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Cannarozzi AL, Latiano A, Massimino L, Bossa F, Giuliani F, Riva M, Ungaro F, Guerra M, Brina ALD, Biscaglia G, Tavano F, Carparelli S, Fiorino G, Danese S, Perri F, Palmieri O. Inflammatory bowel disease genomics, transcriptomics, proteomics and metagenomics meet artificial intelligence. United European Gastroenterol J 2024. [PMID: 39215755 DOI: 10.1002/ueg2.12655] [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: 05/16/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024] Open
Abstract
Various extrinsic and intrinsic factors such as drug exposures, antibiotic treatments, smoking, lifestyle, genetics, immune responses, and the gut microbiome characterize ulcerative colitis and Crohn's disease, collectively called inflammatory bowel disease (IBD). All these factors contribute to the complexity and heterogeneity of the disease etiology and pathogenesis leading to major challenges for the scientific community in improving management, medical treatments, genetic risk, and exposome impact. Understanding the interaction(s) among these factors and their effects on the immune system in IBD patients has prompted advances in multi-omics research, the development of new tools as part of system biology, and more recently, artificial intelligence (AI) approaches. These innovative approaches, supported by the availability of big data and large volumes of digital medical datasets, hold promise in better understanding the natural histories, predictors of disease development, severity, complications and treatment outcomes in complex diseases, providing decision support to doctors, and promising to bring us closer to the realization of the "precision medicine" paradigm. This review aims to provide an overview of current IBD omics based on both individual (genomics, transcriptomics, proteomics, metagenomics) and multi-omics levels, highlighting how AI can facilitate the integration of heterogeneous data to summarize our current understanding of the disease and to identify current gaps in knowledge to inform upcoming research in this field.
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Affiliation(s)
- Anna Lucia Cannarozzi
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Anna Latiano
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Luca Massimino
- Gastroenterology and Digestive Endoscopy Department, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Fabrizio Bossa
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Francesco Giuliani
- Innovation & Research Unit, Fondazione IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Matteo Riva
- Gastroenterology and Digestive Endoscopy Department, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Federica Ungaro
- Gastroenterology and Digestive Endoscopy Department, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Maria Guerra
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Anna Laura Di Brina
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Giuseppe Biscaglia
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Francesca Tavano
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Sonia Carparelli
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Gionata Fiorino
- Gastroenterology and Digestive Endoscopy, San Camillo-Forlanini Hospital, Rome, Italy
| | - Silvio Danese
- Faculty of Medicine, Università Vita-Salute San Raffaele, Milan, Italy
| | - Francesco Perri
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Orazio Palmieri
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
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Kurumi H, Yokoyama Y, Hirano T, Akita K, Hayashi Y, Kazama T, Isomoto H, Nakase H. Cytokine Profile in Predicting the Effectiveness of Advanced Therapy for Ulcerative Colitis: A Narrative Review. Biomedicines 2024; 12:952. [PMID: 38790914 PMCID: PMC11117845 DOI: 10.3390/biomedicines12050952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
Cytokine-targeted therapies have shown efficacy in treating patients with ulcerative colitis (UC), but responses to these advanced therapies can vary. This variability may be due to differences in cytokine profiles among patients with UC. While the etiology of UC is not fully understood, abnormalities of the cytokine profiles are deeply involved in its pathophysiology. Therefore, an approach focused on the cytokine profile of individual patients with UC is ideal. Recent studies have demonstrated that molecular analysis of cytokine profiles in UC can predict response to each advanced therapy. This narrative review summarizes the molecules involved in the efficacy of various advanced therapies for UC. Understanding these associations may be helpful in selecting optimal therapeutic agents.
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Affiliation(s)
- Hiroki Kurumi
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, S-1, W-16, Chuo-ku, Sapporo 060-8543, Hokkaido, Japan; (H.K.)
- Division of Gastroenterology and Nephrology, Department of Multidisciplinary Internal Medicine, Tottori University Faculty of Medicine, 36-1, Nishi-cho, Yonago 683-8504, Tottori, Japan
| | - Yoshihiro Yokoyama
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, S-1, W-16, Chuo-ku, Sapporo 060-8543, Hokkaido, Japan; (H.K.)
| | - Takehiro Hirano
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, S-1, W-16, Chuo-ku, Sapporo 060-8543, Hokkaido, Japan; (H.K.)
| | - Kotaro Akita
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, S-1, W-16, Chuo-ku, Sapporo 060-8543, Hokkaido, Japan; (H.K.)
| | - Yuki Hayashi
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, S-1, W-16, Chuo-ku, Sapporo 060-8543, Hokkaido, Japan; (H.K.)
| | - Tomoe Kazama
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, S-1, W-16, Chuo-ku, Sapporo 060-8543, Hokkaido, Japan; (H.K.)
| | - Hajime Isomoto
- Division of Gastroenterology and Nephrology, Department of Multidisciplinary Internal Medicine, Tottori University Faculty of Medicine, 36-1, Nishi-cho, Yonago 683-8504, Tottori, Japan
| | - Hiroshi Nakase
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, S-1, W-16, Chuo-ku, Sapporo 060-8543, Hokkaido, Japan; (H.K.)
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3
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O'Brien CL, Summers KM, Martin NM, Carter-Cusack D, Yang Y, Barua R, Dixit OVA, Hume DA, Pavli P. The relationship between extreme inter-individual variation in macrophage gene expression and genetic susceptibility to inflammatory bowel disease. Hum Genet 2024; 143:233-261. [PMID: 38421405 PMCID: PMC11043138 DOI: 10.1007/s00439-024-02642-9] [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: 08/25/2023] [Accepted: 01/14/2024] [Indexed: 03/02/2024]
Abstract
The differentiation of resident intestinal macrophages from blood monocytes depends upon signals from the macrophage colony-stimulating factor receptor (CSF1R). Analysis of genome-wide association studies (GWAS) indicates that dysregulation of macrophage differentiation and response to microorganisms contributes to susceptibility to chronic inflammatory bowel disease (IBD). Here, we analyzed transcriptomic variation in monocyte-derived macrophages (MDM) from affected and unaffected sib pairs/trios from 22 IBD families and 6 healthy controls. Transcriptional network analysis of the data revealed no overall or inter-sib distinction between affected and unaffected individuals in basal gene expression or the temporal response to lipopolysaccharide (LPS). However, the basal or LPS-inducible expression of individual genes varied independently by as much as 100-fold between subjects. Extreme independent variation in the expression of pairs of HLA-associated transcripts (HLA-B/C, HLA-A/F and HLA-DRB1/DRB5) in macrophages was associated with HLA genotype. Correlation analysis indicated the downstream impacts of variation in the immediate early response to LPS. For example, variation in early expression of IL1B was significantly associated with local SNV genotype and with subsequent peak expression of target genes including IL23A, CXCL1, CXCL3, CXCL8 and NLRP3. Similarly, variation in early IFNB1 expression was correlated with subsequent expression of IFN target genes. Our results support the view that gene-specific dysregulation in macrophage adaptation to the intestinal milieu is associated with genetic susceptibility to IBD.
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Affiliation(s)
- Claire L O'Brien
- Centre for Research in Therapeutics Solutions, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
- Inflammatory Bowel Disease Research Group, Canberra Hospital, Canberra, ACT, Australia
| | - Kim M Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Natalia M Martin
- Inflammatory Bowel Disease Research Group, Canberra Hospital, Canberra, ACT, Australia
| | - Dylan Carter-Cusack
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Yuanhao Yang
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Rasel Barua
- Inflammatory Bowel Disease Research Group, Canberra Hospital, Canberra, ACT, Australia
| | - Ojas V A Dixit
- Centre for Research in Therapeutics Solutions, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
| | - David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, QLD, Australia.
| | - Paul Pavli
- Inflammatory Bowel Disease Research Group, Canberra Hospital, Canberra, ACT, Australia.
