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Xiao MJ, Pan YT, Tan JH, Li HO, Wang HY. Computed tomography-based radiomics combined with machine learning allows differentiation between primary intestinal lymphoma and Crohn's disease. World J Gastroenterol 2024; 30:3155-3165. [PMID: 39006389 PMCID: PMC11238674 DOI: 10.3748/wjg.v30.i25.3155] [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: 01/09/2024] [Revised: 05/20/2024] [Accepted: 06/07/2024] [Indexed: 07/01/2024] Open
Abstract
BACKGROUND Due to similar clinical manifestations and imaging signs, differential diagnosis of primary intestinal lymphoma (PIL) and Crohn's disease (CD) is a challenge in clinical practice. AIM To investigate the ability of radiomics combined with machine learning methods to differentiate PIL from CD. METHODS We collected contrast-enhanced computed tomography (CECT) and clinical data from 120 patients form center 1. A total of 944 features were extracted single-phase images of CECT scans. Using the last absolute shrinkage and selection operator model, the best predictive radiographic features and clinical indications were screened. Data from 54 patients were collected at center 2 as an external validation set to verify the robustness of the model. The area under the receiver operating characteristic curve, accuracy, sensitivity and specificity were used for evaluation. RESULTS A total of five machine learning models were built to distinguish PIL from CD. Based on the results from the test group, most models performed well with a large area under the curve (AUC) (> 0.850) and high accuracy (> 0.900). The combined clinical and radiomics model (AUC = 1.000, accuracy = 1.000) was the best model among all models. CONCLUSION Based on machine learning, a model combining clinical data with radiologic features was constructed that can effectively differentiate PIL from CD.
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Affiliation(s)
- Meng-Jun Xiao
- Department of Radiology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong Province, China
| | - Yu-Teng Pan
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250000, Shandong Province, China
| | - Jia-He Tan
- University of California, Davis, CA 95616, United States
| | - Hai-Ou Li
- Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong Province, China
| | - Hai-Yan Wang
- Department of Radiology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong Province, 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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Syed S, Boland BS, Bourke LT, Chen LA, Churchill L, Dobes A, Greene A, Heller C, Jayson C, Kostiuk B, Moss A, Najdawi F, Plung L, Rioux JD, Rosen MJ, Torres J, Zulqarnain F, Satsangi J. Challenges in IBD Research 2024: Precision Medicine. Inflamm Bowel Dis 2024; 30:S39-S54. [PMID: 38778628 DOI: 10.1093/ibd/izae084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Indexed: 05/25/2024]
Abstract
Precision medicine is part of 5 focus areas of the Challenges in IBD Research 2024 research document, which also includes preclinical human IBD mechanisms, environmental triggers, novel technologies, and pragmatic clinical research. Building on Challenges in IBD Research 2019, the current Challenges aims to provide a comprehensive overview of current gaps in inflammatory bowel diseases (IBDs) research and deliver actionable approaches to address them with a focus on how these gaps can lead to advancements in interception, remission, and restoration for these diseases. The document is the result of multidisciplinary input from scientists, clinicians, patients, and funders, and represents a valuable resource for patient-centric research prioritization. In particular, the precision medicine section is focused on the main research gaps in elucidating how to bring the best care to the individual patient in IBD. Research gaps were identified in biomarker discovery and validation for predicting disease progression and choosing the most appropriate treatment for each patient. Other gaps were identified in making the best use of existing patient biosamples and clinical data, developing new technologies to analyze large datasets, and overcoming regulatory and payer hurdles to enable clinical use of biomarkers. To address these gaps, the Workgroup suggests focusing on thoroughly validating existing candidate biomarkers, using best-in-class data generation and analysis tools, and establishing cross-disciplinary teams to tackle regulatory hurdles as early as possible. Altogether, the precision medicine group recognizes the importance of bringing basic scientific biomarker discovery and translating it into the clinic to help improve the lives of IBD patients.
