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Hu S, Bourgonje AR, Gacesa R, Jansen BH, Björk JR, Bangma A, Hidding IJ, van Dullemen HM, Visschedijk MC, Faber KN, Dijkstra G, Harmsen HJM, Festen EAM, Vich Vila A, Spekhorst LM, Weersma RK. Mucosal host-microbe interactions associate with clinical phenotypes in inflammatory bowel disease. Nat Commun 2024; 15:1470. [PMID: 38368394 PMCID: PMC10874382 DOI: 10.1038/s41467-024-45855-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/05/2024] [Indexed: 02/19/2024] Open
Abstract
Disrupted host-microbe interactions at the mucosal level are key to the pathophysiology of IBD. This study aimed to comprehensively examine crosstalk between mucosal gene expression and microbiota in patients with IBD. To study tissue-specific interactions, we perform transcriptomic (RNA-seq) and microbial (16S-rRNA-seq) profiling of 697 intestinal biopsies (645 derived from 335 patients with IBD and 52 from 16 non-IBD controls). Mucosal gene expression patterns in IBD are mainly determined by tissue location and inflammation, whereas the mucosal microbiota composition shows a high degree of individual specificity. Analysis of transcript-bacteria interactions identifies six distinct groups of inflammation-related pathways that are associated with intestinal microbiota (adjusted P < 0.05). An increased abundance of Bifidobacterium is associated with higher expression of genes involved in fatty acid metabolism, while Bacteroides correlates with increased metallothionein signaling. In patients with fibrostenosis, a transcriptional network dominated by immunoregulatory genes is associated with Lachnoclostridium bacteria in non-stenotic tissue (adjusted P < 0.05), while being absent in CD without fibrostenosis. In patients using TNF-α-antagonists, a transcriptional network dominated by fatty acid metabolism genes is linked to Ruminococcaceae (adjusted P < 0.05). Mucosal microbiota composition correlates with enrichment of intestinal epithelial cells, macrophages, and NK-cells. Overall, these data demonstrate the presence of context-specific mucosal host-microbe interactions in IBD, revealing significantly altered inflammation-associated gene-taxa modules, particularly in patients with fibrostenotic CD and patients using TNF-α-antagonists. This study provides compelling insights into host-microbe interactions that may guide microbiota-directed precision medicine and fuels the rationale for microbiota-targeted therapeutics as a strategy to alter disease course in IBD.
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Affiliation(s)
- Shixian Hu
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Institute of Precision Medicine, the First Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Arno R Bourgonje
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ranko Gacesa
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Bernadien H Jansen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Johannes R Björk
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Amber Bangma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Iwan J Hidding
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Hendrik M van Dullemen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marijn C Visschedijk
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Hermie J M Harmsen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Eleonora A M Festen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Lieke M Spekhorst
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, Medisch Spectrum Twente, Enschede, the Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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Chen KA, Nishiyama NC, Kennedy Ng MM, Shumway A, Joisa CU, Schaner MR, Lian G, Beasley C, Zhu LC, Bantumilli S, Kapadia MR, Gomez SM, Furey TS, Sheikh SZ. Linking gene expression to clinical outcomes in pediatric Crohn's disease using machine learning. Sci Rep 2024; 14:2667. [PMID: 38302662 PMCID: PMC10834600 DOI: 10.1038/s41598-024-52678-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 01/21/2024] [Indexed: 02/03/2024] Open
Abstract
Pediatric Crohn's disease (CD) is characterized by a severe disease course with frequent complications. We sought to apply machine learning-based models to predict risk of developing future complications in pediatric CD using ileal and colonic gene expression. Gene expression data was generated from 101 formalin-fixed, paraffin-embedded (FFPE) ileal and colonic biopsies obtained from treatment-naïve CD patients and controls. Clinical outcomes including development of strictures or fistulas and progression to surgery were analyzed using differential expression and modeled using machine learning. Differential expression analysis revealed downregulation of pathways related to inflammation and extra-cellular matrix production in patients with strictures. Machine learning-based models were able to incorporate colonic gene expression and clinical characteristics to predict outcomes with high accuracy. Models showed an area under the receiver operating characteristic curve (AUROC) of 0.84 for strictures, 0.83 for remission, and 0.75 for surgery. Genes with potential prognostic importance for strictures (REG1A, MMP3, and DUOX2) were not identified in single gene differential analysis but were found to have strong contributions to predictive models. Our findings in FFPE tissue support the importance of colonic gene expression and the potential for machine learning-based models in predicting outcomes for pediatric CD.