- School of Medicine and Psychology, College of Health and Medicine, Australian National University, Canberra, ACT, Australia.
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4
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Tian QB, Chen SJ, Xiao LJ, Xie JQ, Zhao HB, Zhang X. Potential effects of nutrition-induced alteration of gut microbiota on inflammatory bowel disease: A review. J Dig Dis 2024; 25:78-90. [PMID: 38450936 DOI: 10.1111/1751-2980.13256] [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: 05/15/2023] [Revised: 01/27/2024] [Accepted: 02/06/2024] [Indexed: 03/08/2024]
Abstract
Inflammatory bowel disease (IBD), mainly comprising ulcerative colitis and Crohn's disease, is a group of gradually progressive diseases bringing significant mental anguish and imposes serious economic burdens. Interplay of genetic, environmental, and immunological factors have been implicated in its pathogenesis. Nutrients, as crucial environmental determinants, mainly encompassing carbohydrates, fats, proteins, and micronutrients, are closely related to the pathogenesis and development of IBD. Nutrition is essential for maintaining the dynamic balance of intestinal eco-environments to ensure intestinal barrier and immune homeostasis, while this balance can be disrupted easily by maladjusted nutrition. Research has firmly established that nutrition has the potential to shape the composition and function of gut microbiota to affect the disease course. Unhealthy diet and eating disorders lead to gut microbiota dysbiosis and further destroy the function of intestinal barrier such as the disruption of membrane integrity and increased permeability, thereby triggering intestinal inflammation. Notably, appropriate nutritional interventions, such as the Mediterranean diet, can positively modulate intestinal microecology, which may provide a promising strategy for future IBD prevention. In this review, we provide insights into the interplay between nutrition and gut microbiota and its effects on IBD and present some previously overlooked lines of evidence regarding the role of derived metabolites in IBD processes, such as trimethylamine N-oxide and imidazole propionate. Furthermore, we provide some insights into reducing the risk of onset and exacerbation of IBD by modifying nutrition and discuss several outstanding challenges and opportunities for future study.
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Affiliation(s)
- Qi Bai Tian
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, Hunan Province, China
| | - Shui Jiao Chen
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Li Jun Xiao
- Guangdong Corps Hospital of Chinese People's Armed Police Forces, Guangzhou, Guangdong Province, China
| | - Jia Qi Xie
- Hunan Food and Drug Vocational College, Changsha, Hunan Province, China
| | - Hong Bo Zhao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan Province, China
| | - Xian Zhang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, Hunan Province, China
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Central South University, Changsha, Hunan Province, China
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Caparrós E, García-Martinez I, Pedro Zapater, Lucía Madero, Valverde ÁM, Ana Gutiérrez, Francés R. An altered expression of miR-376a-3p and miR-20a-5p in peripheral blood exosomes regulates the autophagy and inflammatory systemic substrates, and relates to the smoking habit and age in Crohn's disease. FASEB J 2024; 38:e23418. [PMID: 38226870 DOI: 10.1096/fj.202301761r] [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: 08/30/2023] [Revised: 12/11/2023] [Accepted: 12/27/2023] [Indexed: 01/17/2024]
Abstract
miRNAs are short single-stranded noncoding RNAs that participate as epigenetic regulators in inflammatory bowel disease. Most miRNAs detectable in serum are concentrated in exosomes, with relevant cargo for immunobiological processes. We set to evaluate the exosomes miRNAs content in the serum of patients with Crohn's disease (CD) and run a prospective observational study on CD patients on biological monotherapy and healthy controls. miRNA cargo was evaluated in peripheral blood-derived exosomes. Serum autophagy and inflammatory substrates were measured. Patients were followed for 6 months. Patients (n = 28) showed an overexpression of miR-376a-3p and a downregulation of miR-20a-5p compared to controls (n = 10), without significant differences between patients according to biologics. Serum autophagy substrates ATG4C (r = .57; p = .001) and ACRV1C (r = .66; p = .001) inversely correlated with miR-376a-3p expression, whereas IGF1R correlated with miR-20a-5p expression (r = .42; p = .02). Th1-related cytokines correlated with miR-376a-3p expression, whereas the Th17-associated cytokines inversely correlated with miR-20a-5p expression. Smoking (β = -2.301 CI 95% -3.790/-0.811, p = .004) remained as independent factor related to the overexpression of miR-376a-3p, whereas diagnosis before 16 years of age (β = 2.044 CI 95% 0.934/3.154, p = .001) and a younger age of patients (β = -.720 CI 95% -0.108/-0.035, p = .001) were related to decreased miR-20a-5p expression. Seven patients (25%) had a flare in the 6-month follow-up. Patients with overexpression of miR-376a-3p at the baseline showed an increased risk of flare during this period (OR 0.475 [0.237-0.950], p = .035). Finally, a comparative miRNA signature between biologic monotherapies was also explored. Targeting miR-376a-3p and miR-20a-5p epigenetic regulators may yield homeostatic effects on relevant biological processes related to disease progression in CD patients.
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Affiliation(s)
- Esther Caparrós
- Hepatic and Intestinal Immunobiology Group, Dpto. Medicina Clínica, Universidad Miguel Hernández, Alicante, Spain
- IIS ISABIAL, Hospital General Universitario Dr. Balmis, Alicante, Spain
| | - Irma García-Martinez
- Instituto de Investigaciones Biomédicas Sols-Morreale, CSIC/UAM, Madrid, Spain
- CIBERdem, Instituto Salud Carlos III, Madrid, Spain
| | - Pedro Zapater
- Hepatic and Intestinal Immunobiology Group, Dpto. Medicina Clínica, Universidad Miguel Hernández, Alicante, Spain
- IIS ISABIAL, Hospital General Universitario Dr. Balmis, Alicante, Spain
- CIBERehd, Instituto Salud Carlos III, Madrid, Spain
- Instituto IDIBE, Universidad Miguel Hernández, Elche, Spain
| | - Lucía Madero
- IIS ISABIAL, Hospital General Universitario Dr. Balmis, Alicante, Spain
- Servicio Medicina Digestiva, Hospital General Universitario Dr. Balmis, Alicante, Spain
| | - Ángela M Valverde
- Instituto de Investigaciones Biomédicas Sols-Morreale, CSIC/UAM, Madrid, Spain
- CIBERdem, Instituto Salud Carlos III, Madrid, Spain
| | - Ana Gutiérrez
- Hepatic and Intestinal Immunobiology Group, Dpto. Medicina Clínica, Universidad Miguel Hernández, Alicante, Spain
- IIS ISABIAL, Hospital General Universitario Dr. Balmis, Alicante, Spain
- CIBERehd, Instituto Salud Carlos III, Madrid, Spain
- Servicio Medicina Digestiva, Hospital General Universitario Dr. Balmis, Alicante, Spain
| | - Rubén Francés
- Hepatic and Intestinal Immunobiology Group, Dpto. Medicina Clínica, Universidad Miguel Hernández, Alicante, Spain
- IIS ISABIAL, Hospital General Universitario Dr. Balmis, Alicante, Spain
- CIBERehd, Instituto Salud Carlos III, Madrid, Spain
- Instituto IDIBE, Universidad Miguel Hernández, Elche, Spain
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6
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Li F, Yu C, Zhao Q, Wang Z, Wang Z, Chang Y, Xu Z, Han X, Li H, Liu Y, Hu S, Chang S, Tang T, Li Y. Exploring the intestinal ecosystem: from gut microbiota to associations with subtypes of inflammatory bowel disease. Front Cell Infect Microbiol 2024; 13:1304858. [PMID: 38239508 PMCID: PMC10794348 DOI: 10.3389/fcimb.2023.1304858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 12/06/2023] [Indexed: 01/22/2024] Open
Abstract
