.M.)
| | - Mary A Parks
- Price Institute of Surgical Research, Hiram C. Polk Jr. MD Department of Surgery, University of Louisville, Louisville, KY 40202, USA; (K.M.S.); (M.A.P.); (A.M.)
| | - Anne Macleod
- Price Institute of Surgical Research, Hiram C. Polk Jr. MD Department of Surgery, University of Louisville, Louisville, KY 40202, USA; (K.M.S.); (M.A.P.); (A.M.)
| | - Susan Galandiuk
- Price Institute of Surgical Research, Hiram C. Polk Jr. MD Department of Surgery, University of Louisville, Louisville, KY 40202, USA; (K.M.S.); (M.A.P.); (A.M.)
- Division of Colon and Rectal Surgery, Hiram C. Polk Jr. MD Department of Surgery, University of Louisville, Louisville, KY 40202, USA
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20
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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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21
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Affiliation(s)
- Siddharth Singh
- Division of Gastroenterology, University of California San Diego, La Jolla, CA, USA.
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22
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Ventham NT, Kennedy NA, Kalla R, Adams AT, Noble A, Ennis H, Mowat C, Dunlop MG, Satsangi J. Genome-Wide Methylation Profiling in 229 Patients With Crohn's Disease Requiring Intestinal Resection: Epigenetic Analysis of the Trial of Prevention of Post-operative Crohn's Disease (TOPPIC). Cell Mol Gastroenterol Hepatol 2023; 16:431-450. [PMID: 37331566 PMCID: PMC10372903 DOI: 10.1016/j.jcmgh.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 06/02/2023] [Accepted: 06/02/2023] [Indexed: 06/20/2023]
Abstract
BACKGROUND & AIMS DNA methylation alterations may provide important insights into gene-environment interaction in cancer, aging, and complex diseases, such as inflammatory bowel disease (IBD). We aim first to determine whether the circulating DNA methylome in patients requiring surgery may predict Crohn's disease (CD) recurrence following intestinal resection; and second to compare the circulating methylome seen in patients with established CD with that we had reported in a series of inception cohorts. METHODS TOPPIC was a placebo-controlled, randomized controlled trial of 6-mercaptopurine at 29 UK centers in patients with CD undergoing ileocolic resection between 2008 and 2012. Genomic DNA was extracted from whole blood samples from 229 of the 240 patients taken before intestinal surgery and analyzed using 450KHumanMethylation and Infinium Omni Express Exome arrays (Illumina, San Diego, CA). Coprimary objectives were to determine whether methylation alterations may predict clinical disease recurrence; and to assess whether the epigenetic alterations previously reported in newly diagnosed IBD were present in the patients with CD recruited into the TOPPIC study. Differential methylation and variance analysis was performed comparing patients with and without clinical evidence of recurrence. Secondary analyses included investigation of methylation associations with smoking, genotype (MeQTLs), and chronologic age. Validation of our previously published case-control observation of the methylome was performed using historical control data (CD, n = 123; Control, n = 198). RESULTS CD recurrence in patients following surgery is associated with 5 differentially methylated positions (Holm P < .05), including probes mapping to WHSC1 (P = 4.1 × 10-9, Holm P = .002) and EFNA3 (P = 4.9 × 10-8, Holm P = .02). Five differentially variable positions are demonstrated in the group of patients with evidence of disease recurrence including a probe mapping to MAD1L1 (P = 6.4 × 10-5). DNA methylation clock analyses demonstrated significant age acceleration in CD compared with control subjects (GrimAge + 2 years; 95% confidence interval, 1.2-2.7 years), with some evidence for accelerated aging in patients with CD with disease recurrence following surgery (GrimAge +1.04 years; 95% confidence interval, -0.04 to 2.22). Significant methylation differences between CD cases and control subjects were seen by comparing this cohort in conjunction with previously published control data, including validation of our previously described differentially methylated positions (RPS6KA2 P = 1.2 × 10-19, SBNO2 = 1.2 × 10-11) and regions (TXK [false discovery rate, P = 3.6 × 10-14], WRAP73 [false discovery rate, P = 1.9 × 10-9], VMP1 [false discovery rate, P = 1.7 × 10-7], and ITGB2 [false discovery rate, P = 1.4 × 10-7]). CONCLUSIONS We demonstrate differential methylation and differentially variable methylation in patients developing clinical recurrence within 3 years of surgery. Moreover, we report replication of the CD-associated methylome, previously characterized only in adult and pediatric inception cohorts, in patients with medically refractory disease needing surgery.
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Affiliation(s)
- Nicholas T Ventham
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom.
| | - Nicholas A Kennedy
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Rahul Kalla
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Alex T Adams
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Alexandra Noble
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Holly Ennis
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Craig Mowat
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Malcolm G Dunlop
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Jack Satsangi
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
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23
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Hasselblatt P, Reindl W, Gauss A, Neeff H, Fusco S, Klaus J. Questions to consider when caring for patients with ulcerative colitis. ZEITSCHRIFT FUR GASTROENTEROLOGIE 2023; 61:690-700. [PMID: 36257329 DOI: 10.1055/a-1890-6015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Although the management of patients with ulcerative colitis (UC) is well defined by national and international guidelines, there are many debates and open questions related to daily care of UC patients. Here, we aimed to review topics with high clinical relevance including therapy algorithms, potential biomarkers for disease prognosis and response to therapy, the role of interventions targeting the gut microbiota, insights from head-to-head trials, novel UC medications, exit strategies, the impact of COVID19 on UC, care of patients with acute severe disease, cancer screening, and the role of surgery.
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Affiliation(s)
- Peter Hasselblatt
- Department of Medicine II, University Hospital Freiburg, Freiburg, Germany
| | - Wolfgang Reindl
- Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Annika Gauss
- University Hospital Heidelberg, Heidelberg, Germany
| | - Hannes Neeff
- Dept. of General and Visceral Surgery, Medical Center - University of Freiburg, Freiburg, Germany
| | - Stefano Fusco
- Department of Gastroenterology, Eberhard-Karls-Universität Tübingen Medizinische Fakultät, Tübingen, Germany
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24
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Rodríguez-Lago I, Blackwell J, Mateos B, Marigorta UM, Barreiro-de Acosta M, Pollok R. Recent Advances and Potential Multi-Omics Approaches in the Early Phases of Inflammatory Bowel Disease. J Clin Med 2023; 12:jcm12103418. [PMID: 37240524 DOI: 10.3390/jcm12103418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/01/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Inflammatory bowel disease leads to debilitating gastrointestinal symptoms and reduced quality of life, resulting in a significant burden on healthcare utilization and costs. Despite substantial advancements in diagnosis and treatment, there may still be considerable delays in diagnosing some patients. To reduce disease progression before the full disease spectrum appears and improve prognostic outcomes, several strategies have concentrated on early intervention and prevention. Recent evidence shows that initial immune response changes and endoscopic lesions may exist for years before diagnosis, implying the existence of a preclinical phase of inflammatory bowel disease comparable to findings in other immune-mediated disorders. In this review, we highlight the most relevant findings regarding preclinical inflammatory bowel disease and the prospective role of novel omics techniques in this field.
