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Atia O, Buchuk R, Lujan R, Greenfeld S, Kariv R, Loewenberg Weisband Y, Lederman N, Matz E, Ledder O, Zittan E, Yanai H, Shwartz D, Freiman M, Dotan I, Nevo D, Turner D. Predictors of Complicated Disease Course in Children and Adults With Ulcerative Colitis: A Nationwide Study From the epi-IIRN. Inflamm Bowel Dis 2024:izae094. [PMID: 38768390 DOI: 10.1093/ibd/izae094] [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: 11/30/2023] [Indexed: 05/22/2024]
Abstract
BACKGROUND Data on predictors of complicated ulcerative colitis (UC) course from unselected populations cohorts are scarce. We aimed to utilize a nationwide cohort to explore predictors at diagnosis of disease course in children and adults with UC. METHODS Data of patients diagnosed with UC since 2005 were retrieved from the nationwide epi-IIRN cohort. Complicated disease course was defined as colectomy, steroid-dependency, or the need for biologic drugs. Hierarchical clustering categorized disease severity at diagnosis based on complete blood count, albumin, C-reactive protein and erythrocyte sedimentation rate (ESR), analyzed together. RESULTS A total of 13 471 patients with UC (1427 [11%] pediatric-onset) including 103 212 person-years of follow-up were included. Complicated disease course was recorded in 2829 (21%) patients: 1052 (7.9%) escalated to biologics, 1357 (10%) experienced steroid-dependency, and 420 (3.1%) underwent colectomy. Probabilities of complicated disease course at 1 and 5 years from diagnosis were higher in pediatric-onset (11% and 32%, respectively) than adult-onset disease (4% and 16%; P < .001). In a Cox multivariate model, complicated course was predicted by induction therapy with steroids (hazard ratio [HR], 1.5; 95% CI, 1.2-2.0), extraintestinal manifestations (HR, 1.3; 95% CI, 1.03-1.5) and the disease severity clusters of blood tests (HR, 1.8; 95% CI, 1.01-3.1), while induction therapy with enemas (HR, 0.6; 95% CI, 0.5-0.7) and older age (HR, 0.99; 95% CI, 0.98-0.99) were associated with noncomplicated course. CONCLUSION In this nationwide cohort, the probability of complicated disease course during the first 5 years from diagnosis was 32% in pediatric-onset and 16% in adults with UC and was associated with more severe clusters of routinely collected laboratory tests, younger age at diagnosis, extraintestinal manifestations, and type of induction therapy.
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Affiliation(s)
- Ohad Atia
- Juliet Keidan Institute of Pediatric Gastroenterology Hepatology and Nutrition, Shaare Zedek Medical Center, The Hebrew University of Jerusalem, Israel
| | - Rachel Buchuk
- Juliet Keidan Institute of Pediatric Gastroenterology Hepatology and Nutrition, Shaare Zedek Medical Center, The Hebrew University of Jerusalem, Israel
| | - Rona Lujan
- Juliet Keidan Institute of Pediatric Gastroenterology Hepatology and Nutrition, Shaare Zedek Medical Center, The Hebrew University of Jerusalem, Israel
| | - Shira Greenfeld
- Maccabi Health Services, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Israel
| | - Revital Kariv
- Maccabi Health Services, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Israel
| | | | | | - Eran Matz
- Leumit Health Services, Tel Aviv, Israel
| | - Oren Ledder
- Juliet Keidan Institute of Pediatric Gastroenterology Hepatology and Nutrition, Shaare Zedek Medical Center, The Hebrew University of Jerusalem, Israel
| | - Eran Zittan
- The Abraham and Sonia Rochlin IBD Unit, Institute of Gastroenterology and Liver Diseases, Emek Medical Center, Afula, Israel
- The Rappaport Faculty of Medicine Technion-Israel Institute of Technology, Haifa, Israel
| | - Henit Yanai
- Sackler Faculty of Medicine, Tel Aviv University, Israel
- Division of Gastroenterology, Rabin Medical Center, Petah Tikva and the Faculty of Medicine, Tel Aviv University, Israel
| | - Doron Shwartz
- Department of Gastroenterology and Hepatology, Soroka Medical Center, Ben-Gurion University of the Negev, Beer- Sheva, Israel
| | - Moti Freiman
- Faculty of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Iris Dotan
- Sackler Faculty of Medicine, Tel Aviv University, Israel
- Division of Gastroenterology, Rabin Medical Center, Petah Tikva and the Faculty of Medicine, Tel Aviv University, Israel
| | - Daniel Nevo
- Department of Statistics and Operations Research, Tel Aviv University, Israel
| | - Dan Turner
- Juliet Keidan Institute of Pediatric Gastroenterology Hepatology and Nutrition, Shaare Zedek Medical Center, The Hebrew University of Jerusalem, Israel
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2
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Arva NC, Bernieh A, Lopez-Nunez O, Pletneva M, Yang GY, Collins MH. Histopathology of Eosinophilic Gastrointestinal Diseases Beyond Eosinophilic Esophagitis. Immunol Allergy Clin North Am 2024; 44:369-381. [PMID: 38575230 DOI: 10.1016/j.iac.2024.01.008] [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] [Indexed: 04/06/2024]
Abstract
Eosinophilic gastrointestinal diseases (EGID), such as eosinophilic gastritis (EoG), eosinophilic enteritis, and eosinophilic colitis (EoC), are chronic inflammatory conditions characterized by persistent gastrointestinal symptoms and elevated levels of activated eosinophils in the gastrointestinal tract. EoG and eosinophilic duodenitis (EoD) are strongly associated with food allergen triggers and TH2 inflammation, whereas EoC shows minimal transcriptomic overlap with other EGIDs. The level of expression of certain genes associated with TH2 immune response is associated with certain histopathologic findings of EoG, EoD, and EoC. Current immune therapy for EoG depletes tissue eosinophilia with persistence of other histopathologic features of disease.
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Affiliation(s)
- Nicoleta C Arva
- Department of Pathology, Nationwide Children's Hospital, 700 Childrens Drive, Columbus, OH 43205, USA.
| | - Anas Bernieh
- Division of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Oscar Lopez-Nunez
- Division of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Maria Pletneva
- Department of Pathology, University of Utah, 2000 Circle of Hope, Room 3100, Salt Lake City, UT 84112, USA
| | - Guang-Yu Yang
- Department of Pathology, Northwestern University Feinberg School of Medicine, 303 East Chicago Avenue, Chicago, IL 60611, USA
| | - Margaret H Collins
- Division of Pathology and Laboratory Medicine, ML1035, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
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Iacucci M, Maeda Y, Ghosh S. A Baby Step or a Real Giant Stride: Histomic Enabled by Artificial Intelligence to Predict Treatment Response in Pediatric Patients With Ulcerative Colitis. Gastroenterology 2024; 166:730-732. [PMID: 38460608 DOI: 10.1053/j.gastro.2024.03.004] [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: 02/29/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Affiliation(s)
- Marietta Iacucci
- APC Microbiome Ireland, College of Medicine and Health, University College Cork, Cork, Ireland.
| | - Yasuharu Maeda
- APC Microbiome Ireland, College of Medicine and Health, University College Cork, Cork, Ireland
| | - Subrata Ghosh
- APC Microbiome Ireland, College of Medicine and Health, University College Cork, Cork, Ireland
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O'Connell DM, Moses J. Invited commentary to immunotherapy withdrawal by step-down to mesalamine in pediatrics patients with ulcerative colitis. JPGN REPORTS 2024; 5:95-96. [PMID: 38756131 PMCID: PMC11093890 DOI: 10.1002/jpr3.12047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/17/2023] [Accepted: 12/29/2023] [Indexed: 05/18/2024]
Affiliation(s)
- Daniel M. O'Connell
- Department of Pediatrics, Division of Gastroenterology, Hepatology, and NutritionUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Jonathan Moses
- Department of Pediatrics, Division of Pediatric Gastroenterology, Hepatology and NutritionStanford University School of MedicinePalo AltoCaliforniaUSA
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5
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Oliva S, McGowan EC. Associations of Eosinophilic Gastrointestinal Disorders with Other Gastrointestinal and Allergic Diseases. Immunol Allergy Clin North Am 2024; 44:329-348. [PMID: 38575227 DOI: 10.1016/j.iac.2024.01.005] [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] [Indexed: 04/06/2024]
Abstract
Eosinophilic gastrointestinal disorders (EGIDs) are becoming more common causing significant suffering and reduced quality of life. These conditions can affect different parts of the digestive system, either individually or in combination. Recognition of their link to allergic disorders or other gastrointestinal (GI) diseases has raised questions about their shared underlying mechanisms, which has had implications for diagnosis and management. The authors critically examine the current understanding of the connection between EGIDs and allergic conditions (ie, atopic dermatitis, allergic rhinitis, asthma, and food allergy) and GI diseases (ie, inflammatory bowel disease, celiac disease, gastroesophageal reflux disease, and motility disorders).
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Affiliation(s)
- Salvatore Oliva
- Department of Maternal and Child Health, Pediatric Gastroenterology and Liver Unit, Sapienza University of Rome, Viale Regina Elena 324, Rome 00161, Italy.
| | - Emily Clarke McGowan
- Division of Allergy and Immunology, Departments of Internal Medicine and Pediatrics, University of Virginia School of Medicine, P.O. Box 801355, Charlottesville, VA 22908, USA
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6
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Wang C, Gu Y, Chu Q, Wang X, Ding Y, Qin X, Liu T, Wang S, Liu X, Wang B, Cao H. Gut microbiota and metabolites as predictors of biologics response in inflammatory bowel disease: A comprehensive systematic review. Microbiol Res 2024; 282:127660. [PMID: 38442454 DOI: 10.1016/j.micres.2024.127660] [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: 07/25/2023] [Revised: 02/02/2024] [Accepted: 02/19/2024] [Indexed: 03/07/2024]
Abstract
Nonresponse to biologic agents in patients with inflammatory bowel disease (IBD) poses a significant public health burden, and the prediction of response to biologics offers valuable insights for IBD management. Given the pivotal role of gut microbiota and their endogenous metabolites in IBD, we conducted a systematic review to investigate the potential of fecal microbiota and mucosal microbiota and endogenous metabolomic markers as predictors for biotherapy response in IBD patients. A total of 38 studies were included in the review. Following anti-TNF-α treatment, the bacterial community characteristics of IBD patients exhibited a tendency to resemble those observed in healthy controls, indicating an improved clinical response. The levels of endogenous metabolites butyrate and deoxycholic acid were significantly associated with clinical remission following anti-TNF-α therapy. IBD patients who responded well to vedolizumab treatment had higher levels of specific bacteria that produce butyrate, along with increased levels of metabolites such as butyrate, branched-chain amino acids and acetamide following vedolizumab treatment. Crohn's disease patients who responded positively to ustekinumab treatment showed higher levels of Faecalibacterium and lower levels of Escherichia/Shigella. In conclusion, fecal microbiota and mucosal microbiota as well as their endogenous metabolites could provide a predictive tool for assessing the response of IBD patients to various biological agents and serve as a valuable reference for precise drug selection in clinical IBD patients.
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Affiliation(s)
- Chen Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Yu Gu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Qiao Chu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xin Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Yiyun Ding
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xiali Qin
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Tianyu Liu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Sinan Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xiang Liu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Bangmao Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Hailong Cao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China.
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Szigeti R, Kellermayer R. Immunotherapy withdrawal by step-down to mesalamine in pediatric patients with ulcerative colitis. JPGN REPORTS 2024; 5:97-100. [PMID: 38756120 PMCID: PMC11093912 DOI: 10.1002/jpr3.12048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 12/04/2023] [Accepted: 01/14/2024] [Indexed: 05/18/2024]
Abstract
Objective Parents and pediatric patients with ulcerative colitis (UC) who progressed to systemic immunotherapy are concerned about lifelong risks from such treatments. There is limited knowledge about withdrawal of such agents and step-down (SD) to enteral 5-aminosalicylic acid (mesalamine) before transitioning to adult care. Methods We studied nine pediatric cases with moderate to severe UC who after a median of 2.18 years of clinical remission on systemic immunotherapy stepped down to oral mesalamine treatment. Results Average follow-up time from SD was 3.49 years. Five patients (55.5%) had sustained remission (without any flare noted) after SD during follow-up. Sustained clinical remission was 88.9% (8/9) at 1 year, 87.5% (7/8) at 2 years, and 66.7% (4/6) at 3 years after SD. Out of those tested (one patient was not tested), 62.5% (5/8) had fecal calprotectin <50 μg/g. Four out of six patients examined (66.6%) had mucosal healing on post-SD colonoscopy. Conclusion We propose that SD to mesalamine can be a reasonable therapeutic consideration for pediatric patients with UC before transitioning to adult gastroenterology care. Shared decision-making is important before such treatment changes.
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Affiliation(s)
- Reka Szigeti
- Department of Pathology and Genomic MedicineHouston Methodist HospitalHoustonTexasUSA
| | - Richard Kellermayer
- Section of Pediatric Gastroenterology, Hepatology and Nutrition, Texas Children's HospitalBaylor College of MedicineHoustonTexasUSA
- USDA/ARS Children's Nutrition Research CenterHoustonTexasUSA
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8
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Liu X, Prasath S, Siddiqui I, Walters TD, Denson LA, Dhaliwal J. Machine Learning-Based Prediction of Pediatric Ulcerative Colitis Treatment Response Using Diagnostic Histopathology. Gastroenterology 2024; 166:921-924.e4. [PMID: 38309631 DOI: 10.1053/j.gastro.2024.01.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/21/2023] [Accepted: 01/26/2024] [Indexed: 02/05/2024]
Affiliation(s)
- Xiaoxuan Liu
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Biomedical Informatics, University of Cincinnati, Cincinnati, Ohio
| | - Surya Prasath
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Biomedical Informatics, University of Cincinnati, Cincinnati, Ohio
| | - Iram Siddiqui
- Department of Paediatric Laboratory Medicine and Pathobiology, Division of Pathology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Thomas D Walters
- SickKids IBD Centre, Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Lee A Denson
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio
| | - Jasbir Dhaliwal
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Biomedical Informatics, University of Cincinnati, Cincinnati, Ohio; Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, Ohio.