Objective Significant differences have been discovered between subtypes of Crohn's disease (CD) and ulcerative colitis (UC). The role of gut microbiota in promoting the onset of UC and CD is established, but conclusions regarding subtype-specific analyses remain limited. Methods This study aims to explore the influence of gut microbiota on subtypes of UC and CD, offering novel insights into the pathogenesis and treatment of UC and CD.Two-sample Mendelian randomization (MR) analysis was employed to examine the causal relationship between subtypes of UC and CD and gut microbiota composition. Gut microbiota data were sourced from the International Consortium MiBioGen, while UC and CD data were obtained from FINNGEN. Eligible single nucleotide polymorphisms (SNPs) were selected as instrumental variables. Multiple analytical approaches such as inverse variance-weighted (IVW), MR-Egger regression, weighted median, weighted mode, and MR-RAPS were utilized. Sensitivity analyses including MR-Egger intercept test, Cochran's Q test, and leave-one-out analysis were conducted for quality control. Subsequently, we employed multivariable IVW, MR-Egger, weighted median, and LASSO regression methods to identify independently significant genera or families and conducted sensitivity analyses. Results We have determined that Hungatella, Acidaminococcaceae, and 15 other microbial taxa act as protective factors for various CD and UC subtypes, while Terrisporobacter, Anaerostipes, and 23 other microbial taxa are associated with increased risk for different CD and UC subtypes. Furthermore, through multivariable MR analysis, we have identified significant genera or families with independent effects. Conclusion Our study confirms a causal relationship between dysbiosis of gut microbiota and the occurrence of CD and UC subtypes. Furthermore, it validates etiological distinctions among different subtypes of CD and UC. A novel approach to adjunctive therapy involving distinct UC or CD subtypes may involve the use of probiotics and represents a potential avenue for future treatments.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Tongyu Tang
- Department of Gastroenterology, The First Hospital of Jilin University, Changchun, China
| | - Yuqin Li
- Department of Gastroenterology, The First Hospital of Jilin University, Changchun, China
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Forbes AJ, Frampton CMA, Day AS, Kaplan GG, Gearry RB. The Epidemiology of Inflammatory Bowel Disease in Oceania: A Systematic Review and Meta-Analysis of Incidence and Prevalence. Inflamm Bowel Dis 2023:izad295. [PMID: 38159083 DOI: 10.1093/ibd/izad295] [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: 09/18/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Past studies have shown high rates of inflammatory bowel disease (IBD) in Australia and New Zealand (NZ). We aimed to describe the epidemiology of IBD in Australia, NZ, and the surrounding region (collectively termed Oceania) by conducting a systematic review and meta-analysis. METHODS Electronic databases were searched from inception to April 2023 for studies reporting incidence or prevalence rates of IBD, Crohn's disease (CD), or ulcerative colitis (UC) in Oceania. All study designs were included. A meta-analysis calculated pooled estimates of incidence and prevalence, and a sensitivity analysis compared the pooled population-based studies with the non-population-based studies and the Australian and NZ studies separately. RESULTS Nineteen incidence and 11 prevalence studies were included; 2 studies were from the Pacific Islands, with the rest coming from Australia and NZ. Pooled estimates showed high incidence rates of 19.8 (95% confidence interval [CI], 15.8-23.7) for IBD, 8.3 (95% CI, 6.9-9.8) for CD, and 7.4 (95% CI, 5.7-9.1) for CD per 100 000 person-years. CD was more common than UC in most studies. The pooled estimates for the prevalence studies were 303.3 (95% CI, 128.1-478.4) for IBD, 149.8 (95% CI, 71.0-228.5) for CD, and 142.2 (95% CI, 63.1-221.4) for UC per 100 000 persons. Studies using population-based data collection methods showed higher pooled rates for both incidence and prevalence. CONCLUSIONS The incidence and prevalence of IBD in Oceania is high. The studies were heterogeneous and there were several geographic areas with no information, highlighting the need for more epidemiological studies of IBD.
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Affiliation(s)
- Angela J Forbes
- Department of Medicine, University of Otago Christchurch, Christchurch, New Zealand
| | - Chris M A Frampton
- Department of Medicine, University of Otago Christchurch, Christchurch, New Zealand
| | - Andrew S Day
- Department of Paediatrics, University of Otago Christchurch, Christchurch, New Zealand
| | - Gilaad G Kaplan
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Richard B Gearry
- Department of Medicine, University of Otago Christchurch, Christchurch, New Zealand
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Chen H, Lin X, Pan X, Xu H, Zhang X, Liang G, Qiu J, Zhang X, Gao Y, Tan X, Li N, Cai H, Cang X, Qi J, Li W, Li S, Zheng Y, Zhao L, Jin S. Development and validation of a blood routine-based extent and severity clinical decision support tool for ulcerative colitis. Sci Rep 2023; 13:21368. [PMID: 38049548 PMCID: PMC10696009 DOI: 10.1038/s41598-023-48569-5] [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: 05/24/2023] [Accepted: 11/28/2023] [Indexed: 12/06/2023] Open
Abstract
Monitoring extent and severity is vital in the ulcerative colitis (UC) follow-up, however, current assessment is complex and low cost-effectiveness. We aimed to develop a routine blood-based clinical decision support tool, Jin's model, to investigate the extent and severity of UC. The multicentre retrospective cohort study recruited 975 adult UC inpatients and sub-grouped into training, internal validation and external validation set. Model was developed by logistics regression for the extent via Montreal classification and for the severity via Mayo score, Truelove and Witts score (TWS), Mayo endoscopic score (MES) and Degree of Ulcerative colitis Burden of Luminal Inflammation (DUBLIN) score. In Montreal classification, left-sided and extensive versus proctitis model achieved area under the receiver operating characteristic curve (AUROC) of 0.78 and 0.81 retrospectively. For severity, Mayo score model, TWS model, MES model and DUBLIN score model achieved an AUROC of 0.81, 0.70, 0.74 and 0.70 retrospectively. The models also were evaluated with satisfactory calibration and clinical unity. Jin's model was free with open access at http://jinmodel.com:3000/ . Jin's model is a noninvasive, convenient, and efficient approach to assess the extent and severity of UC.
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Affiliation(s)
- Hongliang Chen
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Nangang District, Harbin, 150086, Heilongjiang, China
| | - Xindi Lin
- Department of Statistics, University of Wisconsin, Madison, WI, USA
| | - Xinyue Pan
- School of Economics and Finance, Xi'an Jiaotong University, Xi'an, China
| | - Hongyu Xu
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xuemei Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Jiamusi University, Jiamusi, China
| | - Guoying Liang
- Department of Liver, Spleen and Stomach Diseases, The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, China
| | - Jiawei Qiu
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Nangang District, Harbin, 150086, Heilongjiang, China
| | - Xueyan Zhang
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Nangang District, Harbin, 150086, Heilongjiang, China
| | - Yang Gao
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Nangang District, Harbin, 150086, Heilongjiang, China
| | - Xin Tan
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Ning Li
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Nangang District, Harbin, 150086, Heilongjiang, China
| | - Huimin Cai
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Nangang District, Harbin, 150086, Heilongjiang, China
| | - Xueyu Cang
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Nangang District, Harbin, 150086, Heilongjiang, China
| | - Jihan Qi
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Nangang District, Harbin, 150086, Heilongjiang, China
| | - Wei Li
- Department of Gastroenterology, The First Affiliated Hospital of Jiamusi University, Jiamusi, China
| | - Shuang Li
- Department of Gastroenterology, The First Affiliated Hospital of Jiamusi University, Jiamusi, China
| | - Yutong Zheng
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Nangang District, Harbin, 150086, Heilongjiang, China
| | - Lei Zhao
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Nangang District, Harbin, 150086, Heilongjiang, China
| | - Shizhu Jin
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Nangang District, Harbin, 150086, Heilongjiang, China.