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Affiliation(s)
- Sana Syed
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
- Patient representative for Crohn's & Colitis Foundation, New York, NY, USA
| | - Brigid S Boland
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lauren T Bourke
- Precision Medicine Drug Development, Early Respiratory and Immunology, AstraZeneca, Boston, MA, USA
| | - Lea Ann Chen
- Division of Gastroenterology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Laurie Churchill
- Leona M. and Harry B. Helmsley Charitable Trust, New York, NY, USA
| | | | - Adam Greene
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | | | | | | | - Alan Moss
- Crohn's & Colitis Foundation, New York, NY, USA
| | | | - Lori Plung
- Patient representative for Crohn's & Colitis Foundation, New York, NY, USA
| | - John D Rioux
- Research Center, Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | - Michael J Rosen
- Division of Pediatric Gastroenterology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Joana Torres
- Division of Gastroenterology, Hospital Beatriz Ângelo, Hospital da Luz, Lisbon, Portugal
- Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Fatima Zulqarnain
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | - Jack Satsangi
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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Jagirdhar GSK, Perez JA, Perez AB, Surani S. Integration and implementation of precision medicine in the multifaceted inflammatory bowel disease. World J Gastroenterol 2023; 29:5211-5225. [PMID: 37901450 PMCID: PMC10600960 DOI: 10.3748/wjg.v29.i36.5211] [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: 07/01/2023] [Revised: 07/31/2023] [Accepted: 09/06/2023] [Indexed: 09/20/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a complex disease with variability in genetic, environmental, and lifestyle factors affecting disease presentation and course. Precision medicine has the potential to play a crucial role in managing IBD by tailoring treatment plans based on the heterogeneity of clinical and temporal variability of patients. Precision medicine is a population-based approach to managing IBD by integrating environmental, genomic, epigenomic, transcriptomic, proteomic, and metabolomic factors. It is a recent and rapidly developing medicine. The widespread adoption of precision medicine worldwide has the potential to result in the early detection of diseases, optimal utilization of healthcare resources, enhanced patient outcomes, and, ultimately, improved quality of life for individuals with IBD. Though precision medicine is promising in terms of better quality of patient care, inadequacies exist in the ongoing research. There is discordance in study conduct, and data collection, utilization, interpretation, and analysis. This review aims to describe the current literature on precision medicine, its multiomics approach, and future directions for its application in IBD.
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Affiliation(s)
| | - Jose Andres Perez
- Department of Medicine, Saint Francis Health Systems, Tulsa, OK 74133, United States
| | - Andrea Belen Perez
- Department of Research, Columbia University, New York, NY 10027, United States
| | - Salim Surani
- Department of Medicine and Pharmacology, Texas A&M University, College Station, TX 77413, United States
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Alfonso Perez G, Castillo R. Gene Identification in Inflammatory Bowel Disease via a Machine Learning Approach. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:1218. [PMID: 37512030 PMCID: PMC10383667 DOI: 10.3390/medicina59071218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/24/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023]
Abstract
Inflammatory bowel disease (IBD) is an illness with increasing prevalence, particularly in emerging countries, which can have a substantial impact on the quality of life of the patient. The illness is rather heterogeneous with different evolution among patients. A machine learning approach is followed in this paper to identify potential genes that are related to IBD. This is done by following a Monte Carlo simulation approach. In total, 23 different machine learning techniques were tested (in addition to a base level obtained using artificial neural networks). The best model identified 74 genes selected by the algorithm as being potentially involved in IBD. IBD seems to be a polygenic illness, in which environmental factors might play an important role. Following a machine learning approach, it was possible to obtain a classification accuracy of 84.2% differentiating between patients with IBD and control cases in a large cohort of 2490 total cases. The sensitivity and specificity of the model were 82.6% and 84.4%, respectively. It was also possible to distinguish between the two main types of IBD: (1) Crohn's disease and (2) ulcerative colitis.
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Affiliation(s)
- Gerardo Alfonso Perez
- Biocomp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castello, Spain
| | - Raquel Castillo
- Biocomp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castello, Spain
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Gavrilescu O, Popa IV, Dranga M, Mihai R, Cijevschi Prelipcean C, Mihai C. Laboratory Data and IBDQ-Effective Predictors for the Non-Invasive Machine-Learning-Based Prediction of Endoscopic Activity in Ulcerative Colitis. J Clin Med 2023; 12:jcm12113609. [PMID: 37297804 DOI: 10.3390/jcm12113609] [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: 03/19/2023] [Revised: 05/14/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
A suitable, non-invasive biomarker for assessing endoscopic disease activity (EDA) in ulcerative colitis (UC) has yet to be identified. Our study aimed to develop a cost-effective and non-invasive machine learning (ML) method that utilizes the cost-free Inflammatory Bowel Disease Questionnaire (IBDQ) score and low-cost biological predictors to estimate EDA. Four random forest (RF) and four multilayer perceptron (MLP) classifiers were proposed. The results show that the inclusion of IBDQ in the list of predictors that were fed to the models improved accuracy and the AUC for both the RF and the MLP algorithms. Moreover, the RF technique performed noticeably better than the MLP method on unseen data (the independent patient cohort). This is the first study to propose the use of IBDQ as a predictor in an ML model to estimate UC EDA. The deployment of this ML model can furnish doctors and patients with valuable insights into EDA, a highly beneficial resource for individuals with UC who need long-term treatment.