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9
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Peng N, Wang J, Zhu H, Liu Z, Ren J, Li W, Wang Y. Protective effect of carbon dots as antioxidants on intestinal inflammation by regulating oxidative stress and gut microbiota in nematodes and mouse models. Int Immunopharmacol 2024; 131:111871. [PMID: 38492339 DOI: 10.1016/j.intimp.2024.111871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/12/2024] [Accepted: 03/12/2024] [Indexed: 03/18/2024]
Abstract
Inflammatory bowel disease (IBD) is a recurrent chronic colitis disease with increasing incidence and prevalence year by year. The single efficacy and significant side effects of traditional IBD treatment drugs have promoted the flourishing development of new drugs. Inspired by many health benefits of carbon dots (CDs) based nanomedicine in biomedical applications, a metal-free carbon dots (CP-CDs) was synthesized from citric acid and polyethylene polyamine to treat colitis. Oxidative stress tests at the cellular and nematode levels demonstrated CP-CDs have good antioxidant effects, while the toxicity of CP-CDs to cells and nematodes is low. CP-CDs were further applied to dextran sodium sulfate (DSS)-induced colitis in mice models, and it was found that CP-CDs can reduce the disease activity index (DAI) score of colon tissue and restore the intestinal barrier. Further, the anti-colitis mechanisms of CP-CDs were explored, one of which is to regulate intestinal oxidative stress in inflammatory mice, further reducing the expression of inflammatory cytokines, and thus alleviating colitis. Notably, 16S rRNA sequence analysis showed that the abundance of beneficial bacteria (Ligilactobacillus and Enterorhabdus) in the intestinal tract increased, while that of harmful bacteria (unclassified_Clostridia_UCG_014) decreased after CP-CDs treatment, indicating that CP-CDs rebalancing the gut microbiota destroyed by DSS is another important mechanism. In short, these non-toxic carbon dots not only have the potential for multi-factor combined relief of colitis but also offer an alternative therapy medicine for patients suffering from IBD.
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Affiliation(s)
- Nannan Peng
- School of Life Sciences, Anhui University, Hefei 230601, Anhui, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, China
| | - Jingmin Wang
- School of Life Sciences, Anhui University, Hefei 230601, Anhui, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, China.
| | - Haimei Zhu
- School of Life Sciences, Anhui University, Hefei 230601, Anhui, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, China
| | - Ziyue Liu
- School of Life Sciences, Anhui University, Hefei 230601, Anhui, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, China
| | - Jiayi Ren
- School of Life Sciences, Anhui University, Hefei 230601, Anhui, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, China
| | - Wenjing Li
- School of Life Sciences, Anhui University, Hefei 230601, Anhui, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, China
| | - Yongzhong Wang
- School of Life Sciences, Anhui University, Hefei 230601, Anhui, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, China.
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Wiley KS, Gregg AM, Fox MM, Lagishetty V, Sandman CA, Jacobs JP, Glynn LM. Contact with caregivers is associated with composition of the infant gastrointestinal microbiome in the first 6 months of life. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2024; 183:e24858. [PMID: 37804008 PMCID: PMC10922139 DOI: 10.1002/ajpa.24858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/18/2023] [Accepted: 09/24/2023] [Indexed: 10/08/2023]
Abstract
OBJECTIVES Little is known about how physical contact at birth and early caregiving environments influence the colonization of the infant gastrointestinal microbiome. We investigated how infant contact with caregivers at birth and within the first 2 weeks of life relates to the composition of the gastrointestinal microbiome in a sample of U.S. infants (n = 60). METHODS Skin-to-skin and physical contact with caregivers at birth and early caregiving environments were surveyed at 2 weeks postpartum. Stool samples were collected from infants at 2 weeks, 2, 6, and 12 months of age and underwent 16S rRNA sequencing as a proxy for the gastrointestinal microbiome. Associations between early caregiving environments and alpha and beta diversity, and differential abundance of bacteria at the genus level were assessed using PERMANOVA, and negative binomial mixed models in DEseq2. RESULTS Time in physical contact with caregivers explained 10% of variation in beta diversity at 2 weeks' age. The number of caregivers in the first few weeks of life explained 9% of variation in beta diversity at 2 weeks and the number of individuals in physical contact at birth explained 11% of variation in beta diversity at 6 months. Skin-to-skin contact on the day of birth was positively associated with the abundance of eight genera. Infants held for by more individuals had greater abundance of eight genera. DISCUSSION Results reveal a potential mechanism (skin-to-skin and physical contact) by which caregivers influence the infant gastrointestinal microbiome. Our findings contribute to work exploring the social transmission of microbes.
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Affiliation(s)
- Kyle S Wiley
- Department of Anthropology, UCLA, Los Angeles, California, USA
- Department of Psychiatry & Biobehavioral Sciences, UCLA, Los Angeles, California, USA
| | - Andrew M Gregg
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Molly M Fox
- Department of Anthropology, UCLA, Los Angeles, California, USA
- Department of Psychiatry & Biobehavioral Sciences, UCLA, Los Angeles, California, USA
| | - Venu Lagishetty
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
- UCLA Microbiome Center, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, VA Greater Los Angeles Healthcare System, Los Angeles, California, USA
| | - Curt A Sandman
- Department of Psychiatry and Human Behavior, UC Irvine, Irvine, California, USA
| | - Jonathan P Jacobs
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
- UCLA Microbiome Center, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, VA Greater Los Angeles Healthcare System, Los Angeles, California, USA
| | - Laura M Glynn
- Department of Psychology, Chapman University, Orange, California, USA
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11
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Wang Z, Song X, Waitman LR, Hyams JS, Denson LA. Fitness-for-use of Retrospective Multicenter Electronic Health Records to Conduct Outcome Analysis for Pediatric Ulcerative Colitis. Medicine (Baltimore) 2024; 103:e37395. [PMID: 38489703 PMCID: PMC10939680 DOI: 10.1097/md.0000000000037395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/11/2023] [Accepted: 02/06/2024] [Indexed: 03/17/2024] Open
Abstract
The use of electronic health records has garnered interest as an approach for conducting innovative outcome research and producing real-world evidence at a reduced cost compared to traditional clinical trials. The study aimed to evaluate the utility of deidentified EHR data from a multicenter research network to identify characteristics associated with treatment escalation (TE) in newly diagnosed pediatric ulcerative colitis patients. EHR data (01/2010-12/2021) from 13 Midwest healthcare systems (Greater Plains Collaborative) were collected for pediatric ulcerative colitis patients. We identified standard treatments, excluded missing initial therapy data, and analyzed the TE and time-to-TE outcomes. The clinical and laboratory characteristics at baseline were extracted. Logistic and Cox models were used, and the missing risk factors were imputed. Machine-learning Bayesian additive regression trees were also utilized to create partial dependence plots for assessing the associations between risk factors and clinical outcomes. A total of 502 eligible pediatric patients (aged 4-17 years) who initiated standard treatment were identified. Among them, 205 out of 502 (41%) experienced TE, with a median (P25, P75) duration of 63 (9, 237) days after the initial treatment. Additionally, 20 out of 509 (4%) patients underwent colectomy (COL) with a median (P25, P75) duration of 80 (3, 205) days. Both multivariable logistic regression and Cox proportional hazards regression demonstrated moderate discriminative power in predicting TE and time-to-TE, respectively. Common positive predictors for both TE and time-to-TE included a high monocyte proportion and elevated platelet counts. Conversely, BMI z-score, albumin, hemoglobin levels, and lymphocyte proportion were negatively associated with both TE and time-to-TE. This study demonstrates that multicenter EHR data can be used to identify a trial-comparable study sample of potentially larger size and to identify clinically meaningful endpoints for conducting outcome analysis and generating real-world evidence.
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Affiliation(s)
- Zhu Wang
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN
| | - Xing Song
- Biomedical Informatics, Biostatistics and Medical Epidemiology, University of Missouri, Columbia, MO
| | - Lemuel R Waitman
- Biomedical Informatics, Biostatistics and Medical Epidemiology, University of Missouri, Columbia, MO
| | | | - Lee A Denson
- Cincinnati Children's Medical Center, Cincinnati, OH
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12
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Wang Z, Nie J, Song X, Denson LA, Hyams JS. A comparison of Bayesian and frequentist approaches to incorporating clinical and biological information for the prediction of response to standardized pediatric colitis therapy. PLoS One 2024; 19:e0295814. [PMID: 38446811 PMCID: PMC10917270 DOI: 10.1371/journal.pone.0295814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 11/28/2023] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND The prospective cohort study PROTECT is the largest study in pediatric ulcerative colitis (UC) with standardized treatments, providing valuable data for predicting clinical outcomes. PROTECT and previous studies have identified characteristics associated with clinical outcomes. In this study, we aimed to compare predictive modeling between Bayesian analysis including machine learning and frequentist analysis. METHODS The key outcomes for this analysis were week 4, 12 and 52 corticosteroid (CS)-free remission following standardized treatment from diagnosis. We developed predictive modeling with multivariable Bayesian logistic regression (BLR), Bayesian additive regression trees (BART) and frequentist logistic regression (FLR). The effect estimate of each risk factor was estimated and compared between the BLR and FLR models. The predictive performance of the models was assessed including area under curve (AUC) of the receiver operating characteristic (ROC) curve. Ten-fold cross-validation was performed for internal validation of the models. The estimation contained 95% credible (or confidence) interval (CI). RESULTS The statistically significant associations between the risk factors and early or late outcomes were consistent between all BLR and FLR models. The model performance was similar while BLR and BART models had narrower credible intervals of AUCs. To predict week 4 CS-free remission, the BLR model had AUC of 0.69 (95% CI 0.67-0.70), the BART model had AUC of 0.70 (0.67-0.72), and the FLR had AUC of 0.70 (0.65-0.76). To predict week 12 CS-free remission, the BLR model had AUC of 0.78 (0.77-0.79), the BART model had AUC of 0.78 (0.77-0.79), and the FLR model had AUC of 0.79 (0.74-0.83). To predict week 52 CS-free remission, the BLR model had AUC of 0.69 (0.68-0.70), the BART model had AUC of 0.69 (0.67-0.70), and the FLR model had AUC of 0.69 (0.64-0.74). The BART model identified nonlinear associations. CONCLUSIONS BLR and BART models had intuitive interpretation on interval estimation, better precision in estimating the AUC and can be alternatives for predicting clinical outcomes in pediatric patients with UC. BART model can estimate nonlinear nonparametric association.
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Affiliation(s)
- Zhu Wang
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, United States of America
| | - Jia Nie
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
| | - Xing Song
- Health Management and Informatics, University of Missouri, Columbia, MO, United States of America
| | - Lee A. Denson
- Cincinnati Children’s Hospital and Medical Center, Cincinnati, OH, United States of America
| | - Jeffrey S. Hyams
- Connecticut Children’s Medical Center, Hartford, CT, United States of America
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13
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Greene AC, Mankarious MM, Finkelstein A, El-Mallah JC, Kulaylat AS, Kulaylat AN. Increasing Adoption of Laparoscopy in Urgent and Emergent Colectomies for Pediatric Ulcerative Colitis. J Surg Res 2024; 295:399-406. [PMID: 38070253 DOI: 10.1016/j.jss.2023.11.007] [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: 05/03/2023] [Revised: 09/21/2023] [Accepted: 11/08/2023] [Indexed: 02/25/2024]
Abstract
INTRODUCTION While minimally invasive surgery (MIS) approaches are commonly utilized in the elective surgical setting for pediatric ulcerative colitis (UC), their role in urgent and emergent disease is less clear. We aim to assess trends in the surgical approaches for pediatric UC patients requiring urgent and emergent colectomies and their associated outcomes. METHODS Retrospective review of 81 pediatric UC patients identified in National Surgical Quality Improvement Program Pediatric who underwent urgent or emergent colectomy (2012-2019). Trends in approach were assessed using linear regression. Patient characteristics and clinical outcomes were stratified by approach and compared using standard univariate statistics. Multivariable analysis was used to model the influence of covariates on postoperative length of stay. RESULTS The proportion of MIS cases increased by 5.53% per year (P = 0.01) over the study interval. Sixty-three patients (77.8%) received MIS resections and 18 patients (22.2%) received open resections. Patients undergoing open colectomies were younger and had a higher proportion of preoperative conditions, most notably preoperative sepsis (27.8% versus 4.8%, P = 0.01), and higher American Society of Anesthesiologists [III-IV] classification (83.3% versus 58.8%, P = 0.004). Mean operative time was comparable (open, 173.6 versus MIS, 206.1 min). In the univariate analysis, open approach was associated with increased postoperative length of stay (13.1 versus 7.2 d, P = 0.002). However, after adjusting for confounders, there was no significant difference. CONCLUSIONS There has been a steady increase in the adoption of laparoscopy in urgent and emergent colectomy for pediatric UC. Short-term outcomes between approaches appear comparable.
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Affiliation(s)
- Alicia C Greene
- Department of Surgery, Penn State Hershey Medical Center, Hershey, Pennsylvania
| | - Marc M Mankarious
- Department of Surgery, Penn State Hershey Medical Center, Hershey, Pennsylvania
| | - Adam Finkelstein
- The Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Jessica C El-Mallah
- Department of Surgery, Penn State Hershey Medical Center, Hershey, Pennsylvania
| | - Audrey S Kulaylat
- Division of Colon and Rectal Surgery, Penn State Hershey Medical Center, Hershey, Pennsylvania
| | - Afif N Kulaylat
- Division of Pediatric Surgery, Penn State Children's Hospital, Hershey, Pennsylvania.