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9
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Baldan-Martin M, Rubín de Célix C, Orejudo M, Ortega Moreno L, Fernández-Tomé S, Soleto I, Ramirez C, Arroyo R, Fernández P, Santander C, Moreno-Monteagudo JA, Casanova MJ, Casals F, Casabona S, Becerro I, Lozano JJ, Aransay AM, Chaparro M, Gisbert JP. Long Non-Coding RNA Signatures in the Ileum and Colon of Crohn's Disease Patients and Effect of Anti-TNF-α Treatment on Their Modulation. Int J Mol Sci 2023; 24:15691. [PMID: 37958675 PMCID: PMC10650062 DOI: 10.3390/ijms242115691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
Biological therapies only benefit one-third of patients with Crohn's disease (CD). For this reason, a deeper understanding of the mechanisms by which biologics elicit their effect on intestinal mucosa is needed. Increasing evidence points toward the involvement of long noncoding RNAs (lncRNAs) in the pathogenesis of CD, although their role remains poorly studied. We aimed to characterize lncRNA profiles in the ileum and colon from CD patients and evaluate the effect of anti-TNF-α treatment on their transcription. Terminal ileum and left colon samples from 30 patients (active CD = 10, quiescent CD = 10, and healthy controls (HCs) = 10) were collected for RNA-seq. The patients were classified according to endoscopic activity. Furthermore, biopsies were cultured with infliximab, and their transcriptome was determined by Illumina gene expression array. A total of 678 differentially expressed lncRNAs between the terminal ileum and left colon were identified in HCs, 438 in patients with quiescent CD, and 468 in patients with active CD. Additionally, we identified three new lncRNAs in the ileum associated with CD activity. No differences were observed when comparing the effect of infliximab according to intestinal location, presence of disease (CD vs. HC), and activity (active vs. quiescent). The expression profiles of lncRNAs are associated with the location of intestinal tissue, being very different in the ileum and colon. The presence of CD and disease activity are associated with the differential expression of lncRNAs. No modulatory effect of infliximab has been observed in the lncRNA transcriptome.
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Affiliation(s)
- Montse Baldan-Martin
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - Cristina Rubín de Célix
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - Macarena Orejudo
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - Lorena Ortega Moreno
- Área de Farmacología y Nutrición y Bromatología, Grupo de Investigación de Alto Rendimiento en Fisiopatología del Sistema Digestivo URJC: NeuGut-URJC, Departamento Ciencias Básicas de la Salud, Universidad Rey Juan Carlos, 28922 Madrid, Spain;
| | - Samuel Fernández-Tomé
- Departamento de Nutrición y Ciencia de los Alimentos, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain;
| | - Irene Soleto
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - Cristina Ramirez
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - Ricardo Arroyo
- Instituto de Medicina Molecular Aplicada Nemesio Díez (IMMA-ND), Facultad de Medicina, Universidad San Pablo CEU, 28668 Madrid, Spain (P.F.)
| | - Paloma Fernández
- Instituto de Medicina Molecular Aplicada Nemesio Díez (IMMA-ND), Facultad de Medicina, Universidad San Pablo CEU, 28668 Madrid, Spain (P.F.)
| | - Cecilio Santander
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - José Andrés Moreno-Monteagudo
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - María José Casanova
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - Fernando Casals
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - Sergio Casabona
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - Irene Becerro
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - Juan J. Lozano
- Bioinformatics Platform, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08036 Barcelona, Spain;
| | - Ana M. Aransay
- Genome Analysis Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 48160 Derio, Spain;
| | - María Chaparro
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
| | - Javier P. Gisbert
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006 Madrid, Spain; (C.R.d.C.); (M.O.); (I.S.); (C.R.); (C.S.); (J.A.M.-M.); (M.J.C.); (F.C.); (S.C.); (I.B.); (M.C.); (J.P.G.)
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10
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Song X, Huang Q, Yang Y, Ma L, Liu W, Ou C, Chen Q, Zhao T, Xiao Z, Wang M, Jiang Y, Yang Y, Zhang J, Nan Y, Wu W, Ai K. Efficient Therapy of Inflammatory Bowel Disease (IBD) with Highly Specific and Durable Targeted Ta 2 C Modified with Chondroitin Sulfate (TACS). ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2301585. [PMID: 37224059 DOI: 10.1002/adma.202301585] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 05/06/2023] [Indexed: 05/26/2023]
Abstract
Non-invasive localization of lesions and specific targeted therapy are still the main challenges for inflammatory bowel disease (IBD). Ta, as a medical metal element, has been widely used in the treatment of different diseases because of its excellent physicochemical properties but is still far from being explored in IBD. Here, Ta2 C modified with chondroitin sulfate (CS) (TACS) is evaluated as a highly targeted therapy nanomedicine for IBD. Specifically, TACS is modified with dual targeting CS functions due to IBD lesion-specific positive charges and high expression of CD44 receptors. Thanks to the acid stability, sensitive CT imaging function, and strong reactive oxygen species (ROS) elimination ability, oral TACS can accurately locate and delineate IBD lesions through non-invasive CT imaging, and specifically targeted treat IBD effectively because high levels of ROS are a central factor in the progression of IBD. As expected, TACS has much better imaging and therapeutic effects than clinical CT contrast agent and first-line drug 5-aminosalicylic acid, respectively. The mechanism of TACS treatment mainly involves protection of mitochondria, elimination of oxidative stress, inhibiting macrophage M1 polarization, protection of intestinal barrier, and restoration of intestinal flora balance. Collectively, this work provides unprecedented opportunities for oral nanomedicines to targeted therapy of IBD.
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Affiliation(s)
- Xiangping Song
- Department of Geriatric Surgery, Xiangya Hospital, Central South University, Changsha, 410008, China
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Qiong Huang
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, P. R. China
| | - Yuqi Yang
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, P. R. China
| | - Liang Ma
- Hubei Key Laboratory of Optical Information and Pattern Recognition, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Wenguang Liu
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Chunlin Ou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Qiaohui Chen
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410008, China
- Hunan Provincial Key Laboratory of Cardiovascular Research, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410008, China
| | - Tianjiao Zhao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410008, China
- Hunan Provincial Key Laboratory of Cardiovascular Research, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410008, China
| | - Zuoxiu Xiao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410008, China
- Hunan Provincial Key Laboratory of Cardiovascular Research, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410008, China
| | - Mingyuan Wang
- Department of Geriatric Surgery, Xiangya Hospital, Central South University, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Yitian Jiang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410008, China
- Hunan Provincial Key Laboratory of Cardiovascular Research, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410008, China
| | - Yunrong Yang
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, P. R. China
| | - Jinping Zhang
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, P. R. China
| | - Yayun Nan
- Geriatric Medical Center, People's Hospital of Ningxia Hui Autonomous Region, Yinchuan, 750002, China
| | - Wei Wu
- Department of Geriatric Surgery, Xiangya Hospital, Central South University, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Kelong Ai
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410008, China
- Hunan Provincial Key Laboratory of Cardiovascular Research, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410008, China
- Key Laboratory of Aging-related Bone and Joint Diseases Prevention and Treatment., Ministry of Education, Xiangya Hospital, Central South University, Changsha, 410008, China
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11
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Garrido-Trigo A, Corraliza AM, Veny M, Dotti I, Melón-Ardanaz E, Rill A, Crowell HL, Corbí Á, Gudiño V, Esteller M, Álvarez-Teubel I, Aguilar D, Masamunt MC, Killingbeck E, Kim Y, Leon M, Visvanathan S, Marchese D, Caratù G, Martin-Cardona A, Esteve M, Ordás I, Panés J, Ricart E, Mereu E, Heyn H, Salas A. Macrophage and neutrophil heterogeneity at single-cell spatial resolution in human inflammatory bowel disease. Nat Commun 2023; 14:4506. [PMID: 37495570 PMCID: PMC10372067 DOI: 10.1038/s41467-023-40156-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 07/14/2023] [Indexed: 07/28/2023] Open
Abstract
Ulcerative colitis and Crohn's disease are chronic inflammatory intestinal diseases with perplexing heterogeneity in disease manifestation and response to treatment. While the molecular basis for this heterogeneity remains uncharacterized, single-cell technologies allow us to explore the transcriptional states within tissues at an unprecedented resolution which could further understanding of these complex diseases. Here, we apply single-cell RNA-sequencing to human inflamed intestine and show that the largest differences among patients are present within the myeloid compartment including macrophages and neutrophils. Using spatial transcriptomics in human tissue at single-cell resolution (CosMx Spatial Molecular Imaging) we spatially localize each of the macrophage and neutrophil subsets identified by single-cell RNA-sequencing and unravel further macrophage diversity based on their tissue localization. Finally, single-cell RNA-sequencing combined with single-cell spatial analysis reveals a strong communication network involving macrophages and inflammatory fibroblasts. Our data sheds light on the cellular complexity of these diseases and points towards the myeloid and stromal compartments as important cellular subsets for understanding patient-to-patient heterogeneity.