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Affiliation(s)
- Iago Rodríguez-Lago
- Gastroenterology Department, Hospital Universitario de Galdakao, 48960 Galdakao, Spain
- Biocruces Bizkaia Health Research Institute, 48960 Galdakao, Spain
- Deusto University, 48007 Bilbao, Spain
| | | | - Beatriz Mateos
- Integrative Genomics Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Urko M Marigorta
- Integrative Genomics Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
- IKERBASQUE, Basque Foundation for Sciences, 48009 Bilbao, Spain
| | - Manuel Barreiro-de Acosta
- Gastroenterology Department, Hospital Clínico Universitario de Santiago, 15706 Santiago de Compostela, Spain
| | - Richard Pollok
- Gastroenterology Department, St George's University of London, London SW17 0RE, UK
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25
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Kriger-Sharabi OA, Kopylov U. Harnessing the Power of Precision Medicine and Novel Biomarkers to Treat Crohn’s Disease. J Clin Med 2023; 12:jcm12072696. [PMID: 37048779 PMCID: PMC10094767 DOI: 10.3390/jcm12072696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/11/2023] [Accepted: 03/21/2023] [Indexed: 04/08/2023] Open
Abstract
Crohn’s disease (CD) is a chronic inflammatory condition that affects the gastrointestinal tract. It is part of a spectrum of inflammatory Bowel Diseases (IBD). The disease is complex, characterized by significant inter and intra-individual heterogeneity, which contributes to a diverse and multifaceted portrayal of the disease. Consequently, applying specific and accurate treatment is challenging, and therapeutic success rates remain disappointing and insufficient. In recent years, significant advances in the therapeutic potential of CD have been made. Hope has been provided by these developments in the form of an expanding treatment toolkit. However, even with these beneficial adjustments, patients are frequently treated using an ineffective “one size fits all” treatment protocol, ultimately leading to a plateau in drug effectiveness and a decline in overall treatment success rates. Furthermore, with the advancement in the genome-wide association study, in combination with significant bioinformatic developments, the world of medicine has moved in the direction of personalized, tailored-treatment medicine, and this trend has not escaped the world of IBDs. Prediction models, novel biomarkers, and complex algorithms are emerging and inspiring optimism that CD patients will be treated with “precision medicine” in the near future, meaning that their treatments will be selected based on the patient’s various unique features. In this review, we will outline the current diagnostic and therapeutic limitations that lead to a glass ceiling effect and thus send us in pursuit of discovering novel biomarkers. We will illustrate the challenges and difficulties in discovering relevant and innovative biomarkers and implementing them into everyday clinical practice. We will also heighten the progress made in practicing personalized medicine for CD patients and shed light on future directions and horizons.
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Affiliation(s)
- Ofra Aviva Kriger-Sharabi
- Department of Gatsroenterology, Assuta Ashdod Medical Center, Affiliated to The Ben-Gurion University (BGU) Medical School, Ashdod 7747629, Israel
| | - Uri Kopylov
- Department of Gastroenterology, Sheba Medical Center, Tel Hashomer, Affliated to Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
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26
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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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27
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Cheah E, Huang JG. Precision medicine in inflammatory bowel disease: Individualizing the use of biologics and small molecule therapies. World J Gastroenterol 2023; 29:1539-1550. [PMID: 36970587 PMCID: PMC10037250 DOI: 10.3748/wjg.v29.i10.1539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/17/2023] [Accepted: 02/22/2023] [Indexed: 03/14/2023] Open
Abstract
The advent of biologics and small molecules in inflammatory bowel disease (IBD) has marked a significant turning point in the prognosis of IBD, decreasing the rates of corticosteroid dependence, hospitalizations and improving overall quality of life. The introduction of biosimilars has also increased affordability and enhanced access to these otherwise costly targeted therapies. Biologics do not yet represent a complete panacea: A subset of patients do not respond to first-line anti-tumor necrosis factor (TNF)-alpha agents or may subsequently demonstrate a secondary loss of response. Patients who fail to respond to anti-TNF agents typically have a poorer response rate to second-line biologics. It is uncertain which patient would benefit from a different sequencing of biologics or even a combination of biologic agents. The introduction of newer classes of biologics and small molecules may provide alternative therapeutic targets for patients with refractory disease. This review examines the therapeutic ceiling in current treatment strategies of IBD and the potential paradigm shifts in the future.
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Affiliation(s)
- Eric Cheah
- Department of Gastroenterology and Clinical Nutrition, The Royal Children's Hospital Melbourne, Parkville, VIC 3052, Australia
| | - James Guoxian Huang
- Department of Paediatrics, Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore 119228, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
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28
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Cheah E, Huang JG. Precision medicine in inflammatory bowel disease: Individualizing the use of biologics and small molecule therapies. World J Gastroenterol 2023; 29:1395-1406. [DOI: 10.3748/wjg.v29.i10.1395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/10/2023] Open
Abstract
The advent of biologics and small molecules in inflammatory bowel disease (IBD) has marked a significant turning point in the prognosis of IBD, decreasing the rates of corticosteroid dependence, hospitalizations and improving overall quality of life. The introduction of biosimilars has also increased affordability and enhanced access to these otherwise costly targeted therapies. Biologics do not yet represent a complete panacea: A subset of patients do not respond to first-line anti-tumor necrosis factor (TNF)-alpha agents or may subsequently demonstrate a secondary loss of response. Patients who fail to respond to anti-TNF agents typically have a poorer response rate to second-line biologics. It is uncertain which patient would benefit from a different sequencing of biologics or even a combination of biologic agents. The introduction of newer classes of biologics and small molecules may provide alternative therapeutic targets for patients with refractory disease. This review examines the therapeutic ceiling in current treatment strategies of IBD and the potential paradigm shifts in the future.
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Affiliation(s)
- Eric Cheah
- Department of Gastroenterology and Clinical Nutrition, The Royal Children's Hospital Melbourne, Parkville, VIC 3052, Australia
| | - James Guoxian Huang
- Department of Paediatrics, Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore 119228, Singapore,Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
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29
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Augustin J, McLellan PT, Calderaro J. Mise au point de l’utilisation de l’intelligence artificielle dans la prise en charge des maladies inflammatoires chroniques de l’intestin. Ann Pathol 2023:S0242-6498(23)00075-5. [PMID: 36997441 DOI: 10.1016/j.annpat.2023.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 03/30/2023]
Abstract
Complexity of inflammatory bowel diseases (IBD) lies on their management and their biology. Clinics, blood and fecal samples tests, endoscopy and histology are the main tools guiding IBD treatment, but they generate a large amount of data, difficult to analyze by clinicians. Because of its capacity to analyze large number of data, artificial intelligence is currently generating enthusiasm in medicine, and this technology could be used to improve IBD management. In this review, after a short summary on IBD management and artificial intelligence, we will report pragmatic examples of artificial intelligence utilisation in IBD. Lastly, we will discuss the limitations of this technology.