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Affiliation(s)
- Kevin A Chen
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, 7314 Medical Biomolecular Research Building, 111 Mason Farm Road, Chapel Hill, NC, 27599, USA
- Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Nina C Nishiyama
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, 7314 Medical Biomolecular Research Building, 111 Mason Farm Road, Chapel Hill, NC, 27599, USA
- Departments of Genetics and Biology, Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, 5022 Genetic Medicine Building, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Meaghan M Kennedy Ng
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, 7314 Medical Biomolecular Research Building, 111 Mason Farm Road, Chapel Hill, NC, 27599, USA
- Departments of Genetics and Biology, Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, 5022 Genetic Medicine Building, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Alexandria Shumway
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Chinmaya U Joisa
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, USA
| | - Matthew R Schaner
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, 7314 Medical Biomolecular Research Building, 111 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Grace Lian
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, 7314 Medical Biomolecular Research Building, 111 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Caroline Beasley
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, 7314 Medical Biomolecular Research Building, 111 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Lee-Ching Zhu
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Surekha Bantumilli
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Muneera R Kapadia
- Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Shawn M Gomez
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, USA
| | - Terrence S Furey
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, 7314 Medical Biomolecular Research Building, 111 Mason Farm Road, Chapel Hill, NC, 27599, USA.
- Departments of Genetics and Biology, Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, 5022 Genetic Medicine Building, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA.
| | - Shehzad Z Sheikh
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, 7314 Medical Biomolecular Research Building, 111 Mason Farm Road, Chapel Hill, NC, 27599, USA.
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Wang J, Macoritto M, Guay H, Davis JW, Levesque MC, Cao X. The Clinical Response of Upadacitinib and Risankizumab Is Associated With Reduced Inflammatory Bowel Disease Anti-TNF-α Inadequate Response Mechanisms. Inflamm Bowel Dis 2022; 29:771-782. [PMID: 36515243 DOI: 10.1093/ibd/izac246] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND Janus kinase (JAK) 1 inhibitor upadacitinib and IL-23 inhibitor risankizumab are efficacious in inflammatory bowel disease (IBD) patients who are antitumor necrosis factor (anti-TNF)-α inadequate responders (TNF-IRs). We aimed to understand the mechanisms mediating the response of upadacitinib and risankizumab. METHODS Eight tissue transcriptomic data sets from IBD patients treated with anti-TNF-α therapies along with single-cell RNAseq data from ulcerative colitis were integrated to identify TNF-IR mechanisms. The RNAseq colon tissue data from clinical studies of TNF-IR Crohn's disease patients treated with upadacitinib or risankizumab were used to identify TNF-IR mechanisms that were favorably modified by upadacitinib and risankizumab. RESULTS We found 7 TNF-IR upregulated modules related to innate/adaptive immune responses, interferon signaling, and tissue remodeling and 6 TNF-IR upregulated cell types related to inflammatory fibroblasts, postcapillary venules, inflammatory monocytes, macrophages, dendritic cells, and cycling B cells. Upadacitinib was associated with a significant decrease in the expression of most TNF-IR upregulated modules in JAK1 responders (JAK1-R); in contrast, there was no change in these modules among TNF-IR patients treated with a placebo or among JAK1 inadequate responders (JAK1-IR). In addition, 4 of the 6 TNF-IR upregulated cell types were significantly decreased after upadacitinib treatment in JAK1-R but not among subjects treated with a placebo or among JAK1-IR patients. We observed similar findings from colon biopsy samples from TNF-IR patients treated with risankizumab. CONCLUSIONS Collectively, these data suggest that upadacitinib and risankizumab affect TNF-IR upregulated mechanisms, which may account for their clinical response among TNF-IR IBD patients.