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Affiliation(s)
- Alba Garrido-Trigo
- Inflammatory Bowel Disease Unit, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Ana M Corraliza
- Inflammatory Bowel Disease Unit, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Marisol Veny
- Inflammatory Bowel Disease Unit, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Isabella Dotti
- Inflammatory Bowel Disease Unit, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Elisa Melón-Ardanaz
- Inflammatory Bowel Disease Unit, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Aina Rill
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Helena L Crowell
- Department of Molecular Life Sciences, University of Zurich, Switzerland. SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Ángel Corbí
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Victoria Gudiño
- Inflammatory Bowel Disease Unit, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Miriam Esteller
- Inflammatory Bowel Disease Unit, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Iris Álvarez-Teubel
- Inflammatory Bowel Disease Unit, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Daniel Aguilar
- Inflammatory Bowel Disease Unit, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - M Carme Masamunt
- Inflammatory Bowel Disease Unit, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | | | | | | | - Sudha Visvanathan
- Translational Medicine and Clinical Pharmacology, Boehringer-Ingelheim Pharmaceuticals Inc, Ridgefield, CT, USA
| | - Domenica Marchese
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Ginevra Caratù
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Albert Martin-Cardona
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
- Department of Gastroenterology, Hospital Universitari Mútua Terrassa, Universitat de Barcelona, Terrassa, Spain
| | - Maria Esteve
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
- Department of Gastroenterology, Hospital Universitari Mútua Terrassa, Universitat de Barcelona, Terrassa, Spain
| | - Ingrid Ordás
- Inflammatory Bowel Disease Unit, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Julian Panés
- Inflammatory Bowel Disease Unit, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Elena Ricart
- Inflammatory Bowel Disease Unit, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Elisabetta Mereu
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Azucena Salas
- Inflammatory Bowel Disease Unit, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clínic, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain.
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12
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Andersen V, Bennike TB, Bang C, Rioux JD, Hébert-Milette I, Sato T, Hansen AK, Nielsen OH. Investigating the Crime Scene-Molecular Signatures in Inflammatory Bowel Disease. Int J Mol Sci 2023; 24:11217. [PMID: 37446397 PMCID: PMC10342864 DOI: 10.3390/ijms241311217] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are without cure and troublesome to manage because of the considerable diversity between patients and the lack of reliable biomarkers. Several studies have demonstrated that diet, gut microbiota, genetics and other patient factors are essential for disease occurrence and progression. Understanding the link between these factors is crucial for identifying molecular signatures that identify biomarkers to advance the management of IBD. Recent technological breakthroughs and data integration have fuelled the intensity of this research. This research demonstrates that the effect of diet depends on patient factors and gut microbial activity. It also identifies a range of potential biomarkers for IBD management, including mucosa-derived cytokines, gasdermins and neutrophil extracellular traps, all of which need further evaluation before clinical translation. This review provides an update on cutting-edge research in IBD that aims to improve disease management and patient quality of life.
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Affiliation(s)
- Vibeke Andersen
- Molecular Diagnostic and Clinical Research Unit, University Hospital of Southern Denmark, Institute of Regional Research, University of Southern Denmark, 5000 Odense, Denmark;
- Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark
| | - Tue B. Bennike
- Molecular Diagnostic and Clinical Research Unit, University Hospital of Southern Denmark, Institute of Regional Research, University of Southern Denmark, 5000 Odense, Denmark;
- Medical Microbiology and Immunology, Department of Health Science and Technology, Aalborg University, 9000 Aalborg, Denmark
| | - Corinna Bang
- Institute for Clinical Molecular Biology, Christian-Albrecht’s University, 24105 Kiel, Germany;
| | - John D. Rioux
- Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada; (J.D.R.); (I.H.-M.)
- Montreal Heart Institute Research Institute, Montreal, QC H1T 1C8, Canada
| | - Isabelle Hébert-Milette
- Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada; (J.D.R.); (I.H.-M.)
- Montreal Heart Institute Research Institute, Montreal, QC H1T 1C8, Canada
| | - Toshiro Sato
- Department of Gastroenterology, Keio University School of Medicine, Tokyo 160-8582, Japan;
| | - Axel K. Hansen
- Experimental Animal Models, Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark;
| | - Ole H. Nielsen
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, 2730 Herlev, Denmark
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13
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Rodríguez-Lago I, Blackwell J, Mateos B, Marigorta UM, Barreiro-de Acosta M, Pollok R. Recent Advances and Potential Multi-Omics Approaches in the Early Phases of Inflammatory Bowel Disease. J Clin Med 2023; 12:jcm12103418. [PMID: 37240524 DOI: 10.3390/jcm12103418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/01/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Inflammatory bowel disease leads to debilitating gastrointestinal symptoms and reduced quality of life, resulting in a significant burden on healthcare utilization and costs. Despite substantial advancements in diagnosis and treatment, there may still be considerable delays in diagnosing some patients. To reduce disease progression before the full disease spectrum appears and improve prognostic outcomes, several strategies have concentrated on early intervention and prevention. Recent evidence shows that initial immune response changes and endoscopic lesions may exist for years before diagnosis, implying the existence of a preclinical phase of inflammatory bowel disease comparable to findings in other immune-mediated disorders. In this review, we highlight the most relevant findings regarding preclinical inflammatory bowel disease and the prospective role of novel omics techniques in this field.