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Affiliation(s)
- Jérémy Augustin
- Département de pathologie, hôpital universitaire Henri-Mondor, assistance publique-hôpitaux de Paris, Créteil, France; Inserm U955 Team 18, université Paris-Est-Créteil, faculté de Médecine, Créteil, France.
| | - Paul Thomas McLellan
- Département de gastroentérologie, hôpital Saint-Antoine, assistance publique-hôpitaux de Paris, Sorbonne université, Paris, France
| | - Julien Calderaro
- Département de pathologie, hôpital universitaire Henri-Mondor, assistance publique-hôpitaux de Paris, Créteil, France; Inserm U955 Team 18, université Paris-Est-Créteil, faculté de Médecine, Créteil, France
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30
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Verstockt B, Verstockt S, Cremer J, Sabino J, Ferrante M, Vermeire S, Sudhakar P. Distinct transcriptional signatures in purified circulating immune cells drive heterogeneity in disease location in IBD. BMJ Open Gastroenterol 2023; 10:bmjgast-2022-001003. [PMID: 36746519 PMCID: PMC9906185 DOI: 10.1136/bmjgast-2022-001003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/25/2022] [Indexed: 02/08/2023] Open
Abstract
OBJECTIVE To infer potential mechanisms driving disease subtypes among patients with inflammatory bowel disease (IBD), we profiled the transcriptome of purified circulating monocytes and CD4 T-cells. DESIGN RNA extracted from purified monocytes and CD4 T-cells derived from the peripheral blood of 125 endoscopically active patients with IBD was sequenced using Illumina HiSeq 4000NGS. We used complementary supervised and unsupervised analytical methods to infer gene expression signatures associated with demographic/clinical features. Expression differences and specificity were validated by comparison with publicly available single cell datasets, tissue-specific expression and meta-analyses. Drug target information, druggability and adverse reaction records were used to prioritise disease subtype-specific therapeutic targets. RESULTS Unsupervised/supervised methods identified significant differences in the expression profiles of CD4 T-cells between patients with ileal Crohn's disease (CD) and ulcerative colitis (UC). Following a pathway-based classification (Area Under Receiver Operating Characteristic - AUROC=86%) between ileal-CD and UC patients, we identified MAPK and FOXO pathways to be downregulated in UC. Coexpression module/regulatory network analysis using systems-biology approaches revealed mediatory core transcription factors. We independently confirmed that a subset of the disease location-associated signature is characterised by T-cell-specific and location-specific expression. Integration of drug-target information resulted in the discovery of several new (BCL6, GPR183, TNFAIP3) and repurposable drug targets (TUBB2A, PRKCQ) for ileal CD as well as novel targets (NAPEPLD, SLC35A1) for UC. CONCLUSIONS Transcriptomic profiling of circulating CD4 T-cells in patients with IBD demonstrated marked molecular differences between the IBD-spectrum extremities (UC and predominantly ileal CD, sandwiching colonic CD), which could help in prioritising particular drug targets for IBD subtypes.
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Affiliation(s)
- Bram Verstockt
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID), IBD group, KU Leuven, Leuven, Belgium,Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Sare Verstockt
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID), IBD group, KU Leuven, Leuven, Belgium
| | - Jonathan Cremer
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID), IBD group, KU Leuven, Leuven, Belgium
| | - João Sabino
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID), IBD group, KU Leuven, Leuven, Belgium,Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Marc Ferrante
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID), IBD group, KU Leuven, Leuven, Belgium,Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Severine Vermeire
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID), IBD group, KU Leuven, Leuven, Belgium,Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Padhmanand Sudhakar
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID), IBD group, KU Leuven, Leuven, Belgium
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31
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Liu XY, Tang H, Zhou QY, Zeng YL, Chen D, Xu H, Li Y, Tan B, Qian JM. Advancing the precision management of inflammatory bowel disease in the era of omics approaches and new technology. World J Gastroenterol 2023; 29:272-285. [PMID: 36687128 PMCID: PMC9846940 DOI: 10.3748/wjg.v29.i2.272] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/01/2022] [Accepted: 12/21/2022] [Indexed: 01/06/2023] Open
Abstract
There is great heterogeneity among inflammatory bowel disease (IBD) patients in terms of pathogenesis, clinical manifestation, response to treatment, and prognosis, which requires the individualized and precision management of patients. Many studies have focused on prediction biomarkers and models for assessing IBD disease type, activity, severity, and prognosis. During the era of biologics, how to predict the response and side effects of patients to different treatments and how to quickly recognize the loss of response have also become important topics. Multiomics is a promising area for investigating the complex network of IBD pathogenesis. Integrating numerous amounts of data requires the use of artificial intelligence.
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Affiliation(s)
- Xin-Yu Liu
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
- Eight-year Medical Doctor Program, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
| | - Hao Tang
- Department of Internal Medicine, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
| | - Qing-Yang Zhou
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
| | - Yan-Lin Zeng
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Dan Chen
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing 100730, China
| | - Hui Xu
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
| | - Yue Li
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
| | - Bei Tan
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
| | - Jia-Ming Qian
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
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Bourgonje AR, Kloska D, Grochot-Przęczek A, Feelisch M, Cuadrado A, van Goor H. Personalized redox medicine in inflammatory bowel diseases: an emerging role for HIF-1α and NRF2 as therapeutic targets. Redox Biol 2023; 60:102603. [PMID: 36634466 PMCID: PMC9841059 DOI: 10.1016/j.redox.2023.102603] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 01/05/2023] [Accepted: 01/05/2023] [Indexed: 01/07/2023] Open
Abstract
Inflammatory bowel diseases (IBD), encompassing Crohn's disease (CD) and ulcerative colitis (UC), are intimately associated with inflammation and overproduction of reactive oxygen species (ROS). Temporal and inter-individual variabilities in disease activity and response to therapy pose significant challenges to diagnosis and patient care. Discovery and validation of truly integrative biomarkers would benefit from embracing redox metabolomics approaches with prioritization of central regulatory hubs. We here make a case for applying a personalized redox medicine approach that aims to selectively inhibit pathological overproduction and/or altered expression of specific enzymatic sources of ROS without compromising physiological function. To this end, improved 'clinical-omics integration' may help to better understand which particular redox signaling pathways are disrupted in what patient. Pharmacological interventions capable of activating endogenous antioxidant defense systems may represent viable therapeutic options to restore local/systemic redox status, with HIF-1α and NRF2 holding particular promise in this context. Achieving the implementation of clinically meaningful mechanism-based biomarkers requires development of easy-to-use, robust and cost-effective tools for secure diagnosis and monitoring of treatment efficacy. Ultimately, matching redox-directed pharmacological interventions to individual patient phenotypes using predictive biomarkers may offer new opportunities to break the therapeutic ceiling in IBD.