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Affiliation(s)
- Otilia Gavrilescu
- Medicale I Department, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
- "Saint Spiridon" County Hospital, 700111 Iasi, Romania
| | - Iolanda Valentina Popa
- Medicale II Department, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Mihaela Dranga
- Medicale I Department, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
- "Saint Spiridon" County Hospital, 700111 Iasi, Romania
| | - Ruxandra Mihai
- Medicale II Department, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | | | - Cătălina Mihai
- Medicale I Department, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
- "Saint Spiridon" County Hospital, 700111 Iasi, Romania
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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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Sahu M, Gupta R, Ambasta RK, Kumar P. Artificial intelligence and machine learning in precision medicine: A paradigm shift in big data analysis. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 190:57-100. [PMID: 36008002 DOI: 10.1016/bs.pmbts.2022.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The integration of artificial intelligence in precision medicine has revolutionized healthcare delivery. Precision medicine identifies the phenotype of particular patients with less-common responses to treatment. Recent studies have demonstrated that translational research exploring the convergence between artificial intelligence and precision medicine will help solve the most difficult challenges facing precision medicine. Here, we discuss different aspects of artificial intelligence in precision medicine that improve healthcare delivery. First, we discuss how artificial intelligence changes the landscape of precision medicine and the evolution of artificial intelligence in precision medicine. Second, we highlight the synergies between artificial intelligence and precision medicine and promises of artificial intelligence and precision medicine in healthcare delivery. Third, we briefly explain the promise of big data analytics and the integration of nanomaterials in precision medicine. Last, we highlight the challenges and opportunities of artificial intelligence in precision medicine.
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Affiliation(s)
- Mehar Sahu
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly Delhi College of Engineering), Shahbad Daulatpur, Delhi, India
| | - Rohan Gupta
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly Delhi College of Engineering), Shahbad Daulatpur, Delhi, India
| | - Rashmi K Ambasta
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly Delhi College of Engineering), Shahbad Daulatpur, Delhi, India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly Delhi College of Engineering), Shahbad Daulatpur, Delhi, India.
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Wong ECL, Yusuf A, Pokryszka J, Dulai PS, Colombel JF, Marshall JK, Reinisch W, Narula N. Increased Expression of Interleukin-13 Receptor in Ileum Associated With Nonresponse to Adalimumab in Ileal Crohn's Disease. Inflamm Bowel Dis 2022:6650010. [PMID: 35880680 DOI: 10.1093/ibd/izac157] [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: 05/10/2022] [Indexed: 12/09/2022]
Abstract
BACKGROUND The terminal ileum poses a predilection for Crohn's disease (CD) but is less susceptible to undergo healing to treatment with biologics and small molecules. This study aimed to evaluate histologic features associated with endoscopic remission (ER). METHODS This is a post hoc analysis of patients with moderately to severely active CD, defined as Crohn's disease activity index 220 to 450, and terminal ileal ulceration treated with antitumor necrosis factor (TNF)-α inhibitor adalimumab from the EXTEND trial. We studied whether baseline total Global Histologic Disease Activity Scores (GHAS), any individual histologic element, and specific immunohistochemical (IHC) markers of chronic inflammation from biopsy specimens were associated with postinduction (week 12) and maintenance (week 52) ER, defined as Simple Endoscopic Score for Crohn's Disease of 0. Multivariable logistic regression models adjusted for confounders were used to assess the relationship between histologic markers and 1-year outcomes. RESULTS Seventy-one adult patients with CD affecting the ileum were included in this analysis. Both baseline ileal GHAS scores and individual histologic components were not found to be associated with ER at weeks 12 or 52. Increased expression of interleukin-13 receptor (IL-13R) on IHC stains was associated with reduced likelihood of achieving 1-year ER (adjusted odds ratio, 0.06; 95% CI, 0.01-0.92; P = .044). No other biomarker assessed was associated with 1-year ER. CONCLUSIONS Ileal histologic disease activity and IHC activation markers of chronic mucosal inflammation were not associated with 1-year ER. However, strong staining for IL-13 receptor in the ileum was associated with reduced odds of 1-year ER using adalimumab. Mucosal cellular disease profiles might pose an opportunity to guide treatment of CD.
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Affiliation(s)
- Emily C L Wong
- Department of Medicine, Division of Gastroenterology, and Farncombe Family Digestive Health Research Institute; McMaster University, Hamilton ON, Canada
| | - Arif Yusuf
- Department of Medicine, Division of Gastroenterology, and Farncombe Family Digestive Health Research Institute; McMaster University, Hamilton ON, Canada
| | - Jagoda Pokryszka
- Department of Internal Medicine III, Division of Gastroenterology and Hepatology, Medical University of Vienna, Währinger Gürtel 18-20, Vienna, Austria
| | - Parambir S Dulai
- Division of Gastroenterology, Northwestern University, Chicago, IL, USA
| | - Jean-Frederic Colombel
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John K Marshall
- Department of Medicine, Division of Gastroenterology, and Farncombe Family Digestive Health Research Institute; McMaster University, Hamilton ON, Canada
| | - Walter Reinisch
- Department of Internal Medicine III, Division of Gastroenterology and Hepatology, Medical University of Vienna, Währinger Gürtel 18-20, Vienna, Austria
| | - Neeraj Narula
- Department of Medicine, Division of Gastroenterology, and Farncombe Family Digestive Health Research Institute; McMaster University, Hamilton ON, Canada
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