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Affiliation(s)
- Iago Rodríguez-Lago
- Gastroenterology Department, Hospital Universitario de Galdakao, 48960 Galdakao, Spain
- Biocruces Bizkaia Health Research Institute, 48960 Galdakao, Spain
- Deusto University, 48007 Bilbao, Spain
| | | | - Beatriz Mateos
- Integrative Genomics Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Urko M Marigorta
- Integrative Genomics Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
- IKERBASQUE, Basque Foundation for Sciences, 48009 Bilbao, Spain
| | - Manuel Barreiro-de Acosta
- Gastroenterology Department, Hospital Clínico Universitario de Santiago, 15706 Santiago de Compostela, Spain
| | - Richard Pollok
- Gastroenterology Department, St George's University of London, London SW17 0RE, UK
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14
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Tseng CH. Rosiglitazone Does Not Affect the Risk of Inflammatory Bowel Disease: A Retrospective Cohort Study in Taiwanese Type 2 Diabetes Patients. Pharmaceuticals (Basel) 2023; 16:ph16050679. [PMID: 37242462 DOI: 10.3390/ph16050679] [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: 03/14/2023] [Revised: 04/27/2023] [Accepted: 04/29/2023] [Indexed: 05/28/2023] Open
Abstract
Human studies on the effect of rosiglitazone on inflammatory bowel disease (IBD) are still lacking. We investigated whether rosiglitazone might affect IBD risk by using the reimbursement database of Taiwan's National Health Insurance to enroll a propensity-score-matched cohort of ever users and never users of rosiglitazone. The patients should have been newly diagnosed with diabetes mellitus between 1999 and 2006 and should have been alive on 1 January 2007. We then started to follow the patients from 1 January 2007 until 31 December 2011 for a new diagnosis of IBD. Propensity-score-weighted hazard ratios were estimated with regards to rosiglitazone exposure in terms of ever users versus never users and in terms of cumulative duration and cumulative dose of rosiglitazone therapy for dose-response analyses. The joint effects and interactions between rosiglitazone and risk factors of psoriasis/arthropathies, dorsopathies, and chronic obstructive pulmonary disease/tobacco abuse and the use of metformin were estimated by Cox regression after adjustment for all covariates. A total of 6226 ever users and 6226 never users were identified and the respective numbers of incident IBD were 95 and 111. When we compared the risk of IBD in ever users to that of the never users, the estimated hazard ratio (0.870, 95% confidence interval: 0.661-1.144) was not statistically significant. When cumulative duration and cumulative dose of rosiglitazone therapy were categorized by tertiles and hazard ratios were estimated by comparing the tertiles of rosiglitazone exposure to the never users, none of the hazard ratios reached statistical significance. In secondary analyses, rosiglitazone has a null association with Crohn's disease, but a potential benefit on ulcerative colitis (UC) could not be excluded. However, because of the low incidence of UC, we were not able to perform detailed dose-response analyses for UC. In the joint effect analyses, only the subgroup of psoriasis/arthropathies (-)/rosiglitazone (-) showed a significantly lower risk in comparison to the subgroup of psoriasis/arthropathies (+)/rosiglitazone (-). No interactions between rosiglitazone and the major risk factors or metformin use were observed. We concluded that rosiglitazone has a null effect on the risk of IBD, but the potential benefit on UC awaits further investigation.
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Affiliation(s)
- Chin-Hsiao Tseng
- Department of Internal Medicine, National Taiwan University College of Medicine, Taipei 10051, Taiwan
- Division of Endocrinology and Metabolism, Department of Internal Medicine, National Taiwan University Hospital, Taipei 10002, Taiwan
- National Institute of Environmental Health Sciences of the National Health Research Institutes, Zhunan 35053, Taiwan
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15
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Wang Y, Huang J, Zhang J, Wang F, Tang X. Identifying biomarkers associated with the diagnosis of ulcerative colitis via bioinformatics and machine learning. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:10741-10756. [PMID: 37322958 DOI: 10.3934/mbe.2023476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
BACKGROUND Ulcerative colitis (UC) is an idiopathic inflammatory disease with an increasing incidence. This study aimed to identify potential UC biomarkers and associated immune infiltration characteristics. METHODS Two datasets (GSE87473 and GSE92415) were merged to obtain 193 UC samples and 42 normal samples. Using R, differentially expressed genes (DEGs) between UC and normal samples were filtered out, and their biological functions were investigated using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses. Promising biomarkers were identified using least absolute shrinkage selector operator regression and support vector machine recursive feature elimination, and their diagnostic efficacy was evaluated through receiver operating characteristic (ROC) curves. Finally, CIBERSORT was used to investigate the immune infiltration characteristics in UC, and the relationship between the identified biomarkers and various immune cells was examined. RESULTS We found 102 DEGs, of which 64 were significantly upregulated, and 38 were significantly downregulated. The DEGs were enriched in pathways associated with interleukin-17, cytokine-cytokine receptor interaction and viral protein interactions with cytokines and cytokine receptors, among others. Using machine learning methods and ROC tests, we confirmed DUOX2, DMBT1, CYP2B7P, PITX2 and DEFB1 to be essential diagnostic genes for UC. Immune cell infiltration analysis revealed that all five diagnostic genes were correlated with regulatory T cells, CD8 T cells, activated and resting memory CD4 T cells, activated natural killer cells, neutrophils, activated and resting mast cells, activated and resting dendritic cells and M0, M1 and M2 macrophages. CONCLUSIONS DUOX2, DMBT1, CYP2B7P, PITX2 and DEFB1 were identified as prospective biomarkers for UC. A new perspective on understanding the progression of UC may be provided by these biomarkers and their relationship with immune cell infiltration.
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Affiliation(s)
- Yuedan Wang
- Institute of Digestive Diseases, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing 100091, China
| | - Jinke Huang
- Institute of Digestive Diseases, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing 100091, China
| | - Jiaqi Zhang
- Institute of Digestive Diseases, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing 100091, China
| | - Fengyun Wang
- Institute of Digestive Diseases, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing 100091, China
| | - Xudong Tang
- China Academy of Chinese Medical Sciences, Beijing 100091, China
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16
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Feng Y, Li D, Ma C, Hu X, Chen F. Barley Leaf Ameliorates Citrobacter-rodentium-Induced Colitis through Arginine Enrichment. Nutrients 2023; 15:nu15081890. [PMID: 37111109 PMCID: PMC10145403 DOI: 10.3390/nu15081890] [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: 03/25/2023] [Revised: 04/07/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Inflammatory bowel disease (IBD) has become a global public health challenge. Our previous study showed that barley leaf (BL) significantly reduces Citrobacter-rodentium (CR)-induced colitis, but its mechanism remains elusive. Thus, in this study, we used non-targeted metabolomics techniques to search for potentially effective metabolites. Our results demonstrated that dietary supplementation with BL significantly enriched arginine and that arginine intervention significantly ameliorated CR-induced colitis symptoms such as reduced body weight, shortened colon, wrinkled cecum, and swollen colon wall in mice; in addition, arginine intervention dramatically ameliorated CR-induced histopathological damage to the colon. The gut microbial diversity analysis showed that arginine intervention significantly decreased the relative abundance of CR and significantly increased the relative abundance of Akkermansia, Blautia, Enterorhabdus, and Lachnospiraceae, which modified the CR-induced intestinal flora disorder. Notably, arginine showed a dose-dependent effect on the improvement of colitis caused by CR.