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Affiliation(s)
- Arno R. Bourgonje
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands,Corresponding author.
| | - Damian Kloska
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Anna Grochot-Przęczek
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Martin Feelisch
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Antonio Cuadrado
- Instituto de Investigaciones Biomédicas “Alberto Sols” UAM-CSIC. Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid, Spain
| | - Harry van Goor
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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Vieujean S, Louis E. Precision medicine and drug optimization in adult inflammatory bowel disease patients. Therap Adv Gastroenterol 2023; 16:17562848231173331. [PMID: 37197397 PMCID: PMC10184262 DOI: 10.1177/17562848231173331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/16/2023] [Indexed: 05/19/2023] Open
Abstract
Inflammatory bowel diseases (IBD) encompass two main entities including ulcerative colitis and Crohn's disease. Although having a common global pathophysiological mechanism, IBD patients are characterized by a significant interindividual heterogeneity and may differ by their disease type, disease locations, disease behaviours, disease manifestations, disease course as well as treatment needs. Indeed, although the therapeutic armamentarium for these diseases has expanded rapidly in recent years, a proportion of patients remains with a suboptimal response to medical treatment due to primary non-response, secondary loss of response or intolerance to currently available drugs. Identifying, prior to treatment initiation, which patients are likely to respond to a specific drug would improve the disease management, avoid unnecessary side effects and reduce the healthcare expenses. Precision medicine classifies individuals into subpopulations according to clinical and molecular characteristics with the objective to tailor preventative and therapeutic interventions to the characteristics of each patient. Interventions would thus be performed only on those who will benefit, sparing side effects and expense for those who will not. This review aims to summarize clinical factors, biomarkers (genetic, transcriptomic, proteomic, metabolic, radiomic or from the microbiota) and tools that could predict disease progression to guide towards a step-up or top-down strategy. Predictive factors of response or non-response to treatment will then be reviewed, followed by a discussion about the optimal dose of drug required for patients. The time at which these treatments should be administered (or rather can be stopped in case of a deep remission or in the aftermath of a surgery) will also be addressed. IBD remain biologically complex, with multifactorial etiopathology, clinical heterogeneity as well as temporal and therapeutic variabilities, which makes precision medicine especially challenging in this area. Although applied for many years in oncology, it remains an unmet medical need in IBD.
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Affiliation(s)
- Sophie Vieujean
- Hepato-Gastroenterology and Digestive Oncology, University Hospital CHU of Liège, Liège, Belgium
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Xu YH, Zhu WM, Guo Z. Current status of novel biologics and small molecule drugs in the individualized treatment of inflammatory bowel disease. World J Gastroenterol 2022; 28:6888-6899. [PMID: 36632311 PMCID: PMC9827580 DOI: 10.3748/wjg.v28.i48.6888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/11/2022] [Accepted: 12/01/2022] [Indexed: 12/26/2022] Open
Abstract
Treatment strategies for inflammatory bowel disease (IBD) are rapidly evolving with the development of biologics and small molecule drugs (SMDs). However, these drugs are not guaranteed to be effective in all patients, and a “ceiling effect” of biologic monotherapy may occur. This issue highlights an unmet need for optimizing the use of biologics and predicting therapeutic responses. Thus, the development of new drugs with novel mechanisms of action is urgently needed for patients with primary nonresponse and secondary loss of response to conventional biologics and SMDs. In addition, combining different biologics or SMDs has been proposed as a novel strategy to enhance treatment efficacy in IBD, which theoretically has multidimensional anti-inflammatory potential. Based on the current evidence available for IBD, dual targeted therapy may be a promising strategy for refractory IBD patients who have failed in multiple biologic trea-tments or who have extraintestinal manifestation. Additionally, identifying the subgroup of IBD patients who are responding to biological combination therapies is also equally important in stable disease remission. In this review, we sum-marize the newly developed biologics and SMDs and the current status of bio-logics/SMDs to highlight the development of individualized treatment in IBD.
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Affiliation(s)
- Yi-Han Xu
- Department of General Surgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, Jiangsu Province, China
| | - Wei-Ming Zhu
- Department of General Surgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, Jiangsu Province, China
| | - Zhen Guo
- Department of General Surgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, Jiangsu Province, China
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Ashton JJ, Brooks-Warburton J, Allen PB, Tham TC, Hoque S, Kennedy NA, Dhar A, Sebastian S. The importance of high-quality 'big data' in the application of artificial intelligence in inflammatory bowel disease. Frontline Gastroenterol 2022; 14:258-262. [PMID: 37056322 PMCID: PMC10086732 DOI: 10.1136/flgastro-2022-102342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/06/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- James J Ashton
- Department of Paediatric Gastroenterology, Southampton Children's Hospital, Southampton, UK
- Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
| | - Johanne Brooks-Warburton
- Department of Clinical Pharmacology and Biological Sciences, University of Hertfordshire, Hatfield, UK
- Gastroenterology Department, Lister Hospital, Stevenage, UK
| | - Patrick B Allen
- Department of Gastroenterology, Ulster Hospital, Dundonald, Belfast, UK
| | - Tony C Tham
- Department of Gastroenterology, Ulster Hospital, Dundonald, Belfast, UK
| | - Sami Hoque
- Department of Gastroenterology, Barts Health NHS Trust, London, UK
| | - Nicholas A Kennedy
- Department of Gastroenterology, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
- IBD Pharmacogenetics, University of Exeter, Exeter, UK
| | - Anjan Dhar
- Department of Gastroenterology, County Durham & Darlington NHS Foundation Trust, Darlington, Co. Durham, UK
- Teesside University, Middlesbrough, UK
| | - Shaji Sebastian
- Department of Gastroenterology, Hull University Teaching Hospitals NHS Trust, Hull, UK
- Hull York Medical School, Hull, UK
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36
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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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Globig AM, Mayer LS, Heeg M, Andrieux G, Ku M, Otto-Mora P, Hipp AV, Zoldan K, Pattekar A, Rana N, Schell C, Boerries M, Hofmann M, Neumann-Haefelin C, Kuellmer A, Schmidt A, Boettler T, Tomov V, Thimme R, Hasselblatt P, Bengsch B. Exhaustion of CD39-Expressing CD8 + T Cells in Crohn's Disease Is Linked to Clinical Outcome. Gastroenterology 2022; 163:965-981.e31. [PMID: 35738329 DOI: 10.1053/j.gastro.2022.06.045] [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: 10/03/2021] [Revised: 06/07/2022] [Accepted: 06/14/2022] [Indexed: 12/02/2022]
Abstract
BACKGROUND & AIMS Exhaustion of CD8 T cells has been suggested to inform different clinical outcomes in Crohn's disease, but detailed analyses are lacking. This study aimed to identify the role of exhaustion on a single-cell level and identify relevant CD8 T cell populations in Crohn's disease. METHODS Blood and intestinal tissue from 58 patients with Crohn's disease (active disease or remission) were assessed for CD8 T cell expression of exhaustion markers and their cytokine profile by highly multiplexed flow and mass cytometry. Key disease-associated subsets were sorted and analyzed by RNA sequencing. CD39 inhibition assays were performed in vitro. RESULTS Activated CD39+ and CD39+PD-1+ CD8 T cell subsets expressing multiple exhaustion markers were enriched at low frequency in active Crohn's disease. Their cytokine production capacity was inversely linked to the Harvey-Bradshaw Index. Subset-level protein and transcriptome profiling revealed co-existence of effector and exhaustion programs in CD39+ and CD39+ PD-1+CD8 T cells, with CD39+ cells likely originating from the intestine. CD39 enzymatic activity controlled T cell cytokine production. Importantly, transcriptional exhaustion signatures were enriched in remission in CD39-expressing subsets with up-regulation of TOX. Subset-level transcriptomics revealed a CD39-related gene module that is associated with the clinical course. CONCLUSIONS These data showed a role for the exhaustion of peripheral CD39-expressing CD8 T cell subsets in Crohn's disease. Their low frequency illustrated the utility of single-cell cytometry methods for identification of relevant immune populations. Importantly, the link of their exhaustion status to the clinical activity and their specific gene signatures have implications for exhaustion-based personalized medicine approaches.