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14
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Dhaliwal J, Tertigas D, Carman N, Lawrence S, Debruyn JC, Wine E, Church PC, Huynh HQ, Rashid M, El-Matary W, Deslandres C, Critch J, Ricciuto A, Carroll MW, Benchimol EI, Muise A, Jacobson K, Otley AR, Vallance B, Mack DR, Walters TD, Surette MG, Griffiths AM. Outcomes Following Acute Severe Colitis at Initial Presentation: A Multi-centre, Prospective, Paediatric Cohort Study. J Crohns Colitis 2024; 18:233-245. [PMID: 37602969 PMCID: PMC10896636 DOI: 10.1093/ecco-jcc/jjad143] [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: 04/17/2023] [Indexed: 08/22/2023]
Abstract
AIM To assess contemporary outcomes in children with acute severe ulcerative colitis [ASUC] at initial presentation. METHODS Between April 2014 and January 2019, children aged <17 years, with new onset ASUC (Paediatric Ulcerative Colitis Activity Index [PUCAI ≥65) were prospectively followed in a Canadian inception cohort study. 16S rRNA amplicon sequencing captured microbial composition of baseline faecal samples. Primary endpoint was corticosteroid-free clinical remission with intact colon at 1 year [PUCAI <10, no steroids ≥4 weeks]. RESULTS Of 379 children with new onset UC/IBD-unclassified, 105 [28%] presented with ASUC (42% male; median [interquartile range; [IQR]) age 14 [11-16] years; extensive colitis in all). Compared with mild UC, gut microbiome of ASUC patients had lower α-diversity, decreased beneficial anaerobes, and increased aerobes; 54 [51%] children were steroid-refractory and given infliximab [87% intensified regimen]. Corticosteroid-free remission at 1 year was achieved by 62 [61%] ASUC cohort (by 34 [63%] steroid-refractory patients, all on biologics; by 28 [55%] steroid responders,13 [25%] on 5- aminosalicylic acid [5-ASA], 5 [10%] on thiopurines, 10 [20%] on biologics). By 1 year, 78 [74%] escalated to infliximab including 24 [47%] steroid-responders failed by 5-ASA and/or thiopurines. In multivariable analysis, clinical predictors for commencing infliximab included hypoalbuminaemia, greater PUCAI, higher age, and male sex. Over 18 months, repeat corticosteroid course[s] and repeat hospitalisation were less likely among steroid-refractory versus -responsive but -dependent patients (adjusted odds ratio [aOR] 0.71 [95% CI 0.57-0.89] and 0.54 [95% CI 0.45-0.66], respectively). CONCLUSION The majority of children presenting with ASUC escalate therapy to biologics. Predictors of need for advanced therapy may guide selection of optimal maintenance therapy.
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Affiliation(s)
- Jasbir Dhaliwal
- SickKids IBD Centre, Division of Gastroenterology, Hepatology and Nutrition, Hospital for Sick Children, Department of Paediatrics, University of Toronto, Toronto, ON, Canada
- Child Health and Evaluative Sciences, SickKids Research Institute, Hospital for Sick Children, Toronto, ON, Canada
- Cincinnati Children’s Hospital Medical Center, Division of Gastroenterology, Hepatology and Nutrition, Cincinnati, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, USA
| | - Dominique Tertigas
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Nicholas Carman
- SickKids IBD Centre, Division of Gastroenterology, Hepatology and Nutrition, Hospital for Sick Children, Department of Paediatrics, University of Toronto, Toronto, ON, Canada
| | - Sally Lawrence
- B.C. Children’s Hospital, Division of Gastroenterology, Hepatology and Nutrition, Vancouver, BC, Canada
| | - Jennifer C Debruyn
- Alberta Children’s Hospital, Section of Pediatric Gastroenterology, Hepatology and Nutrition, University of Calgary, Calgary, AB, Canada
| | - Eytan Wine
- Stollery Children’s Hospital, Division of Gastroenterology, Hepatology and Nutrition, Edmonton, AB, Canada
| | - Peter C Church
- SickKids IBD Centre, Division of Gastroenterology, Hepatology and Nutrition, Hospital for Sick Children, Department of Paediatrics, University of Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Hien Q Huynh
- Stollery Children’s Hospital, Division of Gastroenterology, Hepatology and Nutrition, Edmonton, AB, Canada
| | - Mohsin Rashid
- IWK Health Centre, University of Dalhousie, Division of Gastroenterology, Hepatology and Nutrition, Halifax, NS, Canada
| | - Wael El-Matary
- Winnipeg Children’s Hospital, Department of Paediatrics, University of Manitoba, Winnipeg, MN, Canada
| | - Colette Deslandres
- CHU Sainte-Justine, Department of Paediatrics, University of Montreal, Montreal, QC, Canada
| | - Jeffrey Critch
- Janeway Children’s Health and Rehabilitation Centre, Memorial University, St. John’s, NFLD, Canada
| | - Amanda Ricciuto
- SickKids IBD Centre, Division of Gastroenterology, Hepatology and Nutrition, Hospital for Sick Children, Department of Paediatrics, University of Toronto, Toronto, ON, Canada
- Child Health and Evaluative Sciences, SickKids Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Matthew W Carroll
- Stollery Children’s Hospital, Division of Gastroenterology, Hepatology and Nutrition, Edmonton, AB, Canada
| | - Eric I Benchimol
- SickKids IBD Centre, Division of Gastroenterology, Hepatology and Nutrition, Hospital for Sick Children, Department of Paediatrics, University of Toronto, Toronto, ON, Canada
- Child Health and Evaluative Sciences, SickKids Research Institute, Hospital for Sick Children, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Aleixo Muise
- SickKids IBD Centre, Division of Gastroenterology, Hepatology and Nutrition, Hospital for Sick Children, Department of Paediatrics, University of Toronto, Toronto, ON, Canada
| | - Kevan Jacobson
- B.C. Children’s Hospital, Division of Gastroenterology, Hepatology and Nutrition, Vancouver, BC, Canada
| | - Anthony R Otley
- IWK Health Centre, University of Dalhousie, Division of Gastroenterology, Hepatology and Nutrition, Halifax, NS, Canada
| | - Bruce Vallance
- B.C. Children’s Hospital, Division of Gastroenterology, Hepatology and Nutrition, Vancouver, BC, Canada
| | - David R Mack
- Children’s Hospital of Eastern Ontario IBD Centre, Department of Pediatrics, University of Ottawa, Ottawa, ON, Canada
| | - Thomas D Walters
- SickKids IBD Centre, Division of Gastroenterology, Hepatology and Nutrition, Hospital for Sick Children, Department of Paediatrics, University of Toronto, Toronto, ON, Canada
| | - Michael G Surette
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Anne M Griffiths
- SickKids IBD Centre, Division of Gastroenterology, Hepatology and Nutrition, Hospital for Sick Children, Department of Paediatrics, University of Toronto, Toronto, ON, Canada
- Child Health and Evaluative Sciences, SickKids Research Institute, Hospital for Sick Children, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
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15
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Schirmer M, Stražar M, Avila-Pacheco J, Rojas-Tapias DF, Brown EM, Temple E, Deik A, Bullock K, Jeanfavre S, Pierce K, Jin S, Invernizzi R, Pust MM, Costliow Z, Mack DR, Griffiths AM, Walters T, Boyle BM, Kugathasan S, Vlamakis H, Hyams J, Denson L, Clish CB, Xavier RJ. Linking microbial genes to plasma and stool metabolites uncovers host-microbial interactions underlying ulcerative colitis disease course. Cell Host Microbe 2024; 32:209-226.e7. [PMID: 38215740 PMCID: PMC10923022 DOI: 10.1016/j.chom.2023.12.013] [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: 03/13/2023] [Revised: 11/08/2023] [Accepted: 12/15/2023] [Indexed: 01/14/2024]
Abstract
Understanding the role of the microbiome in inflammatory diseases requires the identification of microbial effector molecules. We established an approach to link disease-associated microbes to microbial metabolites by integrating paired metagenomics, stool and plasma metabolomics, and culturomics. We identified host-microbial interactions correlated with disease activity, inflammation, and the clinical course of ulcerative colitis (UC) in the Predicting Response to Standardized Colitis Therapy (PROTECT) pediatric inception cohort. In severe disease, metabolite changes included increased dipeptides and tauro-conjugated bile acids (BAs) and decreased amino-acid-conjugated BAs in stool, whereas in plasma polyamines (N-acetylputrescine and N1-acetylspermidine) increased. Using patient samples and Veillonella parvula as a model, we uncovered nitrate- and lactate-dependent metabolic pathways, experimentally linking V. parvula expansion to immunomodulatory tryptophan metabolite production. Additionally, V. parvula metabolizes immunosuppressive thiopurine drugs through xdhA xanthine dehydrogenase, potentially impairing the therapeutic response. Our findings demonstrate that the microbiome contributes to disease-associated metabolite changes, underscoring the importance of these interactions in disease pathology and treatment.
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Affiliation(s)
- Melanie Schirmer
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Translational Microbiome Data Integration, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany.
| | - Martin Stražar
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Eric M Brown
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Emily Temple
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amy Deik
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kevin Bullock
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sarah Jeanfavre
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kerry Pierce
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shen Jin
- Translational Microbiome Data Integration, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | | | - Marie-Madlen Pust
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Zach Costliow
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David R Mack
- Division of Gastroenterology, Hepatology & Nutrition, Children's Hospital of Eastern Ontario and University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Anne M Griffiths
- Division of Gastroenterology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Thomas Walters
- Division of Gastroenterology, Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Brendan M Boyle
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Subra Kugathasan
- Department of Pediatrics, Emory University, Atlanta, GA 30322, USA
| | - Hera Vlamakis
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jeffrey Hyams
- Connecticut Children's Medical Center, Division of Digestive Diseases, Hartford, CT 06106, USA
| | - Lee Denson
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Clary B Clish
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ramnik J Xavier
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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16
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Scroggins JK, Yang Q, Tully KP, Reuter-Rice K, Brandon D. Examination of Social Determinants of Health Characteristics Influencing Maternal Postpartum Symptom Experiences. J Racial Ethn Health Disparities 2024:10.1007/s40615-023-01901-1. [PMID: 38180636 PMCID: PMC11224138 DOI: 10.1007/s40615-023-01901-1] [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: 08/18/2023] [Revised: 12/05/2023] [Accepted: 12/20/2023] [Indexed: 01/06/2024]
Abstract
Postpartum women experience multiple, co-occurring postpartum symptoms. It is unknown if social determinants of health (SDOH) influence postpartum symptom typologies. This secondary analysis used the Community and Child Health Network study data. Participants included for analysis varied depending on the availability of the SDOH data (N = 851 to 1784). Bivariate and multiple regression analyses were conducted to examine the association between SDOH and previously identified postpartum symptom typologies. Area under the receiver operating characteristics curve (AUROC) was calculated to examine if adding SDOH variables contributes to predicting postpartum symptom typologies. The adjusted odds (aOR) of being in high symptom severity or occurrence typologies were greater for participants who had less than high school education (aOR = 2.29), experienced healthcare discrimination (aOR = 2.21), used governmental aid (aOR = 2.11), or were food insecure (aOR = 2.04). AUROC improved after adding SDOH. Considering experiences of different social-economic hardships influence postpartum symptom typologies, future practice and research should address SDOH to improve postpartum symptom experiences.
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Affiliation(s)
- Jihye Kim Scroggins
- School of Nursing, Columbia University, 560 W 168thStreet, New York, NY, 10032, USA.
- School of Nursing, Duke University, Durham, NC, USA.
| | - Qing Yang
- School of Nursing, Duke University, Durham, NC, USA
| | - Kristin P Tully
- Department of Obstetrics and Gynecology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Karin Reuter-Rice
- School of Nursing, Duke University, Durham, NC, USA
- School of Medicine, Duke University, Durham, NC, USA
| | - Debra Brandon
- School of Nursing, Duke University, Durham, NC, USA
- School of Medicine, Duke University, Durham, NC, USA
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17
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Scarallo L, Fioretti L, Paci M, Naldini S, Renzo S, Barp J, Gissi A, Di Paola M, Villanacci V, Lionetti P. Histological healing as a predictor of sustained clinical remission in paediatric ulcerative colitis. Dig Liver Dis 2024; 56:43-49. [PMID: 37455156 DOI: 10.1016/j.dld.2023.06.020] [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: 03/29/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND The study aimed to assess the longitudinal impact of endoscopic healing (EH) and histological healing (HH) in a cohort of paediatric patients affected by ulcerative colitis (UC). METHODS This was a retrospective single-centre longitudinal study. 86 children with UC who underwent endoscopic re-assessment while in clinical and biochemical remission were included. Partial EH was defined as a Mayo Endoscopic Subscore (MES) of 1 and complete EH was defined as a MES of 0. HH was defined as the absence of active inflammation in all biopsies. The cumulative incidence of clinical relapse was evaluated during follow-up. RESULTS At the second endoscopic re-evaluation, 59 (68.6%) patients achieved EH (MES ≤1). Of these patients, 39 (66%) achieved complete EH. 20 of the 39 patients who achieved complete EH attained complete HH. Patients who achieved partial and complete EH showed higher recurrence-free survival rates compared to those who did not (p < 0.01 and p < 0.01, respectively). Amongst patients with complete EH, those who achieved complete HH had lower recurrence rates when compared to patients who still showed microscopic inflammation (p = 0.049). CONCLUSION Achievement of EH and HH is associated with fewer disease relapses, with patients achieving HH showing longer relapse-free survival rates.
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Affiliation(s)
- Luca Scarallo
- Gastroenterology and Nutrition Unit, Meyer Children Hospital IRCCS, Florence, Italy; Department of NEUROFARBA, University of Florence, Italy
| | - Lorenzo Fioretti
- Gastroenterology and Nutrition Unit, Meyer Children Hospital IRCCS, Florence, Italy
| | - Monica Paci
- Gastroenterology and Nutrition Unit, Meyer Children Hospital IRCCS, Florence, Italy
| | - Sara Naldini
- Gastroenterology and Nutrition Unit, Meyer Children Hospital IRCCS, Florence, Italy
| | - Sara Renzo
- Gastroenterology and Nutrition Unit, Meyer Children Hospital IRCCS, Florence, Italy
| | - Jacopo Barp
- Gastroenterology and Nutrition Unit, Meyer Children Hospital IRCCS, Florence, Italy
| | - Anna Gissi
- Gastroenterology and Nutrition Unit, Meyer Children Hospital IRCCS, Florence, Italy
| | - Monica Di Paola
- Gastroenterology and Nutrition Unit, Meyer Children Hospital IRCCS, Florence, Italy
| | | | - Paolo Lionetti
- Gastroenterology and Nutrition Unit, Meyer Children Hospital IRCCS, Florence, Italy; Department of NEUROFARBA, University of Florence, Italy.