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Affiliation(s)
- Jing Wang
- Genomic Research Center, AbbVie Inc, Cambridge, MA, 02139, USA
| | | | - Heath Guay
- AbbVie Bioresearch Center, Worcester, MA, 01605, USA
| | - Justin W Davis
- Genomic Research Center, AbbVie Inc, North Chicago, IL, 60064, USA
| | | | - Xiaohong Cao
- Genomic Research Center, AbbVie Inc, Cambridge, MA, 02139, USA
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Choi SY, Kim ES, Jeon TY, Lee YM, Lee SM, Choe BH, Choe YH, Kang B. Transmural healing evaluated by magnetic resonance enterography in paediatric patients with Crohn's disease receiving maintenance treatment with biologics. Aliment Pharmacol Ther 2022; 56:1146-1156. [PMID: 35869849 DOI: 10.1111/apt.17161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/10/2022] [Accepted: 07/14/2022] [Indexed: 01/30/2023]
Abstract
BACKGROUND The optimal treatment goal in Crohn's disease (CD) is endoscopic healing (EH). However, transmural healing (TH) facilitated by the development and increasing performance of magnetic resonance enterography (MRE) is emerging as a potential treatment goal. AIMS To assess TH rates after 1 year of treatment by MRE and its relationship with EH in paediatric patients with CD receiving anti-tumour necrosis factor (TNF) agents, and to investigate factors associated with TH after 1 year of treatment. METHODS This multi-centre, prospective, observational study included Korean paediatric patients with luminal CD diagnosed at age < 19 years who were naïve to anti-TNF treatment. They simultaneously underwent ileocolonoscopy and MRE at baseline and after 1 year of treatment with biologics. RESULTS We included 116 patients. At 1 year, EH and TH were achieved in 59.5% (69/116) and 38.8% (45/116) of the patients, respectively. Both EH and TH was observed in 35.3% (41/116), EH without TH in 24.1% (28/116), TH without EH in 3.4% (4/116), and neither EH nor TH in 37.1% (43/116). Moreover, 59.4% (41/69) of patients who achieved EH at 1 year exhibited TH, and 91.1% (41/45) of patients who achieved TH exhibited EH. Baseline MaRIA score was associated with TH according to a multivariate analysis (OR 0.97, 95% CI 0.95-0.99, p = 0.023). CONCLUSION TH is a more stringent goal than EH. Regular follow-up evaluation of transmural status, and efforts to achieve TH, may alter the natural course of CD in the era of treat-to-target.