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Affiliation(s)
- Anna-Maria Globig
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, University Medical Center Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Lena Sophie Mayer
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, University Medical Center Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Maximilian Heeg
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, University Medical Center Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; German Cancer Consortium Partner Site Freiburg, German Cancer Research Center, Heidelberg, Germany
| | - Manching Ku
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | - Patricia Otto-Mora
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, University Medical Center Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Anna Veronika Hipp
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, University Medical Center Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Katharina Zoldan
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, University Medical Center Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Ajinkya Pattekar
- Department of Medicine, Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Nisha Rana
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, University Medical Center Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Christoph Schell
- Institute for Surgical Pathology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; German Cancer Consortium Partner Site Freiburg, German Cancer Research Center, Heidelberg, Germany
| | - Maike Hofmann
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, University Medical Center Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Christoph Neumann-Haefelin
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, University Medical Center Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Armin Kuellmer
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, University Medical Center Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Arthur Schmidt
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, University Medical Center Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Tobias Boettler
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, University Medical Center Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Vesselin Tomov
- Department of Medicine, Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Robert Thimme
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, University Medical Center Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Peter Hasselblatt
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, University Medical Center Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Bertram Bengsch
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, University Medical Center Freiburg, Faculty of Medicine, Freiburg, Germany; German Cancer Consortium Partner Site Freiburg, German Cancer Research Center, Heidelberg, Germany; Centre for Biological Signalling Studies (BIOSS) and Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany.
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Chen H, Li P, Chen J, Wang Y, Yu Q, Wu Y, Chen Y, Cai J. Peripheral blood mononuclear cell microRNAs are novel biomarkers for diagnosing and monitoring Crohn's disease. FASEB J 2022; 36:e22549. [PMID: 36165177 DOI: 10.1096/fj.202200452r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 08/07/2022] [Accepted: 09/02/2022] [Indexed: 11/11/2022]
Abstract
Crohn's disease is a recurrent, progressive, immune-mediated inflammatory disease and merely manifests non-specific symptoms at early stage. In this study, we isolated peripheral blood mononuclear cells (PBMCs) to determine whether PBMC miRNAs are reliable biomarkers for Crohn's disease diagnosing and monitoring. 5 Crohn's disease patients and 5 healthy controls were recruited to find differentially expressed miRNAs by next generation sequencing. Candidate PBMC miRNAs were further validated by qRT-PCR in another cohort consisting of 86 Crohn's disease patients and 39 healthy controls. We found PBMC miR-582-5p could diagnose Crohn's disease with the area under receiver operating characteristic curve (AUROC) of 0.701(95%CI 0.606-0.796, p < .001). While PBMC miR-96-5p was significantly higher in active Crohn's disease and correlated with both clinical (ρ = 0.376, p < .001) and endoscopic activity (ρ = 0.512, p = .015). Furthermore, PBMC miR-96-5p had a better performance in recognizing active Crohn's disease with AUROC of 0.727 (95%CI 0.609-0.844, p = .001) than C-reactive protein (CRP), erythrocyte sedimentation rate (ESR) and fecal calprotectin. In conclusion, PBMC miR-582-5p may be further utilized as a diagnostic biomarker, while miR-96-5p may be a novel and valuable biomarker in monitoring disease activity.
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Affiliation(s)
- Hanwen Chen
- Center of Inflammatory Bowel Disease, Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, P. R. China
| | - Peiwei Li
- Center of Inflammatory Bowel Disease, Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, P. R. China
| | - Jiamin Chen
- Center of Inflammatory Bowel Disease, Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, P. R. China
| | - Yufang Wang
- Department of Gastroenterology, The Third People's Hospital of Hangzhou, Hangzhou, P. R. China
| | - Qiao Yu
- Center of Inflammatory Bowel Disease, Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, P. R. China
| | - Yihua Wu
- Department of Toxicology, Zhejiang University School of Public Health, Hangzhou, P. R. China
| | - Yan Chen
- Center of Inflammatory Bowel Disease, Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, P. R. China
| | - Jianting Cai
- Center of Inflammatory Bowel Disease, Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, P. R. China
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Ashton JJ, Cheng G, Stafford IS, Kellermann M, Seaby EG, Cummings JRF, Coelho TAF, Batra A, Afzal NA, Beattie RM, Ennis S. Prediction of Crohn's Disease Stricturing Phenotype Using a NOD2-derived Genomic Biomarker. Inflamm Bowel Dis 2022; 29:511-521. [PMID: 36161322 PMCID: PMC10069659 DOI: 10.1093/ibd/izac205] [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: 03/14/2022] [Indexed: 12/09/2022]
Abstract
BACKGROUND Crohn's disease (CD) is highly heterogenous and may be complicated by stricturing behavior. Personalized prediction of stricturing will inform management. We aimed to create a stricturing risk stratification model using genomic/clinical data. METHODS Exome sequencing was performed on CD patients, and phenotype data retrieved. Biallelic variants in NOD2 were identified. NOD2 was converted into a per-patient deleteriousness metric ("GenePy"). Using training data, patients were stratified into risk groups for fibrotic stricturing using NOD2. Findings were validated in a testing data set. Models were modified to include disease location at diagnosis. Cox proportional hazards assessed performance. RESULTS Six hundred forty-five patients were included (373 children and 272 adults); 48 patients fulfilled criteria for monogenic NOD2-related disease (7.4%), 24 of whom had strictures. NOD2 GenePy scores stratified patients in training data into 2 risk groups. Within testing data, 30 of 161 patients (18.6%) were classified as high-risk based on the NOD2 biomarker, with stricturing in 17 of 30 (56.7%). In the low-risk group, 28 of 131 (21.4%) had stricturing behavior. Cox proportional hazards using the NOD2 risk groups demonstrated a hazard ratio (HR) of 2.092 (P = 2.4 × 10-5), between risk groups. Limiting analysis to patients diagnosed aged < 18-years improved performance (HR-3.164, P = 1 × 10-6). Models were modified to include disease location, such as terminal ileal (TI) disease or not. Inclusion of NOD2 risk groups added significant additional utility to prediction models. High-risk group pediatric patients presenting with TI disease had a HR of 4.89 (P = 2.3 × 10-5) compared with the low-risk group patients without TI disease. CONCLUSIONS A NOD2 genomic biomarker predicts stricturing risk, with prognostic power improved in pediatric-onset CD. Implementation into a clinical setting can help personalize management.