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18
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Meade S, Liu Chen Kiow J, Massaro C, Kaur G, Squirell E, Bressler B, Lunken G. Gut microbiome-associated predictors as biomarkers of response to advanced therapies in inflammatory bowel disease: a systematic review. Gut Microbes 2023; 15:2287073. [PMID: 38044504 PMCID: PMC10730146 DOI: 10.1080/19490976.2023.2287073] [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: 06/01/2023] [Accepted: 11/20/2023] [Indexed: 12/05/2023] Open
Abstract
Loss of response to therapy in inflammatory bowel disease (IBD) has led to a surge in research focusing on precision medicine. Three systematic reviews have been published investigating the associations between gut microbiota and disease activity or IBD therapy. We performed a systematic review to investigate the microbiome predictors of response to advanced therapy in IBD. Unlike previous studies, our review focused on predictors of response to therapy; so the included studies assessed microbiome predictors before the proposed time of response or remission. We also provide an update of the available data on mycobiomes and viromes. We highlight key themes in the literature that may serve as future biomarkers of treatment response: the abundance of fecal SCFA-producing bacteria and opportunistic bacteria, metabolic pathways related to butyrate synthesis, and non-butyrate metabolomic predictors, including bile acids (BAs), amino acids, and lipids, as well as mycobiome predictors of response.
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Affiliation(s)
- Susanna Meade
- Department of Medicine, University of British Columbia, Vancouver, Canada
- IBD Centre of BC, Vancouver, Canada
| | - Jeremy Liu Chen Kiow
- Department of Medicine, University of British Columbia, Vancouver, Canada
- IBD Centre of BC, Vancouver, Canada
| | - Cristian Massaro
- Department of Pediatrics, Univerisity of British Columbia, Vancouver, Canada
- BC Children’s Hospital Research Institute, Vancouver, Canada
| | - Gurpreet Kaur
- IBD Centre of BC, Vancouver, Canada
- Department of Pediatrics, Univerisity of British Columbia, Vancouver, Canada
| | - Elizabeth Squirell
- Department of Medicine, University of British Columbia, Vancouver, Canada
- IBD Centre of BC, Vancouver, Canada
| | - Brian Bressler
- Department of Medicine, University of British Columbia, Vancouver, Canada
- IBD Centre of BC, Vancouver, Canada
| | - Genelle Lunken
- IBD Centre of BC, Vancouver, Canada
- Department of Pediatrics, Univerisity of British Columbia, Vancouver, Canada
- BC Children’s Hospital Research Institute, Vancouver, Canada
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19
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Ananthakrishnan AN, Adler J, Chachu KA, Nguyen NH, Siddique SM, Weiss JM, Sultan S, Velayos FS, Cohen BL, Singh S. AGA Clinical Practice Guideline on the Role of Biomarkers for the Management of Crohn's Disease. Gastroenterology 2023; 165:1367-1399. [PMID: 37981354 DOI: 10.1053/j.gastro.2023.09.029] [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] [Indexed: 11/21/2023]
Abstract
BACKGROUND & AIMS Biomarkers are used frequently for evaluation and monitoring of patients with Crohn's disease (CD). This American Gastroenterological Association (AGA) guideline is intended to support practitioners in decisions about the use of biomarkers for the management of CD. METHODS A multidisciplinary panel of content experts and guideline methodologists used the Grading of Recommendations Assessment, Development and Evaluation framework to formulate patient-centered clinical questions and review evidence on the performance of fecal calprotectin, serum C-reactive protein (CRP), and Endoscopic Healing Index in patients with established CD who were asymptomatic, had symptoms of varying severity, or were in surgically induced remission. Biomarker performance was assessed against the gold standard of endoscopic activity, defined as a Simple Endoscopic Score for Crohn's Disease ≥3. The panel used the Grading of Recommendations Assessment, Development and Evaluation Evidence-to-Decision framework to develop recommendations for use of biomarkers in various settings. Implementation considerations were formulated for each recommendation to inform clinical practice. RESULTS The guideline panel made 11 conditional recommendations. In patients with CD in symptomatic remission, the panel suggests use of a biomarker- and symptom-based monitoring strategy over symptoms alone. In patients in symptomatic remission, a fecal calprotectin <150 μg/g and normal CRP rules out active inflammation, avoiding endoscopic evaluation for assessment of disease activity. However, elevated biomarkers in this setting merit confirmation with endoscopy before treatment adjustment. In patients with CD with mild symptoms, neither normal nor elevated biomarkers alone are sufficiently accurate to determine endoscopic activity. In patients with CD with moderate to severe symptoms, elevated fecal calprotectin or serum CRP suggests endoscopic activity, precluding routine endoscopic assessment for disease activity. In patients with CD in surgically induced remission in low-risk patients on pharmacologic prophylaxis, a normal fecal calprotectin reliably rules out endoscopic recurrence. In other postoperative settings, the panel suggests endoscopic assessment for establishing postoperative recurrence. CONCLUSIONS In patients with CD, fecal calprotectin and serum CRP can inform disease management in both asymptomatic and symptomatic disease. Discordance between symptom assessment and biomarker value may merit endoscopic evaluation for confirmation of status of disease activity.
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Affiliation(s)
- Ashwin N Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jeremy Adler
- Division of Pediatric Gastroenterology, C.S. Mott Children's Hospital, Michigan Medicine, University of Michigan, Ann Arbor, Michigan; Susan B. Meister Child Health Evaluation and Research Center, University of Michigan, Ann Arbor, Michigan
| | - Karen A Chachu
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, North Carolina
| | - Nghia H Nguyen
- Division of Gastroenterology, Kaiser Permanente Medical Group, Riverside, California
| | - Shazia M Siddique
- Division of Gastroenterology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania; Center for Evidence-Based Practice, University of Pennsylvania Health System, Philadelphia, Pennsylvania
| | - Jennifer M Weiss
- Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Shahnaz Sultan
- Division of Gastroenterology, Hepatology, and Nutrition, University of Minnesota, Minneapolis, Minnesota, and Veterans Affairs Healthcare System, Minneapolis, Minnesota
| | - Fernando S Velayos
- Division of Gastroenterology, Kaiser Permanente Medical Group, San Francisco, California
| | - Benjamin L Cohen
- Division of Gastroenterology, Hepatology, and Nutrition, Digestive Disease Institute, Cleveland Clinic, Cleveland, Ohio
| | - Siddharth Singh
- Division of Gastroenterology and Hepatology, University of California San Diego, La Jolla, California; Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, California
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20
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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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21
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Green Z, Beattie RM, Ashton JJ. Recent developments in the assessment and management of inflammatory bowel disease in childhood: a narrative review. Transl Pediatr 2023; 12:1853-1874. [PMID: 37969128 PMCID: PMC10644027 DOI: 10.21037/tp-23-210] [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: 03/28/2023] [Accepted: 09/15/2023] [Indexed: 11/17/2023] Open
Abstract
Background and Objective The landscape of paediatric inflammatory bowel disease (pIBD) continues to evolve in an era of increasing incidence. There have been rapid developments in understanding, as we begin to perceive IBD as a spectrum of conditions, alongside advancements in monitoring and treatment. The objective of this article was to provide an overview of recent advances and challenges in the management of pIBD, with a focus on sustainable healthcare, personalised therapy, genomics, new drugs and avenues for future optimisation. Methods We present a narrative review that synthesises and summarises recent research (2017-2022) related to pIBD. We undertook a structured search of the literature (PubMed and Medline) and additional articles were identified through manual searches of reference lists. Evidence tables were compiled for disease outcomes. Key Content and Findings In this review we outline current practice, integrating clinical guidelines and contemporary research. We discuss initial investigations (including suggested threshold for paediatric faecal calprotectin), specialist investigations for disease monitoring [with reference to video capsule endoscopy (VCE) and therapeutic drug levels] and outline new and established treatment options. Biomarkers and genomic testing are examined as important tools for individualising care and identifying potential therapeutic targets, including for top-down therapy. Despite these advances, significant challenges remain, including the need for further research to understand the mechanisms of disease and the translation of these advances into real-world improvements in practice. Conclusions Recent advances in understanding of the pathogenesis of pIBD, alongside genomic and pharmacological developments have added more tools to the armamentarium for the treatment of these conditions and highlighted ongoing areas of research need.
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Affiliation(s)
- Zachary Green
- Department of Paediatric Gastroenterology, Southampton Children’s Hospital, Southampton, UK
- Department of Paediatric Gastroenterology, Noah’s Ark Children’s Hospital for Wales, Cardiff, UK
| | - Robert Mark Beattie
- Department of Paediatric Gastroenterology, Southampton Children’s Hospital, Southampton, UK
| | - James J. Ashton
- Department of Paediatric Gastroenterology, Southampton Children’s Hospital, Southampton, UK
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
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22
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Honda K, Furuichi M, Kawaguchi T, Pust MM, Yasuma-Mitobe K, Plichta D, Hasegawa N, Ohya T, Bhattarai S, Sasajima S, Yoshimasa A, Tuganbaev T, Yaginuma M, Ueda M, Okahashi N, Amafuji K, Kiridooshi Y, Sugita K, Stražar M, Skelly A, Suda W, Hattori M, Nakamoto N, Caballero S, Norman J, Olle B, Tanoue T, Arita M, Bucci V, Atarashi K, Xavier R. Rationally-defined microbial consortia suppress multidrug-resistant proinflammatory Enterobacteriaceae via ecological control. RESEARCH SQUARE 2023:rs.3.rs-3462622. [PMID: 37961431 PMCID: PMC10635318 DOI: 10.21203/rs.3.rs-3462622/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Persistent colonization and outgrowth of pathogenic organisms in the intestine may occur due to long-term antibiotic usage or inflammatory conditions, which perpetuate dysregulated immunity and tissue damage1,2. Gram-negative Enterobacteriaceae gut pathobionts are particularly recalcitrant to conventional antibiotic treatment3,4, though an emerging body of evidence suggests that manipulation of the commensal microbiota may be a practical alternative therapeutic strategy5-7. In this study, we rationally isolated and down-selected commensal bacterial consortia from healthy human stool samples capable of strongly and specifically suppressing intestinal Enterobacteriaceae. One of the elaborated consortia, consisting of 18 commensal strains, effectively controlled ecological niches by regulating gluconate availability, thereby reestablishing colonization resistance and alleviating antibiotic-resistant Klebsiella-driven intestinal inflammation in mice. Harnessing these microbial activities in the form of live bacterial therapeutics may represent a promising solution to combat the growing threat of proinflammatory, antimicrobial-resistant bacterial infection.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Aoto Yoshimasa
- JSR-Keio University Medical and Chemical Innovation Center
| | | | | | | | | | | | | | | | | | | | - Wataru Suda
- RIKEN Center for Integrative Medical Sciences
| | | | | | - Silvia Caballero
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center
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23
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Abu Hanna F, Atia O, Yerushalmy Feler A, Shouval D, Weiss B, Mresat H, Magen-Rimon R, Zifman E, Turner D, Rinawi F. Thiopurines Maintenance Therapy in Children With Ulcerative Colitis: A Multicenter Retrospective Study. J Pediatr Gastroenterol Nutr 2023; 77:505-511. [PMID: 37491713 DOI: 10.1097/mpg.0000000000003899] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
BACKGROUND AND AIMS Thiopurines are an established treatment for pediatric ulcerative colitis (UC). However, data regarding safety and efficacy are lacking. We aimed to determine short and long-term outcome following thiopurines use in children with UC. METHODS We conducted a retrospective review of children (2-18 years) with UC treated with thiopurines between January 2008 and January 2019 at 7 medical centers in Israel. The primary outcome was corticosteroid (CS)-free clinical remission at week 52 following thiopurines initiation without the need for rescue therapy (infliximab, calcineurin inhibitors, or colectomy). RESULTS A total of 133 children were included [median age at diagnosis of 12.4 (interquartile range 11.0-15.8) years, 30 (23%) left-sided colitis, 113 (85%) with moderate or severe disease at diagnosis]. At diagnosis 58 patients (44%) were treated with 5-aminosalicylates and 72 (54%) with CS. Sixty patients (45%) received thiopurines as 1st line maintenance therapy. Seventy-four patients (56%) had CS-free clinical remission at week 52 without rescue therapy. Predictors of clinical remission were not identified. In a sub-analysis among patients with steroid-responsive moderate to severe UC, 59 (55%) patients achieved this outcome. The likelihood of remaining free of rescue therapy among thiopurines-treated patients was 83%, 62%, 45%, and 37% at 1, 2, 3, and 4 years, respectively. CONCLUSION More than half of children with UC starting thiopurines without previous or concomitant biologic therapy have CS-free clinical remission at 52 weeks later without the need for rescue therapy. Thiopurines are effective in pediatric UC and could be considered prior to biologics.
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Affiliation(s)
- Firas Abu Hanna
- From the Pediatric Gastroenterology Unit, Emek Medical Centre, Afula, Israel
| | - Ohad Atia
- The Juliet Keiden Institute of Pediatric Gastroenterology and Nutrition, Shaare Zedek Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Anat Yerushalmy Feler
- Pediatric Gastroenterology Institute, "Dana-Dwek" Children's Hospital, Tel Aviv Sourasky Medical Center and the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Dror Shouval
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children's Medical Center and the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Batia Weiss
- the Pediatric Gastroenterology and Nutrition Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Hadeel Mresat
- From the Pediatric Gastroenterology Unit, Emek Medical Centre, Afula, Israel
| | - Ramit Magen-Rimon
- Pediatric Gastroenterology and Nutrition Institute, Ruth Children's Hospital of Haifa, Rambam Medical Center, Faculty of Medicine, Technion, Haifa, Israel
| | - Eyal Zifman
- the Pediatric Gastroenterology Unit, Meir Medical Center, Kfar-Saba, Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Dan Turner
- The Juliet Keiden Institute of Pediatric Gastroenterology and Nutrition, Shaare Zedek Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Firas Rinawi
- From the Pediatric Gastroenterology Unit, Emek Medical Centre, Afula, Israel
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24
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Zhang X, Rosh JR. Safety Summary of Pediatric Inflammatory Bowel Disease Therapies. Gastroenterol Clin North Am 2023; 52:535-548. [PMID: 37543398 DOI: 10.1016/j.gtc.2023.05.007] [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: 08/07/2023]
Abstract
Therapeutic options for the treatment of pediatric inflammatory bowel disease include aminosalicylates, enteral nutrition, corticosteroids, immunomodulators, biologics, and emerging small molecule agents. Infectious risk due to systemic immunosuppression should be mitigated by appropriate screening before therapy initiation. Rare but serious malignancies have been associated with thiopurine use alone and in combination with anti-tumor necrosis factor agents, often in the setting of a primary Epstein-Barr virus infection. Potential agent-specific adverse events such as cytopenias, hepatotoxicity, and nephrotoxicity warrant regular clinical and laboratory monitoring.