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Affiliation(s)
- Yu Feng
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruit and Vegetables Processing Ministry of Agriculture, Engineering Research Centre for Engineering Vegetables Processing, Ministry of Education, China Agricultural University, Beijing 100083, China
| | - Daotong Li
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruit and Vegetables Processing Ministry of Agriculture, Engineering Research Centre for Engineering Vegetables Processing, Ministry of Education, China Agricultural University, Beijing 100083, China
| | - Chen Ma
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruit and Vegetables Processing Ministry of Agriculture, Engineering Research Centre for Engineering Vegetables Processing, Ministry of Education, China Agricultural University, Beijing 100083, China
| | - Xiaosong Hu
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruit and Vegetables Processing Ministry of Agriculture, Engineering Research Centre for Engineering Vegetables Processing, Ministry of Education, China Agricultural University, Beijing 100083, China
| | - Fang Chen
- College of Food Science and Nutritional Engineering, National Engineering Research Center for Fruit and Vegetable Processing, Key Laboratory of Fruit and Vegetables Processing Ministry of Agriculture, Engineering Research Centre for Engineering Vegetables Processing, Ministry of Education, China Agricultural University, Beijing 100083, China
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17
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Verstockt B, Verstockt S, Cremer J, Sabino J, Ferrante M, Vermeire S, Sudhakar P. Distinct transcriptional signatures in purified circulating immune cells drive heterogeneity in disease location in IBD. BMJ Open Gastroenterol 2023; 10:bmjgast-2022-001003. [PMID: 36746519 PMCID: PMC9906185 DOI: 10.1136/bmjgast-2022-001003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/25/2022] [Indexed: 02/08/2023] Open
Abstract
OBJECTIVE To infer potential mechanisms driving disease subtypes among patients with inflammatory bowel disease (IBD), we profiled the transcriptome of purified circulating monocytes and CD4 T-cells. DESIGN RNA extracted from purified monocytes and CD4 T-cells derived from the peripheral blood of 125 endoscopically active patients with IBD was sequenced using Illumina HiSeq 4000NGS. We used complementary supervised and unsupervised analytical methods to infer gene expression signatures associated with demographic/clinical features. Expression differences and specificity were validated by comparison with publicly available single cell datasets, tissue-specific expression and meta-analyses. Drug target information, druggability and adverse reaction records were used to prioritise disease subtype-specific therapeutic targets. RESULTS Unsupervised/supervised methods identified significant differences in the expression profiles of CD4 T-cells between patients with ileal Crohn's disease (CD) and ulcerative colitis (UC). Following a pathway-based classification (Area Under Receiver Operating Characteristic - AUROC=86%) between ileal-CD and UC patients, we identified MAPK and FOXO pathways to be downregulated in UC. Coexpression module/regulatory network analysis using systems-biology approaches revealed mediatory core transcription factors. We independently confirmed that a subset of the disease location-associated signature is characterised by T-cell-specific and location-specific expression. Integration of drug-target information resulted in the discovery of several new (BCL6, GPR183, TNFAIP3) and repurposable drug targets (TUBB2A, PRKCQ) for ileal CD as well as novel targets (NAPEPLD, SLC35A1) for UC. CONCLUSIONS Transcriptomic profiling of circulating CD4 T-cells in patients with IBD demonstrated marked molecular differences between the IBD-spectrum extremities (UC and predominantly ileal CD, sandwiching colonic CD), which could help in prioritising particular drug targets for IBD subtypes.
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Affiliation(s)
- Bram Verstockt
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID), IBD group, KU Leuven, Leuven, Belgium,Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Sare Verstockt
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID), IBD group, KU Leuven, Leuven, Belgium
| | - Jonathan Cremer
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID), IBD group, KU Leuven, Leuven, Belgium
| | - João Sabino
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID), IBD group, KU Leuven, Leuven, Belgium,Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Marc Ferrante
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID), IBD group, KU Leuven, Leuven, Belgium,Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Severine Vermeire
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID), IBD group, KU Leuven, Leuven, Belgium,Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Padhmanand Sudhakar
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID), IBD group, KU Leuven, Leuven, Belgium
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18
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Bourgonje AR, Kloska D, Grochot-Przęczek A, Feelisch M, Cuadrado A, van Goor H. Personalized redox medicine in inflammatory bowel diseases: an emerging role for HIF-1α and NRF2 as therapeutic targets. Redox Biol 2023; 60:102603. [PMID: 36634466 PMCID: PMC9841059 DOI: 10.1016/j.redox.2023.102603] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 01/05/2023] [Accepted: 01/05/2023] [Indexed: 01/07/2023] Open
Abstract
Inflammatory bowel diseases (IBD), encompassing Crohn's disease (CD) and ulcerative colitis (UC), are intimately associated with inflammation and overproduction of reactive oxygen species (ROS). Temporal and inter-individual variabilities in disease activity and response to therapy pose significant challenges to diagnosis and patient care. Discovery and validation of truly integrative biomarkers would benefit from embracing redox metabolomics approaches with prioritization of central regulatory hubs. We here make a case for applying a personalized redox medicine approach that aims to selectively inhibit pathological overproduction and/or altered expression of specific enzymatic sources of ROS without compromising physiological function. To this end, improved 'clinical-omics integration' may help to better understand which particular redox signaling pathways are disrupted in what patient. Pharmacological interventions capable of activating endogenous antioxidant defense systems may represent viable therapeutic options to restore local/systemic redox status, with HIF-1α and NRF2 holding particular promise in this context. Achieving the implementation of clinically meaningful mechanism-based biomarkers requires development of easy-to-use, robust and cost-effective tools for secure diagnosis and monitoring of treatment efficacy. Ultimately, matching redox-directed pharmacological interventions to individual patient phenotypes using predictive biomarkers may offer new opportunities to break the therapeutic ceiling in IBD.
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Affiliation(s)
- Arno R. Bourgonje
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands,Corresponding author.
| | - Damian Kloska
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Anna Grochot-Przęczek
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Martin Feelisch
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Antonio Cuadrado
- Instituto de Investigaciones Biomédicas “Alberto Sols” UAM-CSIC. Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid, Spain
| | - Harry van Goor
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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19
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Yan XX, Wu D. Intestinal microecology-based treatment for inflammatory bowel disease: Progress and prospects. World J Clin Cases 2023; 11:47-56. [PMID: 36687179 PMCID: PMC9846986 DOI: 10.12998/wjcc.v11.i1.47] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/11/2022] [Accepted: 12/15/2022] [Indexed: 01/04/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic, recurrent, and debilitating disorder, and includes Crohn’s disease and ulcerative colitis. The pathogenesis of IBD is closely associated with intestinal dysbiosis, but has not yet been fully clarified. Genetic and environmental factors can influence IBD patients’ gut microbiota and metabolism, disrupt intestinal barriers, and trigger abnormal immune responses. Studies have reported the alteration of gut microbiota and metabolites in IBD, providing the basis for potential therapeutic options. Intestinal microbiota-based treatments such as pre/probiotics, metabolite supplementation, and fecal microbiota transplantation have been extensively studied, but their clinical efficacy remains controversial. Repairing the intestinal barrier and promoting mucosal healing have also been proposed. We here review the current clinical trials on intestinal microecology and discuss the prospect of research and practice in this field.
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Affiliation(s)
- Xia-Xiao Yan
- Department of Gastroenterology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100730, China
| | - Dong Wu
- Department of Gastroenterology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100730, China
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20
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Cao D, Qian K, Zhao Y, Hong J, Chen H, Wang X, Yang N, Zhang C, Cao J, Jia K, Wu G, Zhu M, Shen J, Zhang Y, Cui Z, Wang Z. Association of neutrophil extracellular traps with fistula healing in patients with complex perianal fistulising Crohn's disease. J Crohns Colitis 2022; 17:580-592. [PMID: 36322703 DOI: 10.1093/ecco-jcc/jjac171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Indexed: 02/08/2023]
Abstract
BACKGROUND AND AIMS Perianal fistulising Crohn's disease (pfCD) is a disabling phenotype of Crohn's disease (CD) with suboptimal outcomes. We assessed neutrophil extracellular traps (NETs) in perianal fistulas and implicated their roles in pfCD healing. METHODS Patients with complex pfCD who developed preplaced seton drainage were recruited during the verified maintenance of remission in CD. Fistula tracts were sampled during definitive surgery plus seton removal. Patient demographics, CD classification, medication strategy, and healing of pfCD were recorded. RNA sequencing was applied for transcriptomic profile analysis. NETs components, including myeloperoxidase (MPO), neutrophil elastase (NE), and citrullinated histone H3 (CitH3), were identified using immunofluorescence. Serum infliximab (IFX), anti-IFX antibodies, and tissue levels of IFX, adalimumab (ADA), MPO and CitH3 were determined using enzyme-linked immunosorbent assays. Peptidyl arginine deiminase IV (PAD4), tumour necrosis factor (TNF)-α, and NE were detected using immunohistochemistry. Gene expression levels of PAD family members were assessed with qPCR. RESULTS Twenty-one patients were included, 15 of whom adopted IFX as maintenance treatment. RNA-seq revealed difference in neutrophil associated pathways between unhealed and healed fistulas. NETs components (MPO/NE/CitH3) were detectable in the fistulas and were parallel with the PAD4 levels. Eleven of 21 (52%) patients experienced complete healing of the pfCD 108 weeks post-operatively. Fistula NETs were significantly increased in patients with unhealed pfCD. Increased NETs were associated with abundant TNF-α production and the absence of IFX in fistulas. CONCLUSIONS NETs exist in pfCD fistulas, which are associated with unhealed post-operative fistulas in pfCD, suggesting their prognostic roles in pfCD.