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Affiliation(s)
- James J Ashton
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK.,Department of Paediatric Gastroenterology, Southampton Children's Hospital, Southampton, UK
| | - Guo Cheng
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
| | - Imogen S Stafford
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK.,Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Melina Kellermann
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
| | - Eleanor G Seaby
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
| | - J R Fraser Cummings
- Department of Gastroenterology, University Hospital Southampton, Southampton, UK
| | - Tracy A F Coelho
- Department of Paediatric Gastroenterology, Southampton Children's Hospital, Southampton, UK
| | - Akshay Batra
- Department of Paediatric Gastroenterology, Southampton Children's Hospital, Southampton, UK
| | - Nadeem A Afzal
- Department of Paediatric Gastroenterology, Southampton Children's Hospital, Southampton, UK
| | - R Mark Beattie
- Department of Paediatric Gastroenterology, Southampton Children's Hospital, Southampton, UK
| | - Sarah Ennis
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
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Longitudinal multi-omics analysis identifies early blood-based predictors of anti-TNF therapy response in inflammatory bowel disease. Genome Med 2022; 14:110. [PMID: 36153599 PMCID: PMC9509553 DOI: 10.1186/s13073-022-01112-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 09/02/2022] [Indexed: 11/10/2022] Open
Abstract
Background and aims Treatment with tumor necrosis factor α (TNFα) antagonists in IBD patients suffers from primary non-response rates of up to 40%. Biomarkers for early prediction of therapy success are missing. We investigated the dynamics of gene expression and DNA methylation in blood samples of IBD patients treated with the TNF antagonist infliximab and analyzed the predictive potential regarding therapy outcome. Methods We performed a longitudinal, blood-based multi-omics study in two prospective IBD patient cohorts receiving first-time infliximab therapy (discovery: 14 patients, replication: 23 patients). Samples were collected at up to 7 time points (from baseline to 14 weeks after therapy induction). RNA-sequencing and genome-wide DNA methylation data were analyzed and correlated with clinical remission at week 14 as a primary endpoint. Results We found no consistent ex ante predictive signature across the two cohorts. Longitudinally upregulated transcripts in the non-remitter group comprised TH2- and eosinophil-related genes including ALOX15, FCER1A, and OLIG2. Network construction identified transcript modules that were coherently expressed at baseline and in non-remitting patients but were disrupted at early time points in remitting patients. These modules reflected processes such as interferon signaling, erythropoiesis, and platelet aggregation. DNA methylation analysis identified remission-specific temporal changes, which partially overlapped with transcriptomic signals. Machine learning approaches identified features from differentially expressed genes cis-linked to DNA methylation changes at week 2 as a robust predictor of therapy outcome at week 14, which was validated in a publicly available dataset of 20 infliximab-treated CD patients. Conclusions Integrative multi-omics analysis reveals early shifts of gene expression and DNA methylation as predictors for efficient response to anti-TNF treatment. Lack of such signatures might be used to identify patients with IBD unlikely to benefit from TNF antagonists at an early time point. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01112-z.
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Nowak JK, Adams AT, Kalla R, Lindstrøm JC, Vatn S, Bergemalm D, Keita ÅV, Gomollón F, Jahnsen J, Vatn MH, Ricanek P, Ostrowski J, Walkowiak J, Halfvarson J, Satsangi J. Characterisation of the Circulating Transcriptomic Landscape in Inflammatory Bowel Disease Provides Evidence for Dysregulation of Multiple Transcription Factors Including NFE2, SPI1, CEBPB, and IRF2. J Crohns Colitis 2022; 16:1255-1268. [PMID: 35212366 PMCID: PMC9426667 DOI: 10.1093/ecco-jcc/jjac033] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 01/11/2022] [Accepted: 02/23/2022] [Indexed: 01/11/2023]
Abstract
AIM To assess the pathobiological and translational importance of whole-blood transcriptomic analysis in inflammatory bowel disease [IBD]. METHODS We analysed whole-blood expression profiles from paired-end sequencing in a discovery cohort of 590 Europeans recruited across six countries in the IBD Character initiative (newly diagnosed patients with Crohn's disease [CD; n = 156], ulcerative colitis [UC; n = 167], and controls [n = 267]), exploring differential expression [DESeq2], co-expression networks [WGCNA], and transcription factor involvement [EPEE, ChEA, DoRothEA]. Findings were validated by analysis of an independent replication cohort [99 CD, 100 UC, 95 controls]. In the discovery cohort, we also defined baseline expression correlates of future treatment escalation using cross-validated elastic-net and random forest modelling, along with a pragmatic ratio detection procedure. RESULTS Disease-specific transcriptomes were defined in IBD [8697 transcripts], CD [7152], and UC [8521], with the most highly significant changes in single genes, including CD177 (log2-fold change [LFC] = 4.63, p = 4.05 × 10-118), MCEMP1 [LFC = 2.45, p = 7.37 × 10-109], and S100A12 [LFC = 2.31, p = 2.15 × 10-93]. Significantly over-represented pathways included IL-1 [p = 1.58 × 10-11], IL-4, and IL-13 [p = 8.96 × 10-9]. Highly concordant results were obtained using multiple regulatory activity inference tools applied to the discovery and replication cohorts. These analyses demonstrated central roles in IBD for the transcription factors NFE2, SPI1 [PU.1], CEBPB, and IRF2, all regulators of cytokine signalling, based on a consistent signal across cohorts and transcription factor ranking methods. A number of simple transcriptome-based models were associated with the need for treatment escalation, including the binary CLEC5A/CDH2 expression ratio in UC (hazard ratio = 23.4, 95% confidence interval [CI] 5.3-102.0). CONCLUSIONS Transcriptomic analysis has allowed for a detailed characterisation of IBD pathobiology, with important potential translational implications.
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Affiliation(s)
- Jan K Nowak
- Corresponding authors: Dr Jan K. Nowak, Translational Gastroenterology Unit, Experimental Medicine Division, John Radcliffe Hospital, Headley Way, Headington, Oxford OX3 9DU, UK.
| | | | - Rahul Kalla
- MRC Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Jonas C Lindstrøm
- Health Services Research Unit, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Simen Vatn
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
| | - Daniel Bergemalm
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Åsa V Keita
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | | | - Jørgen Jahnsen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
| | - Morten H Vatn
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- EpiGen Institute, Akershus University Hospital, University of Oslo, Oslo, Norway
| | - Petr Ricanek
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
| | - Jerzy Ostrowski
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre for Postgraduate Medical Education, Warsaw, Poland
| | - Jaroslaw Walkowiak
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Jack Satsangi
- Jack Satsangi, Translational Gastroenterology Unit, Experimental Medicine Division, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK.