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Affiliation(s)
- Xiaoyi Zhang
- Pediatric Gastroenterology, Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Indiana University, 705 Riley Hospital Drive, ROC 4210, Indianapolis, IN 46202, USA. https://twitter.com/xtzhang
| | - Joel R Rosh
- Pediatric Gastroenterology, Division of Pediatric Gastroenterology, Liver Disease, and Nutrition, Cohen Children's Medical Center of New York, 1991 Marcus Avenue, Suite M100, Lake Success, NY 11042, USA.
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25
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Dolinger MT. The Role of Noninvasive Surrogates of Inflammation in Monitoring Pediatric Inflammatory Bowel Diseases: The Old and the New. Gastroenterol Clin North Am 2023; 52:497-515. [PMID: 37543396 DOI: 10.1016/j.gtc.2023.05.003] [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] [Indexed: 08/07/2023]
Abstract
Effectiveness of limited available therapies for pediatric inflammatory bowel disease has reached stagnation. Previous non-invasive monitoring strategies have relied upon cumbersome tools to evaluate clinical symptoms and biochemical markers that do not reflect endoscopic activity or respond quickly to treatments. Novel, patient-centric, and highly accurate, monitoring strategies with a focus on intestinal ultrasound for a direct, precise monitoring of activity to achieve disease modification are now possible. Ultimately, research on the optimal tight control monitoring strategies, individualized to each pediatric inflammatory bowel disease patient, are in development and offer a hope to potential therapeutic ceiling breakthrough on the horizon.
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Affiliation(s)
- Michael Todd Dolinger
- Division of Pediatric Gastroenterology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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26
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Annese V, Annese M. Precision Medicine in Inflammatory Bowel Disease. Diagnostics (Basel) 2023; 13:2797. [PMID: 37685335 PMCID: PMC10487169 DOI: 10.3390/diagnostics13172797] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/24/2023] [Accepted: 08/26/2023] [Indexed: 09/10/2023] Open
Abstract
Ulcerative colitis and Crohn's disease are traditionally defined as the two main subtypes of inflammatory bowel disease. However, a more recent view considers IBD as a spectrum of heterogeneous phenotypes with consistent differences in clinical presentation and behaviors, likely explained by differences in underlying pathogenetic mechanisms. The etiology is still elusive, and the suggested pathogenesis is a complex interplay among genetic predisposition and abnormal immune response at the mucosal intestinal level, activated by only partially identified environmental triggers leading to altered intestinal permeability and impaired handling of gut microbiota. The undeniable continuous progress of medical therapy with more frequent shifts from traditional to more advanced modalities also underlines the actual unmet needs. We are using medications with completely different mechanisms of action, with a lack of predictive factors of outcomes and response and still an unsatisfactory rate of success. In addition, we are missing still valuable and accurate markers to predict disease progression and severity in order to avoid under- or over-treatment. In such a complex scenario, it is undoubtful that the application of artificial intelligence and machine learning algorithms may improve the management and pave the way for precision and eventually personalized medicine in these patients; however, there are still several challenges that will be the focus of this review.
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Affiliation(s)
- Vito Annese
- Department Gastroenterology IRCCS San Donato Policlinic, Vita-Salute San Raffaele University, 20100 Milan, Italy
| | - Monica Annese
- Department Gastroenterology, IRCCS Hospital Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy
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27
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Bolia R, Goel A, Semwal P, Srivastava A. Oral Tacrolimus in Steroid Refractory and Dependent Pediatric Ulcerative Colitis-A Systematic Review and Meta-Analysis. J Pediatr Gastroenterol Nutr 2023; 77:228-234. [PMID: 37184447 DOI: 10.1097/mpg.0000000000003827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
BACKGROUND There are limited treatment options for children with steroid-refractory or dependent ulcerative colitis (UC). A few observational studies suggest efficacy of oral tacrolimus. We performed a systematic review and meta-analysis to assess the efficacy of tacrolimus in pediatric UC. METHODS PubMed and Scopus were searched for publications related to the use of oral tacrolimus in pediatric UC. Data regarding the clinical response and colectomy-free survival were extracted from studies that met the selection criteria. RESULTS The search strategy yielded 492 articles of which 7 studies were included in the final review. They included 166 children (111 steroid-refractory, 52 steroid-dependent, 3 no steroids). Majority of cases (150/166 [90%]) were naïve to biologics. An initial response to tacrolimus therapy was seen in 84% (95% CI: 73%-93%) (n = 7 studies). No difference was observed between children with high (>10 ng/mL) or low tacrolimus levels (127/150 [85%] vs 12/16 [75%], P = 0.3). No difference in initial response between the children who were steroid refractory or dependent (92/111 [83%] vs 46/52 [88%], P = 0.36). The response in the biologic-exposed group (n = 10) was 70%. At 1-year follow-up, 15.2% (95% CI: 7%-21%) (n = 2 studies, 85 patients) had a sustained response on only tacrolimus. The pooled frequency of 1-year colectomy-free survival in children treated with initial oral tacrolimus was 64% (95% CI: 53%-75%). Twelve (7.2%) patients required cessation of therapy because of side effects. CONCLUSION Tacrolimus has a high initial response in biologic naïve UC children. It can be effectively used as a bridge to other therapies with a 1-year colectomy-free survival of 64%.
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Affiliation(s)
- Rishi Bolia
- From the Department of Gastroenterology, Hepatology and Liver Transplant, Queensland Children's Hospital, Brisbane, Australia
| | - Akhil Goel
- the Department of Community and Family Medicine, All India Institute of Medical Sciences, Jodhpur, India
| | - Pooja Semwal
- the Division of Paediatric Gastroenterology, Department of Paediatrics, All India Institute of Medical Sciences, Rishikesh, India
| | - Anshu Srivastava
- the Department of Paediatric Gastroenterology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
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Braun T, Sosnovski KE, Amir A, BenShoshan M, VanDussen KL, Karns R, Levhar N, Abbas-Egbariya H, Hadar R, Efroni G, Castel D, Avivi C, Rosen MJ, Grifiths AM, Walters TD, Mack DR, Boyle BM, Ali SA, Moore SR, Schirmer M, Xavier RJ, Kugathasan S, Jegga AG, Weiss B, Mayer C, Barshack I, Ben-Horin S, Ulitsky I, Beucher A, Ferrer J, Hyams JS, Denson LA, Haberman Y. Mucosal transcriptomics highlight lncRNAs implicated in ulcerative colitis, Crohn's disease, and celiac disease. JCI Insight 2023; 8:e170181. [PMID: 37261910 PMCID: PMC10443795 DOI: 10.1172/jci.insight.170181] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/31/2023] [Indexed: 06/03/2023] Open
Abstract
Ulcerative colitis (UC), Crohn's disease (CD), and celiac disease are prevalent intestinal inflammatory disorders with nonsatisfactory therapeutic interventions. Analyzing patient data-driven cohorts can highlight disease pathways and new targets for interventions. Long noncoding RNAs (lncRNAs) are attractive candidates, since they are readily targetable by RNA therapeutics, show relative cell-specific expression, and play key cellular functions. Uniformly analyzing gut mucosal transcriptomics from 696 subjects, we have highlighted lncRNA expression along the gastrointestinal (GI) tract, demonstrating that, in control samples, lncRNAs have a more location-specific expression in comparison with protein-coding genes. We defined dysregulation of lncRNAs in treatment-naive UC, CD, and celiac diseases using independent test and validation cohorts. Using the Predicting Response to Standardized Pediatric Colitis Therapy (PROTECT) inception UC cohort, we defined and prioritized lncRNA linked with UC severity and prospective outcomes, and we highlighted lncRNAs linked with gut microbes previously implicated in mucosal homeostasis. HNF1A-AS1 lncRNA was reduced in all 3 conditions and was further reduced in more severe UC form. Similarly, the reduction of HNF1A-AS1 ortholog in mice gut epithelia showed higher sensitivity to dextran sodium sulfate-induced colitis, which was coupled with alteration in the gut microbial community. These analyses highlight prioritized dysregulated lncRNAs that can guide future preclinical studies for testing them as potential targets.
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Affiliation(s)
- Tzipi Braun
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Katya E. Sosnovski
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amnon Amir
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Marina BenShoshan
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Kelli L. VanDussen
- Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Rebekah Karns
- Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Nina Levhar
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Haya Abbas-Egbariya
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Rotem Hadar
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Gilat Efroni
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - David Castel
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Camila Avivi
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Michael J. Rosen
- Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
- Center for Pediatric IBD and Celiac Disease, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | | | | | - David R. Mack
- Children’s Hospital of East Ontario, Ottawa, Ontario, Canada
| | | | - Syed Asad Ali
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sean R. Moore
- Department of Pediatrics, University of Virginia, Charlottesville, Virginia, USA
| | | | - Ramnik J. Xavier
- Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Anil G. Jegga
- Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
- Department of Computer Science, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Engineering, Cincinnati, Ohio, USA
| | - Batya Weiss
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chen Mayer
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Iris Barshack
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shomron Ben-Horin
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Igor Ulitsky
- Departments of Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Anthony Beucher
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Jorge Ferrer
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
- Regulatory Genomics and Diabetes, Centre for Genomic Regulation, the Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en red Diabetes y enfermedades metabólicas asociadas (CIBERDEM), Spain
| | - Jeffrey S. Hyams
- Connecticut Children’s Medical Center, Hartford, Connecticut, USA
| | - Lee A. Denson
- Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Yael Haberman
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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Venkateswaran S, Somineni HK, Matthews JD, Kilaru V, Hyams JS, Denson LA, Kellamayer R, Gibson G, Cutler DJ, Conneely KN, Smith AK, Kugathasan S. Longitudinal DNA methylation profiling of the rectal mucosa identifies cell-specific signatures of disease status, severity and clinical outcomes in ulcerative colitis cell-specific DNA methylation signatures of UC. Clin Epigenetics 2023; 15:50. [PMID: 36964596 PMCID: PMC10039532 DOI: 10.1186/s13148-023-01462-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 03/07/2023] [Indexed: 03/26/2023] Open
Abstract
BACKGROUND In peripheral blood, DNA methylation (DNAm) patterns in inflammatory bowel disease patients reflect inflammatory status rather than disease status. Here, we examined DNAm in diseased rectal mucosa from ulcerative colitis (UC) patients, focusing on constituent cell types with the goal of identifying therapeutic targets for UC other than the immune system. We profiled DNAm of rectal mucosal biopsies of pediatric UC at diagnosis (n = 211) and non-IBD control (n = 85) patients and performed epigenome-wide association studies (EWAS) of specific cell types to understand DNAm changes in epithelial, immune and fibroblast cells across disease states, course, and clinical outcomes. We also examined longitudinal analysis on follow-up samples (n = 73), and comparisons were made among patients with clinical outcomes including those undergoing colectomy versus those who did not. Additionally, we included RNA-seq from the same subjects to assess the impact of CpG sites on the transcription of nearby genes during the disease course. RESULTS At diagnosis, UC rectal mucosa exhibited a lower proportion of epithelial cells and fibroblasts, and higher proportion of immune cells, in conjunction with variation in the DNAm pattern. While treatment had significant effects on the methylation signature of immune cells, its effects on fibroblasts and epithelial cells were attenuated. Individuals who required colectomy exhibited cell composition and DNAm patterns at follow-up more similar to disease onset than patients who did not require colectomy. Combining these results with gene expression profiles, we identify CpG sites whose methylation patterns are most consistent with a contribution to poor disease outcomes and could thus be potential therapeutic targets. CONCLUSIONS Cell-specific epigenetic changes in the rectal mucosa in UC are associated with disease severity and outcome. Current therapeutics may more effectively target the immune than the epithelial and fibroblast compartments.
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Affiliation(s)
- Suresh Venkateswaran
- Division of Pediatric Gastroenterology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, 1760 Haygood Drive, W-427, Atlanta, GA, 30322, USA
| | - Hari K Somineni
- Division of Pediatric Gastroenterology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, 1760 Haygood Drive, W-427, Atlanta, GA, 30322, USA
| | - Jason D Matthews
- Division of Pediatric Gastroenterology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, 1760 Haygood Drive, W-427, Atlanta, GA, 30322, USA
| | - Varun Kilaru
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Jeffrey S Hyams
- Division of Digestive Diseases, Hepatology, and Nutrition, Connecticut Children's Medical Center, Hartford, CT, USA
| | - Lee A Denson
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Richard Kellamayer
- Section of Pediatric Gastroenterology, Texas Children's Hospital Baylor College of Medicine, Houston, TX, USA
| | - Greg Gibson
- Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA, USA
| | - David J Cutler
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Karen N Conneely
- Department of Human Genetics, Emory University, Atlanta, GA, USA
- Genetics and Molecular Biology Program, Emory University, Atlanta, GA, USA
| | - Alicia K Smith
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, USA
- Genetics and Molecular Biology Program, Emory University, Atlanta, GA, USA
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Subra Kugathasan
- Division of Pediatric Gastroenterology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, 1760 Haygood Drive, W-427, Atlanta, GA, 30322, USA.
- Department of Human Genetics, Emory University, Atlanta, GA, USA.
- Genetics and Molecular Biology Program, Emory University, Atlanta, GA, USA.
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Nambu R, Arai K, Kudo T, Murakoshi T, Kunisaki R, Mizuochi T, Kato S, Kumagai H, Inoue M, Ishige T, Saito T, Noguchi A, Yodoshi T, Hagiwara SI, Iwata N, Nishimata S, Kakuta F, Tajiri H, Hiejima E, Toita N, Mochizuki T, Shimizu H, Iwama I, Hirano Y, Shimizu T. Clinical outcome of ulcerative colitis with severe onset in children: a multicenter prospective cohort study. J Gastroenterol 2023; 58:472-480. [PMID: 36884071 DOI: 10.1007/s00535-023-01972-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/14/2023] [Indexed: 03/09/2023]
Abstract
BACKGROUND As best practices for treating children with severe-onset ulcerative colitis remain controversial in the era of biologic agents, we prospectively investigated treatments and outcomes in a multicenter cohort. METHODS Using a Web-based data registry maintained in Japan between October 2012 and March 2020, we compared management and treatment outcomes in an S1 group defined by a Pediatric Ulcerative Colitis Activity Index of 65 or more points at diagnosis with those in an S0 group defined by an index value below 65. RESULTS Three hundred one children with ulcerative colitis treated at 21 institutions were included, with follow-up for 3.6 ± 1.9 years. Among them, 75 (25.0%) were in S1; their age at diagnosis was 12.3 ± 2.9 years, and 93% had pancolitis. Colectomy free rates in S1 were 89% after 1 year, 79% after 2, and 74% after 5, significantly lower than for S0 (P = 0.0003). Calcineurin inhibitors and biologic agents, respectively, were given to 53% and 56% of S1 patients, significantly more than for S0 patients (P < 0.0001). Among S1 patients treated with calcineurin inhibitors when steroids failed, 23% required neither biologic agents nor colectomy, similarly to the S0 group (P = 0.46). CONCLUSIONS Children with severe ulcerative colitis are likely to require powerful agents such as calcineurin inhibitors and biologic agents; sometimes colectomy ultimately proves necessary. Need for biologic agents in steroid-resistant patients might be reduced to an extent by interposing a therapeutic trial of CI rather than turning to biologic agents or colectomy immediately.