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Affiliation(s)
- So Yoon Choi
- Department of Pediatrics, Kosin University Gospel Hospital, Kosin University College of Medicine, Busan, South Korea
| | - Eun Sil Kim
- Department of Pediatrics, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Tae Yeon Jeon
- Department of Radiology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Yoo Min Lee
- Department of Pediatrics, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon, South Korea
| | - So Mi Lee
- Department of Radiology, Kyungpook National University School of Medicine, Daegu, South Korea
| | - Byung-Ho Choe
- Department of Pediatrics, Kyungpook National University School of Medicine, Daegu, South Korea
| | - Yon Ho Choe
- Department of Pediatrics, Samsung Medical Center, School of Medicine, Sungkyunkwan University, Seoul, South Korea
| | - Ben Kang
- Department of Pediatrics, Kyungpook National University School of Medicine, Daegu, South Korea
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Gordon IO, Abushamma S, Kurowski JA, Holubar SD, Kou L, Lyu R, Rieder F. Paediatric Ulcerative Colitis Is a Fibrotic Disease and Is Linked with Chronicity of Inflammation. J Crohns Colitis 2021; 16:804-821. [PMID: 34849664 PMCID: PMC9228908 DOI: 10.1093/ecco-jcc/jjab216] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/20/2021] [Accepted: 11/25/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND AIMS Intestinal fibrosis has recently been characterised in adult ulcerative colitis and may affect motility, diarrhoea, and the symptom of urgency. We aimed to charactersze the presence of fibrosis in paediatric patients with ulcerative colitis, and its link to severity and chronicity of mucosal inflammation, as well as clinical factors of severity. METHODS We performed a single-centre cross-sectional study in children ages 1-18 years with ulcerative colitis, undergoing colectomy or proctocolectomy. Tissue cross-sections were derived from proximal, mid, and distal colon and rectum, and inflammation and fibrosis were graded based on previously developed scores. Clinical data were collected prospectively. RESULTS From 62 patients, 205 intestinal sections were evaluated. Median age at diagnosis was 13 years, 100% had extensive colitis, and all resections were done for refractory disease. The presence, chronicity, and degree of inflammation were linked with the presence of fibrosis. Thickness of the muscularis mucosa was also linked with presence and chronicity of inflammation. The overall submucosal fibrosis burden was associated with prior anti-tumour necrosis factor use. CONCLUSIONS Paediatric patients with ulcerative colitis exhibit colorectal submucosal fibrosis and muscularis mucosa thickening, which correlate with the presence, chronicity, and degree of mucosal inflammation. Fibrosis should be recognised as a complication of paediatric ulcerative colitis, and ulcerative colitis should be considered a progressive disease.
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Affiliation(s)
- Ilyssa O Gordon
- Department of Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Suha Abushamma
- Department of Gastroenterology, Washington University School of Medicine, Barnes Jewish Hospital, St Louis, MO,USA
| | - Jacob A Kurowski
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Stefan D Holubar
- Department of Colorectal Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Lei Kou
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Ruishen Lyu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Florian Rieder
- Corresponding author: Florian Rieder, MD, Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute, 9500 Euclid Avenue – A3, Cleveland, OH, 44195, USA. Tel.: +1 [216] 445 4916; fax: +1 [216] 636 0104;
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Beck LC, Granger CL, Masi AC, Stewart CJ. Use of omic technologies in early life gastrointestinal health and disease: from bench to bedside. Expert Rev Proteomics 2021; 18:247-259. [PMID: 33896313 DOI: 10.1080/14789450.2021.1922278] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Introduction: At birth, the gastrointestinal (GI) tract is colonized by a complex community of microorganisms, forming the basis of the gut microbiome. The gut microbiome plays a fundamental role in host health, disorders of which can lead to an array of GI diseases, both short and long term. Pediatric GI diseases are responsible for significant morbidity and mortality, but many remain poorly understood. Recent advancements in high-throughput technologies have enabled deeper profiling of GI morbidities. Technologies, such as metagenomics, transcriptomics, proteomics and metabolomics, have already been used to identify associations with specific pathologies, and highlight an exciting area of research. However, since these diseases are often complex and multifactorial by nature, reliance on a single experimental approach may not capture the true biological complexity. Therefore, multi-omics aims to integrate singular omic data to further enhance our understanding of disease.Areas covered: This review will discuss and provide an overview of the main omic technologies that are used to study complex GI pathologies in early life.Expert opinion: Multi-omic technologies can help to unravel the complexities of several diseases during early life, aiding in biomarker discovery and enabling the development of novel therapeutics and augment predictive models.
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Affiliation(s)
- Lauren C Beck
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Claire L Granger
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK.,Newcastle Neonatal Service, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, UK
| | - Andrea C Masi
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Christopher J Stewart
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
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