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42
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Noor NM, Sousa P, Paul S, Roblin X. Early Diagnosis, Early Stratification, and Early Intervention to Deliver Precision Medicine in IBD. Inflamm Bowel Dis 2022; 28:1254-1264. [PMID: 34480558 PMCID: PMC9340521 DOI: 10.1093/ibd/izab228] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Indexed: 12/15/2022]
Abstract
Despite huge advances in understanding the molecular basis of IBD, clinical management has continued to rely on a "trial and error" approach. In addition, a therapeutic ceiling has emerged whereby even the most effective interventions are only beneficial for approximately 30% of patients. Consequently, several tools have been developed to aid stratification and guide treatment-decisions. We review the potential application for many of these precision medicine approaches, which are now almost within reach. We highlight the importance of early action (and avoiding inaction) to ensure the best outcomes for patients and how combining early action with precision tools will likely ensure the right treatment is delivered at the right time and place for each individual person living with IBD. The lack of clinical impact to date from precision medicine, despite much hype and investment, should be tempered with the knowledge that clinical translation can take a long time, and many promising breakthroughs might be ready for clinical implementation in the near future. We discuss some of the remaining challenges and barriers to overcome for clinical adoption. We also highlight that early recognition, early diagnosis, early stratification, and early intervention go hand in hand with precision medicine tools. It is the combination of these approaches that offer the greatest opportunity to finally deliver on the promise of precision medicine in IBD.
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Affiliation(s)
- Nurulamin M Noor
- Department of Gastroenterology, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Trust, Cambridge, United Kingdom
- Medical Research Council Clinical Trials Unit, University College London, London, United Kingdom
| | - Paula Sousa
- Department of Gastroenterology, Viseu Unit, Tondela-Viseu Hospital Centre, 3504–509 Viseu, Portugal
| | - Stéphane Paul
- Faculty of Medicine of Saint-Etienne, Immunology Unit University Hospital of Saint-Etienne, CIC INSERM 1408, Saint-Etienne, France
| | - Xavier Roblin
- Department of Gastroenterology, University Hospital of Sain- Etienne, Saint-Etienne, France
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43
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Swaminathan A, Mules TC, Gearry RB. Editorial: measuring disease severity in inflammatory bowel disease-the whole is greater than the sum of its parts. Authors' reply. Aliment Pharmacol Ther 2022; 56:746-747. [PMID: 35879891 DOI: 10.1111/apt.17126] [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: 12/09/2022]
Affiliation(s)
- Akhilesh Swaminathan
- Department of Medicine, University of Otago, Christchurch, Christchurch, New Zealand.,Department of Gastroenterology, Christchurch Hospital, Christchurch, New Zealand
| | - Thomas C Mules
- Department of Gastroenterology, Christchurch Hospital, Christchurch, New Zealand
| | - Richard B Gearry
- Department of Medicine, University of Otago, Christchurch, Christchurch, New Zealand.,Department of Gastroenterology, Christchurch Hospital, Christchurch, New Zealand
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44
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Swaminathan A, Fan D, Borichevsky GM, Mules TC, Hirschfeld E, Frampton CM, Day AS, Siegel CA, Gearry RB. The disease severity index for inflammatory bowel disease is associated with psychological symptoms and quality of life, and predicts a more complicated disease course. Aliment Pharmacol Ther 2022; 56:664-674. [PMID: 35633043 PMCID: PMC9545845 DOI: 10.1111/apt.17058] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/10/2022] [Accepted: 05/17/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND The Disease Severity Index (DSI) is a novel tool to predict disease severity in inflammatory bowel disease (IBD). However, its ability to predict disease complications and the presence of psychosocial comorbidity is unclear. AIMS To assess prospectively associations between the DSI and psychological symptoms, quality-of-life (QoL) and disease outcomes in an IBD cohort. METHODS Patients with IBD undergoing ileocolonoscopy were followed prospectively for 12 months. DSI, psychological symptoms (perceived stress (PSS-10), depression (PHQ-9), anxiety (GAD-7)) and QoL (IBDQ-32) scores were assessed at baseline. Logistic regression identified variables predicting a complicated IBD course at 12 months (composite outcome of need for escalation of biological/immunomodulator for disease relapse, recurrent corticosteroid use, IBD-related hospitalisation and surgery). Receiver operating characteristics (ROC) analysis identified optimal DSI thresholds predicting a complicated disease course and multivariable logistic regression assessed the risk of reaching this outcome. RESULTS One hundred and seventy-two patients were recruited (100 Crohn's disease, 91 female). Median DSI was 21 (IQR 11-32) and 97 patients had endoscopically active disease at baseline. The DSI was significantly higher in patients with symptoms of moderate-severe stress (PSS-10 > 14, p < 0.01), depression (PHQ-9 ≥ 10, p < 0.01), anxiety (GAD-7 ≥ 10, p < 0.05) and impaired quality-of-life (IBDQ-32 < 168, p < 0.01). Only the baseline DSI (OR 1.05, p < 0.01) and endoscopically active disease (OR 6.12, p < 0.01) were associated with a complicated IBD course. A DSI > 23 was strongly predictive of a complicated IBD course (OR 8.31, p < 0.001). CONCLUSIONS The DSI is associated with psychological distress, impaired QoL and predicts a more complicated disease course in patients with IBD.
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Affiliation(s)
- Akhilesh Swaminathan
- Department of MedicineUniversity of OtagoChristchurchNew Zealand,Department of GastroenterologyChristchurch hospitalChristchurchNew Zealand
| | - Dali Fan
- Department of GastroenterologyChristchurch hospitalChristchurchNew Zealand
| | | | - Thomas C. Mules
- Department of GastroenterologyChristchurch hospitalChristchurchNew Zealand
| | | | | | - Andrew S. Day
- Department of PaediatricsUniversity of OtagoChristchurchNew Zealand
| | - Corey A. Siegel
- Inflammatory Bowel Disease Centre, Section of Gastroenterology and HepatologyDartmouth Hitchcock Medical CentreLebanonNew HampshireUSA
| | - Richard B. Gearry
- Department of MedicineUniversity of OtagoChristchurchNew Zealand,Department of GastroenterologyChristchurch hospitalChristchurchNew Zealand
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45
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Noor N, Brezina B, Negro JDLR, Dowling F, Bond S, Whitehead L, Lee J, Lyons P, McKinney E, Smith K, Lee J, Parkes M. Predicting outcomes for Crohn's disease using a molecular biomarker: profile trial. Clin Med (Lond) 2022; 22 Suppl 4:22-23. [PMID: 38614568 PMCID: PMC9600841 DOI: 10.7861/clinmed.22-4-s22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Nurulamin Noor
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Biljana Brezina
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | | | - Simon Bond
- Cambridge Clinical Trials Unit, Cambridge, UK
| | - Lynne Whitehead
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jacinta Lee
- University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Paul Lyons
- University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Eoin McKinney
- University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Kenneth Smith
- University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - James Lee
- The Francis Crick Institute, London, UK
| | - Miles Parkes
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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46
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High-dimensional profiling reveals Tc17 cell enrichment in active Crohn's disease and identifies a potentially targetable signature. Nat Commun 2022; 13:3688. [PMID: 35760777 PMCID: PMC9237103 DOI: 10.1038/s41467-022-31229-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 05/25/2022] [Indexed: 11/20/2022] Open
Abstract
The immune-pathology in Crohn’s disease is linked to dysregulated CD4+ T cell responses biased towards pathogenic TH17 cells. However, the role of CD8+ T cells able to produce IL-17 (Tc17 cells) remains unclear. Here we characterize the peripheral blood and intestinal tissue of Crohn’s disease patients (n = 61) with flow and mass cytometry and reveal a strong increase of Tc17 cells in active disease, mainly due to induction of conventional T cells. Mass cytometry shows that Tc17 cells express a distinct immune signature (CD6high, CD39, CD69, PD-1, CD27low) which was validated in an independent patient cohort. This signature stratifies patients into groups with distinct flare-free survival associated with differential CD6 expression. Targeting of CD6 in vitro reduces IL-17, IFN-γ and TNF production. These results identify a distinct Tc17 cell population in Crohn’s disease with proinflammatory features linked to disease activity. The Tc17 signature informs clinical outcomes and may guide personalized treatment decisions. The T cell compartment in patients with Crohn's disease is dysregulated. Here the authors use cytometric profiling to reveal an enrichment of distinct Tc17 cells during active Crohn's disease and may suggest CD6 as a potential target for therapeutic studies.