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Affiliation(s)
- Ryusuke Nambu
- Division of Gastroenterology and Hepatology, Saitama Children's Medical Center, 1-2 Shintoshin, Chuo-Ku, Saitama, 3308777, Japan.
| | - Katsuhiro Arai
- Center for Pediatric Inflammatory Bowel Disease, Division of Gastroenterology, National Center for Child Health and Development, Tokyo, Japan
| | - Takahiro Kudo
- Department of Pediatrics, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Takatsugu Murakoshi
- Department of Gastroenterology, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Reiko Kunisaki
- Inflammatory Bowel Disease Center, Yokohama City University Medical Center, Kanagawa, Japan
| | - Tatsuki Mizuochi
- Department of Pediatrics and Child Health, Kurume University School of Medicine, Fukuoka, Japan
| | - Sawako Kato
- Department of Pediatrics, Shinshu University School of Medicine, Nagano, Japan
| | - Hideki Kumagai
- Department of Pediatrics, Jichi Medical University, Tochigi, Japan
| | - Mikihiro Inoue
- Department of Pediatric Surgery, Fujita Health University, Aichi, Japan
| | - Takashi Ishige
- Department of Pediatrics, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Takeshi Saito
- Division of Pediatric Surgery, Chiba Children's Hospital, Chiba, Japan
| | - Atsuko Noguchi
- Department of Pediatrics, Akita University Graduate School of Medicine, Akita, Japan
| | | | - Shin-Ichiro Hagiwara
- Department of Gastroenterology, Nutrition and Endocrinology, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Naomi Iwata
- Department of Infection and Immunology, Aichi Children's Health and Medical Center, Aichi, Japan
| | - Shigeo Nishimata
- Department of Pediatrics and Adolescent Medicine, Tokyo Medical University, Tokyo, Japan
| | - Fumihiko Kakuta
- Department of General Pediatrics and Gastroenterology, Miyagi Children's Hospital, Miyagi, Japan
| | - Hitoshi Tajiri
- Department of Pediatrics, Osaka General Medical Center, Osaka, Japan
| | - Eitaro Hiejima
- Department of Pediatrics, Kyoto University Hospital, Kyoto, Japan
| | - Nariaki Toita
- Department of Pediatrics, Sapporo Kosei General Hospital, Hokkaido, Japan
| | | | - Hirotaka Shimizu
- Center for Pediatric Inflammatory Bowel Disease, Division of Gastroenterology, National Center for Child Health and Development, Tokyo, Japan
| | - Itaru Iwama
- Division of Gastroenterology and Hepatology, Saitama Children's Medical Center, 1-2 Shintoshin, Chuo-Ku, Saitama, 3308777, Japan
| | - Yuri Hirano
- Center for Pediatric Inflammatory Bowel Disease, Division of Gastroenterology, National Center for Child Health and Development, Tokyo, Japan
| | - Toshiaki Shimizu
- Department of Pediatrics, Faculty of Medicine, Juntendo University, Tokyo, Japan
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Mehta RS, Mayers JR, Zhang Y, Bhosle A, Glasser NR, Nguyen LH, Ma W, Bae S, Branck T, Song K, Sebastian L, Pacheco JA, Seo HS, Clish C, Dhe-Paganon S, Ananthakrishnan AN, Franzosa EA, Balskus EP, Chan AT, Huttenhower C. Gut microbial metabolism of 5-ASA diminishes its clinical efficacy in inflammatory bowel disease. Nat Med 2023; 29:700-709. [PMID: 36823301 PMCID: PMC10928503 DOI: 10.1038/s41591-023-02217-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 01/10/2023] [Indexed: 02/25/2023]
Abstract
For decades, variability in clinical efficacy of the widely used inflammatory bowel disease (IBD) drug 5-aminosalicylic acid (5-ASA) has been attributed, in part, to its acetylation and inactivation by gut microbes. Identification of the responsible microbes and enzyme(s), however, has proved elusive. To uncover the source of this metabolism, we developed a multi-omics workflow combining gut microbiome metagenomics, metatranscriptomics and metabolomics from the longitudinal IBDMDB cohort of 132 controls and patients with IBD. This associated 12 previously uncharacterized microbial acetyltransferases with 5-ASA inactivation, belonging to two protein superfamilies: thiolases and acyl-CoA N-acyltransferases. In vitro characterization of representatives from both families confirmed the ability of these enzymes to acetylate 5-ASA. A cross-sectional analysis within the discovery cohort and subsequent prospective validation within the independent SPARC IBD cohort (n = 208) found three of these microbial thiolases and one acyl-CoA N-acyltransferase to be epidemiologically associated with an increased risk of treatment failure among 5-ASA users. Together, these data address a longstanding challenge in IBD management, outline a method for the discovery of previously uncharacterized gut microbial activities and advance the possibility of microbiome-based personalized medicine.
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Affiliation(s)
- Raaj S Mehta
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Jared R Mayers
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yancong Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Harvard Chan Microbiome in Public Health Center, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Amrisha Bhosle
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Harvard Chan Microbiome in Public Health Center, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Nathaniel R Glasser
- Resnick Sustainability Institute, California Institute of Technology, Pasadena, CA, USA
| | - Long H Nguyen
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Wenjie Ma
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Sena Bae
- Department of Immunology & Infectious Disease, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Tobyn Branck
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Kijun Song
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Luke Sebastian
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | | | - Hyuk-Soo Seo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Ashwin N Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Eric A Franzosa
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Emily P Balskus
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Immunology & Infectious Disease, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biostatistics, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA.
- Harvard Chan Microbiome in Public Health Center, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA.
- Department of Immunology & Infectious Disease, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA.
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Singh S, Ananthakrishnan AN, Nguyen NH, Cohen BL, Velayos FS, Weiss JM, Sultan S, Siddique SM, Adler J, Chachu KA. AGA Clinical Practice Guideline on the Role of Biomarkers for the Management of Ulcerative Colitis. Gastroenterology 2023; 164:344-372. [PMID: 36822736 DOI: 10.1053/j.gastro.2022.12.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
BACKGROUND & AIMS Biomarkers are used frequently for noninvasive monitoring and treatment decision making in the management of patients with ulcerative colitis (UC). This American Gastroenterological Association (AGA) guideline is intended to support practitioners in decisions about the use of biomarkers for the management of UC. METHODS A multidisciplinary panel of content experts and guideline methodologists used the Grading of Recommendations Assessment, Development and Evaluation framework to prioritize clinical questions, identify patient-centered outcomes, and conduct an evidence synthesis on the clinical performance of serum C-reactive protein (CRP), fecal calprotectin, and fecal lactoferrin as biomarkers of disease activity in patients with established UC in symptomatic remission or with active symptoms. The guideline panel used the Evidence-to-Decision framework to develop recommendations for the use of biomarkers for monitoring and management of UC and provided implementation considerations for clinical practice. RESULTS The guideline panel made 7 conditional recommendations. In patients with UC in symptomatic remission, the panel suggests the use of a biomarker- and symptom-based monitoring strategy over a symptom-based monitoring strategy. For patients in symptomatic remission, the panel suggests using fecal calprotectin <150 μg/g, normal fecal lactoferrin, and/or normal CRP to rule out active inflammation and avoid routine endoscopic assessment of disease. In patients with UC with moderate to severe symptoms, the panel suggests using fecal calprotectin >150 μg/g, elevated fecal lactoferrin, or elevated CRP to inform treatment decisions and avoid routine endoscopic assessment of disease. However, in patients in symptomatic remission but elevated biomarkers, and in patients with moderate to severe symptoms with normal biomarkers, the panel suggests endoscopic assessment of disease to inform treatment decisions. In patients with UC with mild symptoms, the panel suggests endoscopic assessment of disease activity to inform treatment decisions. The panel identified the use of a biomarker-based monitoring strategy over an endoscopy-based monitoring strategy as a knowledge gap. The panel also proposed key implementation considerations for optimal use of biomarkers, and identified areas for future research. CONCLUSIONS In patients with UC, noninvasive biomarkers, including fecal calprotectin, fecal lactoferrin, and serum CRP can inform disease monitoring and management.
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Affiliation(s)
- Siddharth Singh
- Division of Gastroenterology and Hepatology, Department of Medicine, University of California San Diego, La Jolla, California; Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, California
| | - Ashwin N Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts; Harvard Medical School, Boston, Massachusetts
| | - Nghia H Nguyen
- Division of Gastroenterology and Hepatology, Department of Medicine, University of California San Diego, La Jolla, California
| | - Benjamin L Cohen
- Division of Gastroenterology, Hepatology, and Nutrition, Digestive Disease and Surgery Institute, Cleveland Clinic, Cleveland, Ohio
| | - Fernando S Velayos
- Division of Gastroenterology, Kaiser Permanente Medical Group, San Francisco, California
| | - Jennifer M Weiss
- Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Shahnaz Sultan
- Division of Gastroenterology, Hepatology, and Nutrition, University of Minnesota, Minneapolis, Minnesota; Veterans Affairs Healthcare System, Minneapolis, Minnesota
| | - Shazia M Siddique
- Division of Gastroenterology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania; Center for Evidence-Based Practice, University of Pennsylvania Health System, Philadelphia, Pennsylvania
| | - Jeremy Adler
- Division of Pediatric Gastroenterology, CS Mott Children's Hospital, Michigan Medicine, University of Michigan, Ann Arbor, Michigan; Susan B. Meister Child Health Evaluation and Research Center, University of Michigan, Ann Arbor, Michigan
| | - Karen A Chachu
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, North Carolina
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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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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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Using machine learning to impact on long-term clinical care: principles, challenges, and practicalities. Pediatr Res 2023; 93:324-333. [PMID: 35906306 PMCID: PMC9937918 DOI: 10.1038/s41390-022-02194-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/10/2022] [Accepted: 06/22/2022] [Indexed: 11/08/2022]
Abstract
The rise of machine learning in healthcare has significant implications for paediatrics. Long-term conditions with significant disease heterogeneity comprise large portions of the routine work performed by paediatricians. Improving outcomes through discovery of disease and treatment prediction models, alongside novel subgroup clustering of patients, are some of the areas in which machine learning holds significant promise. While artificial intelligence has percolated into routine use in our day to day lives through advertising algorithms, song or movie selections and sifting of spam emails, the ability of machine learning to utilise highly complex and dimensional data has not yet reached its full potential in healthcare. In this review article, we discuss some of the foundations of machine learning, including some of the basic algorithms. We emphasise the importance of correct utilisation of machine learning, including adequate data preparation and external validation. Using nutrition in preterm infants and paediatric inflammatory bowel disease as examples, we discuss the evidence and potential utility of machine learning in paediatrics. Finally, we review some of the future applications, alongside challenges and ethical considerations related to application of artificial intelligence. IMPACT: Machine learning is a widely used term; however, understanding of the process and application to healthcare is lacking. This article uses clinical examples to explore complex machine learning terms and algorithms. We discuss limitations and potential future applications within paediatrics and neonatal medicine.
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Asadzadeh-Aghdaei H, Rejali L, Nourian M, Chaleshi V, Zamani N, Baradaran-Ghavami S, Nemati M, Shahrokh S, Norouzinia M, Vosough M, Nazemalhosseini-Mojarad E, Zali M. Toll-Like Receptor 7 a Novel Non-Invasive Inflammatory Genetic Sensor for Ulcerative Colitis Remission Monitoring. Adv Biomed Res 2023; 12:54. [PMID: 37057238 PMCID: PMC10086669 DOI: 10.4103/abr.abr_24_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/06/2022] [Accepted: 03/07/2022] [Indexed: 04/15/2023] Open
Abstract
Background Ulcerative colitis (UC) and Crohn's disease (CD) are two major types of inflammatory bowel diseases (IBDs). Toll-like receptors (TLRs) are expressed in the innate immune system compartments, in charge of identifying a wide range of microorganisms. The aim of the present study was to evaluate the expression of TLR-2, -7, and -8 in peripheral blood mononuclear cells (PBMC) of UC patients as a novel non-invasive primary inflammation sensor for monitoring the clinical course of UC candidates. Materials and Methods In this cross-sectional study, total RNA was extracted from the PBMC of 42 UC patients along with 20 healthy donors. The mRNA levels of TLR-2, -7, and -8 were assessed using the quantitative real-time polymerase chain (qRT-PCR) reaction. Results The present research study demonstrated no significant changes in TLR-2 mRNA expression in UC patients in comparison with the control group (P = 0.1264), whereas significant elevation (P = 0.0008) was distinguished in the TLR-7 expression of UC participants specifically during the remission course compared with healthy donors and flareup patients (P = 0.0004 and P = 0.0063, respectively). The last selected TLR, TLR-8 was not shown remarkable changes either between UC patients and the control group or between clinical courses of the disease. Conclusion Here, among three nominated TLRs for predicting UC patients, TLR-7 was potentially selected according to the significant difference in mRNA expression in flareup UC patients and control donors. TLR-7 could be used as a novel non-invasive biomarker for monitoring UC patients in the active course of the disease.