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47
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Söderman J, Berglind L, Almer S. Inverse and Concordant Mucosal Pathway Gene Expressions in Inflamed and Non-Inflamed Ulcerative Colitis Patients: Potential Relevance to Aetiology and Pathogenesis. Int J Mol Sci 2022; 23:ijms23136944. [PMID: 35805947 PMCID: PMC9266769 DOI: 10.3390/ijms23136944] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/17/2022] [Accepted: 06/21/2022] [Indexed: 02/05/2023] Open
Abstract
Ulcerative colitis (UC) arises from a complex interplay between host and environmental factors, but with a largely unsolved pathophysiology. The pathophysiology was outlined by RNA-sequencing of mucosal biopsies from non-inflamed and inflamed colon of UC patients (14 and 17, respectively), and from 27 patients without intestinal inflammation. Genes differentially expressed (DE), or present in enriched gene sets, were investigated using statistical text analysis of functional protein information. Compared with controls, inflamed and non-inflamed UC mucosa displayed 9360 and 52 DE genes, respectively. Seventy-three non-pseudogenes were DE relative to both gender and inflammation. Mitochondrial processes were downregulated in inflamed and upregulated in non-inflamed UC mucosa, whereas angiogenesis and endoplasmic reticulum (ER) stress were upregulated in both tissue states. Immune responses were upregulated in inflamed mucosa, whereas the non-inflamed UC mucosa presented both up- and downregulated gene sets. DE and enriched genes overlapped with genes present in inflammatory bowel disease genome-wide associated loci (p = 1.43 × 10−18), especially regarding immune responses, respiratory chain, angiogenesis, ER stress, and steroid hormone metabolism. Apart from confirming established pathophysiological mechanisms of immune cells, our study provides evidence for involvement of less described pathways (e.g., respiratory chain, ER stress, fatty-acid oxidation, steroid hormone metabolism and angiogenesis).
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Affiliation(s)
- Jan Söderman
- Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden
- Laboratory Medicine, Region Jönköping County, 551 85 Jönköping, Sweden;
- Correspondence:
| | - Linda Berglind
- Laboratory Medicine, Region Jönköping County, 551 85 Jönköping, Sweden;
| | - Sven Almer
- Department of Medicine, Solna, Karolinska Institutet, 171 77 Stockholm, Sweden;
- IBD Unit, Division of Gastroenterology, Karolinska University Hospital, 171 76 Stockholm, Sweden
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48
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Noor NM, Lee JC. The Endoscopic Healing Index in Crohn's Disease: A Serum Proteomic Biomarker for Monitoring Disease Activity. Inflamm Bowel Dis 2022; 29:669-671. [PMID: 35704706 DOI: 10.1093/ibd/izac126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Indexed: 12/09/2022]
Affiliation(s)
- Nurulamin M Noor
- Department of Gastroenterology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom.,Medical Research Council Clinical Trials Unit, University College London, London, United Kingdom
| | - James C Lee
- Francis Crick Institute, London, United Kingdom.,Institute of Liver and Digestive Health, Division of Medicine, University College London London, United Kingdom
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49
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Stafford IS, Gosink MM, Mossotto E, Ennis S, Hauben M. A Systematic Review of Artificial Intelligence and Machine Learning Applications to Inflammatory Bowel Disease, with Practical Guidelines for Interpretation. Inflamm Bowel Dis 2022; 28:1573-1583. [PMID: 35699597 PMCID: PMC9527612 DOI: 10.1093/ibd/izac115] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND Inflammatory bowel disease (IBD) is a gastrointestinal chronic disease with an unpredictable disease course. Computational methods such as machine learning (ML) have the potential to stratify IBD patients for the provision of individualized care. The use of ML methods for IBD was surveyed, with an additional focus on how the field has changed over time. METHODS On May 6, 2021, a systematic review was conducted through a search of MEDLINE and Embase databases, with the search structure ("machine learning" OR "artificial intelligence") AND ("Crohn* Disease" OR "Ulcerative Colitis" OR "Inflammatory Bowel Disease"). Exclusion criteria included studies not written in English, no human patient data, publication before 2001, studies that were not peer reviewed, nonautoimmune disease comorbidity research, and record types that were not primary research. RESULTS Seventy-eight (of 409) records met the inclusion criteria. Random forest methods were most prevalent, and there was an increase in neural networks, mainly applied to imaging data sets. The main applications of ML to clinical tasks were diagnosis (18 of 78), disease course (22 of 78), and disease severity (16 of 78). The median sample size was 263. Clinical and microbiome-related data sets were most popular. Five percent of studies used an external data set after training and testing for additional model validation. DISCUSSION Availability of longitudinal and deep phenotyping data could lead to better modeling. Machine learning pipelines that consider imbalanced data and that feature selection only on training data will generate more generalizable models. Machine learning models are increasingly being applied to more complex clinical tasks for specific phenotypes, indicating progress towards personalized medicine for IBD.
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Affiliation(s)
| | | | - Enrico Mossotto
- Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
| | - Sarah Ennis
- Address correspondence to: Sarah Ennis, Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK ()
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50
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Gergely M, Deepak P. Tools for the Diagnosis and Management of Crohn's Disease. Gastroenterol Clin North Am 2022; 51:213-239. [PMID: 35595412 DOI: 10.1016/j.gtc.2021.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Numerous tools have emerged over recent decades to aid in the increasingly complex management of patients with Crohn's disease (CD) beyond endoscopy, including video capsule endoscopy, magnetic resonance enterography, computed tomography enterography, a variety of biomarkers, and even wearable biosensors and smartphone applications. These tools have allowed for a more sophisticated and less invasive complementary approach to the evaluation of disease activity and treatment response in patients with CD. This article details the characteristics, practical application, and limitations of these various modalities and discusses how updated guidelines are now incorporating many of them into a treat-to-target strategy.
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Affiliation(s)
- Maté Gergely
- Division of Gastroenterology, Inflammatory Bowel Diseases Center, Washington University School of Medicine, 600 South Euclid Avenue, Campus Box 8124, Saint Louis, MO 63110, USA
| | - Parakkal Deepak
- Division of Gastroenterology, Inflammatory Bowel Diseases Center, Washington University School of Medicine, 600 South Euclid Avenue, Campus Box 8124, Saint Louis, MO 63110, USA.
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