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Affiliation(s)
- Hamid Asadzadeh-Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Leili Rejali
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahyar Nourian
- Mahak Hematology Oncology Research Center (Mahak-HORC), Mahak Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Vahid Chaleshi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Naghmeh Zamani
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shaghayegh Baradaran-Ghavami
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohsen Nemati
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shabnam Shahrokh
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohsen Norouzinia
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Massoud Vosough
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Ehsan Nazemalhosseini-Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Address for correspondence: Dr. Ehsan Nazemalhosseini-Mojarad, Gastroenterology, and Liver Disease Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Yeman St, Chamran Expressway, Thran, Iran. E-mail:
| | - Mohammadreza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Impact of international travel and diarrhea on gut microbiome and resistome dynamics. Nat Commun 2022; 13:7485. [PMID: 36470885 PMCID: PMC9722912 DOI: 10.1038/s41467-022-34862-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 11/08/2022] [Indexed: 12/11/2022] Open
Abstract
International travel contributes to the global spread of antimicrobial resistance. Travelers' diarrhea exacerbates the risk of acquiring multidrug-resistant organisms and can lead to persistent gastrointestinal disturbance post-travel. However, little is known about the impact of diarrhea on travelers' gut microbiomes, and the dynamics of these changes throughout travel. Here, we assembled a cohort of 159 international students visiting the Andean city of Cusco, Peru and applied next-generation sequencing techniques to 718 longitudinally-collected stool samples. We find that gut microbiome composition changed significantly throughout travel, but taxonomic diversity remained stable. However, diarrhea disrupted this stability and resulted in an increased abundance of antimicrobial resistance genes that can remain high for weeks. We also identified taxa differentially abundant between diarrheal and non-diarrheal samples, which were used to develop a classification model that distinguishes between these disease states. Additionally, we sequenced the genomes of 212 diarrheagenic Escherichia coli isolates and found those from travelers who experienced diarrhea encoded more antimicrobial resistance genes than those who did not. In this work, we find the gut microbiomes of international travelers' are resilient to dysbiosis; however, they are also susceptible to colonization by multidrug-resistant bacteria, a risk that is more pronounced in travelers with diarrhea.
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Prognostic Factors of Biologic Therapy in Pediatric IBD. CHILDREN (BASEL, SWITZERLAND) 2022; 9:children9101558. [PMID: 36291494 PMCID: PMC9600413 DOI: 10.3390/children9101558] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/04/2022] [Accepted: 10/09/2022] [Indexed: 11/06/2022]
Abstract
This was a retrospective cohort study aimed at identifying parameters measured at diagnosis of pediatric IBD to predict subsequent biologic therapy, as an equivalent to an unfavorable clinical course. Identification of predictors of poor outcomes is an important issue in current ECCO guidelines on pIBD. The study population consisted of 119 children with Crohn’s disease and 112 with ulcerative colitis, diagnosed and monitored for at least 1 year from 2009–2019. The population was divided into the study groups separately: 39 children with CD and 14 with UC who received biologics before the age of 18 y compared to 80 with CD and 98 with UC who did not. The combined analysis of 53 biologic therapy recipients vs. 178 non-recipients with IBD was also conducted. Logistic regression tests (OR, RR) and sensitivity, specificity, PPV, and NPV were used. Factors significantly correlated with subsequent biologic therapy were perianal disease, complicated disease behavior, high PCDAI (CD), fatigue, hypoalbuminemia, high PUCAI (UC) and fever, fatigue, hypoalbuminemia, hypoproteinemia, and elevated CRP (IBD). Marginally significant factors were ileocecal disease, elevated serum IgA, anemia, and L4a–L4b coexistence. Apart from parameters already accepted as POPO (B2/3, perianal disease), interesting observations are the significance of IgA, L4a–L4b in CD, and hypoalbuminemia in UC.
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Bertani L. Treatment and Management of Chronic Inflammatory Bowel Diseases: Optimizing Present and Future Therapeutic Choices. J Clin Med 2022; 11:jcm11185267. [PMID: 36142914 PMCID: PMC9501929 DOI: 10.3390/jcm11185267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 08/31/2022] [Accepted: 09/03/2022] [Indexed: 11/16/2022] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic relapsing diseases of the gastrointestinal tract of unknown origin, resulting from an aberrant immune response to microbial and gut-specific antigens in genetically susceptible patients [...]
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Affiliation(s)
- Lorenzo Bertani
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy;
- Department of Surgery, Tuscany North-West ASL, Pontedera Hospital, 56025 Pontedera, Italy
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Aloi M, D'Arcangelo G, Rossetti D, Bucherini S, Felici E, Romano C, Martinelli M, Dipasquale V, Lionetti P, Oliva S. Occurrence and Clinical Impact of Eosinophilic Esophagitis in a Large Cohort of Children With Inflammatory Bowel Disease. Inflamm Bowel Dis 2022:6658537. [PMID: 35942651 DOI: 10.1093/ibd/izac172] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Indexed: 12/09/2022]
Abstract
BACKGROUND Scarce data have investigated the association between pediatric inflammatory bowel disease (IBD) and eosinophilic esophagitis (EoE). We, therefore, aimed to describe the epidemiology and the possible peculiar phenotype and natural history of such an association. METHODS Case-control study is based on the Italian Society for Pediatric Gastroenterology (SIGENP) national registry. All children with a combined diagnosis of IBD and EoE were included. The overall prevalence and incidence in 2 periods, 2009 to 2015, and 2016 to 2021, were calculated. Cases were matched with IBD only and EoE only patients in a 1:3:3 ratio. Phenotype and outcomes (courses of steroids, risk of complications, surgery, treatment escalation, and hospitalization) were compared between groups. RESULTS Eleven patients (age 11.2 ± 2.8 years, Males 91%) with EoE-IBD out of 3090 patients with IBD were identified, resulting in an overall prevalence of 0.35% and an incidence of 0.18% for 2009 to 2015 and 0.45% for 2016 to 2021. Treatment escalation rates for IBD were significantly higher in patients with IBD compared with EoE-IBD at 12- and 24-month follow-up (0% vs 30%, P = .04; and 9% vs 45.5%, P = .03, respectively). Furthermore, patients with IBD were at a significantly higher risk of hospitalization than both EoE-IBD and EoE patients (log rank P < .001). We found no significant differences in major outcomes related to the EoE course in EoE-IBD patients compared with EoE ones. CONCLUSIONS The incidence and prevalence of EoE in children with IBD are low, although the incidence seems to be rising in recent years. Having EoE appears to be associated with a milder IBD disease course, whereas having IBD does not seem to affect the natural history of EoE. More data are needed to better define the phenotype of such association.
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Affiliation(s)
- Marina Aloi
- Sapienza University of Rome - Umberto I Hospital, Rome, Italy
| | | | - Danilo Rossetti
- Sapienza University of Rome - Umberto I Hospital, Rome, Italy
| | | | - Enrico Felici
- Sapienza University of Rome - Umberto I Hospital, Rome, Italy
| | - Claudio Romano
- Sapienza University of Rome - Umberto I Hospital, Rome, Italy
| | | | | | - Paolo Lionetti
- Sapienza University of Rome - Umberto I Hospital, Rome, Italy
| | - Salvatore Oliva
- Sapienza University of Rome - Umberto I Hospital, Rome, Italy
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Haifer C, Luu LDW, Paramsothy S, Borody TJ, Leong RW, Kaakoush NO. Microbial determinants of effective donors in faecal microbiota transplantation for UC. Gut 2022; 72:gutjnl-2022-327742. [PMID: 35879048 DOI: 10.1136/gutjnl-2022-327742] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/13/2022] [Indexed: 02/04/2023]
Abstract
OBJECTIVE Faecal microbiota transplantation (FMT) has variable efficacy in treating UC. Recently, oral lyophilised FMT was found to induce remission in patients with UC, with one donor having 100% efficacy compared with a second donor (36% efficacy). We characterised differences in the gut microbiota of these two donors with the aim of improving FMT donor selection. DESIGN Faecal samples from the two donors were collected over a period of 44 (donor 1) or 70 (donor 2) weeks. The microbiome and metabolome were profiled using shotgun metagenomics and untargeted metabolomics RESULTS: Gut microbiome long-term stability was highly evident in the effective donor. Donor microbiota species evenness was a robust feature associated with clinical efficacy across two clinical trials of FMT in UC, leading to increased donor species engraftment in patients. Alpha diversity and beta diversity of donor gut microbiotas significantly differed. 90 bacterial species and one archaeon were differentially abundant between donors, 44 of which were >0.1% in relative abundance. 17/44 species were enriched in the effective donor, 11 of which (64.7%) were assembled into high-quality genomes that were prevalent (≥75% samples) in that donor, and six showed evidence of engraftment in patients. Taxonomic differences between donors translated to substantial microbial functional differences that were validated using metabolomics. CONCLUSION Donor microbiota stability and species evenness were identified as novel metrics that were associated with therapeutic efficacy in UC, beyond individual microbial species or metabolites. These metrics may represent community resilience that translates to better engraftment in the host. TRIAL REGISTRATION NUMBER ACTRN12619000611123.
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Affiliation(s)
- Craig Haifer
- Concord Clinical School, University of Sydney, Sydney, NSW, Australia
- Department of Gastroenterology, Concord Repatriation General Hospital, Sydney, NSW, Australia
- Department of Gastroenterology, St Vincent's Hospital, Sydney, NSW, Australia
| | - Laurence Don Wai Luu
- School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Sudarshan Paramsothy
- Concord Clinical School, University of Sydney, Sydney, NSW, Australia
- Department of Gastroenterology, Concord Repatriation General Hospital, Sydney, NSW, Australia
| | | | - Rupert W Leong
- Concord Clinical School, University of Sydney, Sydney, NSW, Australia
- Department of Gastroenterology, Concord Repatriation General Hospital, Sydney, NSW, Australia
| | - Nadeem O Kaakoush
- School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia
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Borren NZ, Ananthakrishnan AN. Precision medicine: how multiomics will shape the future of inflammatory bowel disease? Curr Opin Gastroenterol 2022; 38:382-387. [PMID: 35762697 PMCID: PMC9472771 DOI: 10.1097/mog.0000000000000847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
PURPOSE OF REVIEW In this article, we provide an overview of studies examining multiomic profiling in various clinical scenarios in the management of inflammatory bowel diseases (IBDs). RECENT FINDINGS IBD arises as a result of an interplay between genetic, environmental, microbial and immunologic perturbations. The access to high throughput technology as well as the decrease in costs associated with such studies has led to a growing wealth of literature examining the utility of single or multiomic profiles in the management of IBD. Such studies have commonly examined the genome (and less frequently the epigenome), transcriptome, metabolome, proteome and the gut microbial metagenome in the context of overall IBD status or specific clinical scenarios, including the disease progression or response to treatment. The findings have provided important insight into how each of these compartments reflect underlying disease pathophysiologic processes and, in turn, can influence stratification of patients for clinical management. SUMMARY Multiomic profiling in IBD has the potential to advance the field of personalized precision medicine in the management of IBDs.
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Affiliation(s)
- Nienke Z Borren
- Department of Gastroenterology & Hepatology, Erasmus University Medical Center, Rotterdam, the Netherlands
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Elhag DA, Kumar M, Saadaoui M, Akobeng AK, Al-Mudahka F, Elawad M, Al Khodor S. Inflammatory Bowel Disease Treatments and Predictive Biomarkers of Therapeutic Response. Int J Mol Sci 2022; 23:ijms23136966. [PMID: 35805965 PMCID: PMC9266456 DOI: 10.3390/ijms23136966] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/05/2022] [Accepted: 06/06/2022] [Indexed: 02/08/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic immune-mediated inflammation of the gastrointestinal tract with a highly heterogeneous presentation. It has a relapsing and remitting clinical course that necessitates lifelong monitoring and treatment. Although the availability of a variety of effective therapeutic options including immunomodulators and biologics (such as TNF, CAM inhibitors) has led to a paradigm shift in the treatment outcomes and clinical management of IBD patients, some patients still either fail to respond or lose their responsiveness to therapy over time. Therefore, according to the recent Selecting Therapeutic Targets in Inflammatory Bowel Disease (STRIDE-II) recommendations, continuous disease monitoring from symptomatic relief to endoscopic healing along with short- and long-term therapeutic responses are critical for providing IBD patients with a tailored therapy algorithm. Moreover, considering the high unmet need for novel therapeutic approaches for IBD patients, various new modulators of cytokine signaling events (for example, JAK/TYK inhibitors), inhibitors of cytokines (for example IL-12/IL-23, IL-22, IL-36, and IL-6 inhibitors), anti-adhesion and migration strategies (for example, β7 integrin, sphingosine 1-phosphate receptors, and stem cells), as well as microbial-based therapeutics to decolonize the bed buds (for example, fecal microbiota transplantation and bacterial inhibitors) are currently being evaluated in different phases of controlled clinical trials. This review aims to offer a comprehensive overview of available treatment options and emerging therapeutic approaches for IBD patients. Furthermore, predictive biomarkers for monitoring the therapeutic response to different IBD therapies are also discussed.
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Affiliation(s)
- Duaa Ahmed Elhag
- Research Department, Sidra Medicine, Doha 26999, Qatar; (D.A.E.); (M.K.); (M.S.)
| | - Manoj Kumar
- Research Department, Sidra Medicine, Doha 26999, Qatar; (D.A.E.); (M.K.); (M.S.)
| | - Marwa Saadaoui
- Research Department, Sidra Medicine, Doha 26999, Qatar; (D.A.E.); (M.K.); (M.S.)
| | - Anthony K. Akobeng
- Division of Gastroenterology, Hepatology and Nutrition, Sidra Medicine, Doha 26999, Qatar; (A.K.A.); (F.A.-M.); (M.E.)
| | - Fatma Al-Mudahka
- Division of Gastroenterology, Hepatology and Nutrition, Sidra Medicine, Doha 26999, Qatar; (A.K.A.); (F.A.-M.); (M.E.)
| | - Mamoun Elawad
- Division of Gastroenterology, Hepatology and Nutrition, Sidra Medicine, Doha 26999, Qatar; (A.K.A.); (F.A.-M.); (M.E.)
| | - Souhaila Al Khodor
- Research Department, Sidra Medicine, Doha 26999, Qatar; (D.A.E.); (M.K.); (M.S.)
- Correspondence:
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45
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Clarkston K, Karns R, Jegga AG, Sharma M, Fox S, Ojo BA, Minar P, Walters TD, Griffiths AM, Mack DR, Boyle B, LeLeiko NS, Markowitz J, Rosh JR, Patel AS, Shah S, Baldassano RN, Pfefferkorn M, Sauer C, Kugathasan S, Haberman Y, Hyams JS, Denson LA, Rosen MJ. Targeted Assessment of Mucosal Immune Gene Expression Predicts Clinical Outcomes in Children with Ulcerative Colitis. J Crohns Colitis 2022; 16:1735-1750. [PMID: 35665804 PMCID: PMC9683081 DOI: 10.1093/ecco-jcc/jjac075] [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] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS We aimed to determine whether a targeted gene expression panel could predict clinical outcomes in paediatric ulcerative colitis [UC] and investigated putative pathogenic roles of predictive genes. METHODS In total, 313 rectal RNA samples from a cohort of newly diagnosed paediatric UC patients (PROTECT) were analysed by a real-time PCR microfluidic array for expression of type 1, 2 and 17 inflammation genes. Associations between expression and clinical outcomes were assessed by logistic regression. Identified prognostic markers were further analysed using existing RNA sequencing (RNA-seq) data sets and tissue immunostaining. RESULTS IL13RA2 was associated with a lower likelihood of corticosteroid-free remission (CSFR) on mesalamine at week 52 (p = .002). A model including IL13RA2 and only baseline clinical parameters was as accurate as an established clinical model, which requires week 4 remission status. RORC was associated with a lower likelihood of colectomy by week 52. A model including RORC and PUCAI predicted colectomy by 52 weeks (area under the receiver operating characteristic curve 0.71). Bulk RNA-seq identified IL13RA2 and RORC as hub genes within UC outcome-associated expression networks related to extracellular matrix and innate immune response, and lipid metabolism and microvillus assembly, respectively. Adult UC single-cell RNA-seq data revealed IL13RA2 and RORC co-expressed genes were localized to inflammatory fibroblasts and undifferentiated epithelial cells, respectively, which was supported by protein immunostaining. CONCLUSION Targeted assessment of rectal mucosal immune gene expression predicts 52-week CSFR in treatment-naïve paediatric UC patients. Further exploration of IL-13Rɑ2 as a therapeutic target in UC and future studies of the epithelial-specific role of RORC in UC pathogenesis are warranted.
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Affiliation(s)
- Kathryn Clarkston
- Division of Gastroenterology, Hepatology and Nutrition,Division of Pediatric Gastroenterology, Children’s Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Rebekah Karns
- Division of Gastroenterology, Hepatology and Nutrition
| | - Anil G Jegga
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Mihika Sharma
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Sejal Fox
- Division of Gastroenterology, Hepatology and Nutrition
| | - Babajide A Ojo
- Division of Pediatric Gastroenterology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Phillip Minar
- Division of Gastroenterology, Hepatology and Nutrition,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Thomas D Walters
- Division of Pediatric Gastroenterology, Hospital for Sick Children, Toronto, ON, Canada
| | - Anne M Griffiths
- Division of Pediatric Gastroenterology, Hospital for Sick Children, Toronto, ON, Canada
| | - David R Mack
- Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Eastern Ontario and University of Ottawa, Ottawa, ON, Canada
| | - Brendan Boyle
- Division of Gastroenterology, Hepatology, and Nutrition, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Neal S LeLeiko
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons and NewYork-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, USA
| | - James Markowitz
- Division of Gastroenterology, Hepatology, and Nutrition, Cohen Children’s Medical Center of New York, New Hyde Park, NY, USA
| | - Joel R Rosh
- Division of Gastroenterology, Hepatology, and Nutrition, Goryeb Children’s Hospital, Atlantic Health, Morristown, NJ, USA
| | - Ashish S Patel
- Division of Gastroenterology, Phoenix Children’s Hospital, Phoenix, AZ, USA
| | - Sapana Shah
- Division of Gastroenterology, Hepatology and Nutrition, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Robert N Baldassano
- Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marian Pfefferkorn
- Division of Gastroenterology, Hepatology, and Nutrition, Riley Children’s Hospital, Indianapolis, IN, USA
| | - Cary Sauer
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Emory University and Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Subra Kugathasan
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Emory University and Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Yael Haberman
- Division of Gastroenterology, Hepatology and Nutrition,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA,Sheba Medical Center, Tel Hashomer, Israel
| | - Jeffrey S Hyams
- Division of Digestive Diseases, Hepatology, and Nutrition, Connecticut Children’s Medical Center, Hartford, CT, USA
| | - Lee A Denson
- Division of Gastroenterology, Hepatology and Nutrition,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Michael J Rosen
- Corresponding author: Michael J. Rosen, MD, MSCI, Division of Pediatric Gastroenterology, Department of Pediatrics, Stanford University School of Medicine, 750 Welch Rd, Suite 116, Palo Alto, CA 94304, USA. E-mail:
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Leite-Gomes E, Dias AM, Azevedo CM, Santos-Pereira B, Magalhães M, Garrido M, Amorim R, Lago P, Marcos-Pinto R, Pinho SS. Bringing to Light the Risk of Colorectal Cancer in Inflammatory Bowel Disease: Mucosal Glycosylation as a Key Player. Inflamm Bowel Dis 2022; 28:947-962. [PMID: 34849933 DOI: 10.1093/ibd/izab291] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Indexed: 02/06/2023]
Abstract
Colitis-associated cancer is a major complication of inflammatory bowel disease remaining an important clinical challenge in terms of diagnosis, screening, and prognosis. Inflammation is a driving factor both in inflammatory bowel disease and cancer, but the mechanism underlying the transition from colon inflammation to cancer remains to be defined. Dysregulation of mucosal glycosylation has been described as a key regulatory mechanism associated both with colon inflammation and colorectal cancer development. In this review, we discuss the major molecular mechanisms of colitis-associated cancer pathogenesis, highlighting the role of glycans expressed at gut epithelial cells, at lamina propria T cells, and in serum proteins in the regulation of intestinal inflammation and its progression to colon cancer, further discussing its potential clinical and therapeutic applications.
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Affiliation(s)
- Eduarda Leite-Gomes
- i3S-Institute for Research and Innovation in Health, University of Porto, Porto, Portugal
| | - Ana M Dias
- i3S-Institute for Research and Innovation in Health, University of Porto, Porto, Portugal
| | - Catarina M Azevedo
- i3S-Institute for Research and Innovation in Health, University of Porto, Porto, Portugal
| | - Beatriz Santos-Pereira
- i3S-Institute for Research and Innovation in Health, University of Porto, Porto, Portugal
| | - Mariana Magalhães
- i3S-Institute for Research and Innovation in Health, University of Porto, Porto, Portugal.,Department of Gastroenterology, Centro Hospitalar e Universitário do Porto, Porto, Portugal
| | - Mónica Garrido
- Department of Gastroenterology, Centro Hospitalar e Universitário do Porto, Porto, Portugal
| | - Rita Amorim
- i3S-Institute for Research and Innovation in Health, University of Porto, Porto, Portugal.,Pediatrics Department, Centro Hospitalar e Universitário São João, Porto, Portugal.,Medical Faculty, University of Porto, Porto, Portugal
| | - Paula Lago
- Department of Gastroenterology, Centro Hospitalar e Universitário do Porto, Porto, Portugal
| | - Ricardo Marcos-Pinto
- Department of Gastroenterology, Centro Hospitalar e Universitário do Porto, Porto, Portugal.,School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal.,Centre for Research in Health Technologies and Information Systems, University of Porto, Portugal
| | - Salomé S Pinho
- i3S-Institute for Research and Innovation in Health, University of Porto, Porto, Portugal.,School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal.,Medical Faculty, University of Porto, Porto, Portugal
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Targeted RNAseq Improves Clinical Diagnosis of Very Early-Onset Pediatric Immune Dysregulation. J Pers Med 2022; 12:jpm12060919. [PMID: 35743704 PMCID: PMC9224647 DOI: 10.3390/jpm12060919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 02/05/2023] Open
Abstract
Despite increased use of whole exome sequencing (WES) for the clinical analysis of rare disease, overall diagnostic yield for most disorders hovers around 30%. Previous studies of mRNA have succeeded in increasing diagnoses for clearly defined disorders of monogenic inheritance. We asked if targeted RNA sequencing could provide similar benefits for primary immunodeficiencies (PIDs) and very early-onset inflammatory bowel disease (VEOIBD), both of which are difficult to diagnose due to high heterogeneity and variable severity. We performed targeted RNA sequencing of a panel of 260 immune-related genes for a cohort of 13 patients (seven suspected PID cases and six VEOIBD) and analyzed variants, splicing, and exon usage. Exonic variants were identified in seven cases, some of which had been previously prioritized by exome sequencing. For four cases, allele specific expression or lack thereof provided additional insights into possible disease mechanisms. In addition, we identified five instances of aberrant splicing associated with four variants. Three of these variants had been previously classified as benign in ClinVar based on population frequency. Digenic or oligogenic inheritance is suggested for at least two patients. In addition to validating the use of targeted RNA sequencing, our results show that rare disease research will benefit from incorporating contributing genetic factors into the diagnostic approach.
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Brown RE, Jacobse J, Anant SA, Blunt KM, Chen B, Vega PN, Jones CT, Pilat JM, Revetta F, Gorby AH, Stengel KR, Choksi YA, Palin K, Piazuelo MB, Washington MK, Lau KS, Goettel JA, Hiebert SW, Short SP, Williams CS. MTG16 (CBFA2T3) regulates colonic epithelial differentiation, colitis, and tumorigenesis by repressing E protein transcription factors. JCI Insight 2022; 7:153045. [PMID: 35503250 PMCID: PMC9220854 DOI: 10.1172/jci.insight.153045] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/13/2022] [Indexed: 12/04/2022] Open
Abstract
Aberrant epithelial differentiation and regeneration contribute to colon pathologies including inflammatory bowel disease (IBD) and colitis-associated cancer (CAC). MTG16 (CBFA2T3) is a transcriptional corepressor expressed in the colonic epithelium. MTG16 deficiency in mice exacerbates colitis and increases tumor burden in CAC, though the underlying mechanisms remain unclear. Here, we identified MTG16 as a central mediator of epithelial differentiation, promoting goblet and restraining enteroendocrine cell development in homeostasis and enabling regeneration following dextran sulfate sodium (DSS)-induced colitis. Transcriptomic analyses implicated increased E box-binding transcription factor (E protein) activity in MTG16-deficient colon crypts. Using a novel mouse model with a point mutation that attenuates MTG16:E protein interactions (Mtg16P209T), we established that MTG16 exerts control over colonic epithelial differentiation and regeneration by repressing E protein-mediated transcription. Mimicking murine colitis, MTG16 expression was increased in biopsies from patients with active IBD compared to unaffected controls. Finally, uncoupling MTG16:E protein interactions partially phenocopied the enhanced tumorigenicity of Mtg16-/- colon in the azoxymethane(AOM)/DSS-induced model of CAC, indicating that MTG16 protects from tumorigenesis through additional mechanisms. Collectively, our results demonstrate that MTG16, via its repression of E protein targets, is a key regulator of cell fate decisions during colon homeostasis, colitis, and cancer.
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Affiliation(s)
- Rachel E Brown
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Justin Jacobse
- Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, Netherlands
| | - Shruti A Anant
- Department of Medicine, Health, and Society, Vanderbilt University, Nashville, United States of America
| | - Koral M Blunt
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
| | - Bob Chen
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Paige N Vega
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Chase T Jones
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
| | - Jennifer M Pilat
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Frank Revetta
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, United States of America
| | - Aidan H Gorby
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
| | - Kristy R Stengel
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Yash A Choksi
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
| | - Kimmo Palin
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - M Blanca Piazuelo
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
| | - Mary K Washington
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, United States of America
| | - Ken S Lau
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Jeremy A Goettel
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
| | - Scott W Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Sarah P Short
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
| | - Christopher S Williams
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
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Kellermayer R, Chang A, Patel K. Sirolimus (Rapamycin) Induced Mucosal Healing in Anti-Tumor Necrosis Factor Refractory Pediatric Ulcerative Colitis. JPGN REPORTS 2022; 3:e183. [PMID: 37168909 PMCID: PMC10158451 DOI: 10.1097/pg9.0000000000000183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/20/2022] [Indexed: 05/13/2023]
Abstract
Sirolimus (rapamycin) has been sparsely reported in the treatment of pediatric ulcerative colitis (PUC). Mucosal healing has not been examined in responders to the drug. We describe a case of infliximab refractory PUC where rapamycin induced sustained clinical remission along with mucosal healing. We conclude that rapamycin should be positioned into the expanding treatment repertoire of PUC.
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Affiliation(s)
- Richard Kellermayer
- Section of Pediatric Gastroenterology, Texas Children’s Hospital Baylor College of Medicine
- USDA/ARS Children’s Nutrition Research Center
| | | | - Kalyani Patel
- Department of Pathology, Baylor College of Medicine, Houston, TX
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Verstockt B, Parkes M, Lee JC. How Do We Predict a Patient's Disease Course and Whether They Will Respond to Specific Treatments? Gastroenterology 2022; 162:1383-1395. [PMID: 34995535 DOI: 10.1053/j.gastro.2021.12.245] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 12/09/2021] [Accepted: 12/09/2021] [Indexed: 02/07/2023]
Abstract
Gastroenterologists will be all too familiar with the difficult decisions that managing inflammatory bowel disease often presents. How aggressively should I treat this patient? Do I expect them to have a mild or aggressive form of disease? Do they need a biologic? If so, which one? And when should I start it? The reality is that the answers that would be right for one patient might be disastrous for another. The growing therapeutic armamentarium will only make these decisions more difficult, and yet, we have seen how other specialties have begun to use the molecular heterogeneity in their diseases to provide some answers. Here, we review the progress that has been made in predicting the future for any given patient with inflammatory bowel disease-whether that is the course of disease that they will experience or whether or not they will respond to, or indeed tolerate, a particular therapy.
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Affiliation(s)
- Bram Verstockt
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Katholieke Universiteit Leuven, Leuven, Belgium; Department of Chronic Diseases and Metabolism, Translational Research Center for Gastrointestinal Disorders-Inflammatory Bowel Disease (TARGID-IBD), Katholieke Universiteit Leuven, Leuven, Belgium
| | - Miles Parkes
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - James C Lee
- Genetic Mechanisms of Disease Laboratory, Francis Crick Institute, London, United Kingdom; Institute for Liver & Digestive Health, Royal Free London Hospital, University College London, London, United Kingdom.
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