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Affiliation(s)
- Dongxing Cao
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Keyu Qian
- Laboratory of Medicine, Baoshan Branch, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200444, China
| | - Ying Zhao
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology & Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology; Shanghai Cancer Institute; Shanghai Institute of Digestive Disease; Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine. Shanghai 200001, China
| | - Jie Hong
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology & Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology; Shanghai Cancer Institute; Shanghai Institute of Digestive Disease; Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine. Shanghai 200001, China
| | - Haoyan Chen
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology & Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology; Shanghai Cancer Institute; Shanghai Institute of Digestive Disease; Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine. Shanghai 200001, China
| | - Xiaohui Wang
- Department of General Surgery, Baoshan Branch, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200444, China
| | - Nailin Yang
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Cheng Zhang
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Jingkai Cao
- Department of General Surgery, Baoshan Branch, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200444, China
| | - Keyu Jia
- Laboratory of Medicine, Baoshan Branch, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200444, China
| | - Guangyu Wu
- Department of Radiology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200444, China
| | - Mingming Zhu
- Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Jun Shen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Disease Research Center, Ren Ji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai Jiao Tong University, Shanghai, China
| | - Ye Zhang
- Laboratory of Medicine, Baoshan Branch, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200444, China
| | - Zhe Cui
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China; Department of General Surgery, Baoshan Branch, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, No.1058, Huan Zhen Bei Rd, Baoshan District, Shanghai 200444, China
| | - Zheng Wang
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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21
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Spencer EA, Agrawal M, Jess T. Prognostication in inflammatory bowel disease. Front Med (Lausanne) 2022; 9:1025375. [PMID: 36275829 PMCID: PMC9582521 DOI: 10.3389/fmed.2022.1025375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/14/2022] [Indexed: 11/13/2022] Open
Abstract
Personalized care in inflammatory bowel diseases (IBD) hinges on parsing the heterogeneity of IBD patients through prognostication of their disease course and therapeutic response to allow for tailor-made treatment and monitoring strategies to optimize care. Herein we review the currently available predictors of outcomes in IBD and those on the both near and far horizons. We additionally discuss the importance of worldwide collaborative efforts and tools to support clinical use of these prognostication tools.
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Affiliation(s)
- Elizabeth A. Spencer
- Division of Pediatric Gastroenterology and Nutrition, Icahn School of Medicine, Mount Sinai Hospital, New York, NY, United States,*Correspondence: Elizabeth A. Spencer
| | - Manasi Agrawal
- Division of Gastroenterology, Icahn School of Medicine, Mount Sinai Hospital, New York, NY, United States,Center for Molecular Prediction of Inflammatory Bowel Disease, PREDICT, Aalborg University, Aalborg, Denmark
| | - Tine Jess
- Center for Molecular Prediction of Inflammatory Bowel Disease, PREDICT, Aalborg University, Aalborg, Denmark,Department of Gastroenterology and Hepatology, Aalborg University Hospital, Aalborg, Denmark
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22
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Swaminathan A, Fan D, Borichevsky GM, Mules TC, Hirschfeld E, Frampton CM, Day AS, Siegel CA, Gearry RB. The disease severity index for inflammatory bowel disease is associated with psychological symptoms and quality of life, and predicts a more complicated disease course. Aliment Pharmacol Ther 2022; 56:664-674. [PMID: 35633043 PMCID: PMC9545845 DOI: 10.1111/apt.17058] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/10/2022] [Accepted: 05/17/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND The Disease Severity Index (DSI) is a novel tool to predict disease severity in inflammatory bowel disease (IBD). However, its ability to predict disease complications and the presence of psychosocial comorbidity is unclear. AIMS To assess prospectively associations between the DSI and psychological symptoms, quality-of-life (QoL) and disease outcomes in an IBD cohort. METHODS Patients with IBD undergoing ileocolonoscopy were followed prospectively for 12 months. DSI, psychological symptoms (perceived stress (PSS-10), depression (PHQ-9), anxiety (GAD-7)) and QoL (IBDQ-32) scores were assessed at baseline. Logistic regression identified variables predicting a complicated IBD course at 12 months (composite outcome of need for escalation of biological/immunomodulator for disease relapse, recurrent corticosteroid use, IBD-related hospitalisation and surgery). Receiver operating characteristics (ROC) analysis identified optimal DSI thresholds predicting a complicated disease course and multivariable logistic regression assessed the risk of reaching this outcome. RESULTS One hundred and seventy-two patients were recruited (100 Crohn's disease, 91 female). Median DSI was 21 (IQR 11-32) and 97 patients had endoscopically active disease at baseline. The DSI was significantly higher in patients with symptoms of moderate-severe stress (PSS-10 > 14, p < 0.01), depression (PHQ-9 ≥ 10, p < 0.01), anxiety (GAD-7 ≥ 10, p < 0.05) and impaired quality-of-life (IBDQ-32 < 168, p < 0.01). Only the baseline DSI (OR 1.05, p < 0.01) and endoscopically active disease (OR 6.12, p < 0.01) were associated with a complicated IBD course. A DSI > 23 was strongly predictive of a complicated IBD course (OR 8.31, p < 0.001). CONCLUSIONS The DSI is associated with psychological distress, impaired QoL and predicts a more complicated disease course in patients with IBD.
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Affiliation(s)
- Akhilesh Swaminathan
- Department of MedicineUniversity of OtagoChristchurchNew Zealand,Department of GastroenterologyChristchurch hospitalChristchurchNew Zealand
| | - Dali Fan
- Department of GastroenterologyChristchurch hospitalChristchurchNew Zealand
| | | | - Thomas C. Mules
- Department of GastroenterologyChristchurch hospitalChristchurchNew Zealand
| | | | | | - Andrew S. Day
- Department of PaediatricsUniversity of OtagoChristchurchNew Zealand
| | - Corey A. Siegel
- Inflammatory Bowel Disease Centre, Section of Gastroenterology and HepatologyDartmouth Hitchcock Medical CentreLebanonNew HampshireUSA
| | - Richard B. Gearry
- Department of MedicineUniversity of OtagoChristchurchNew Zealand,Department of GastroenterologyChristchurch hospitalChristchurchNew Zealand
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23
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Elhag DA, Kumar M, Saadaoui M, Akobeng AK, Al-Mudahka F, Elawad M, Al Khodor S. Inflammatory Bowel Disease Treatments and Predictive Biomarkers of Therapeutic Response. Int J Mol Sci 2022; 23:ijms23136966. [PMID: 35805965 PMCID: PMC9266456 DOI: 10.3390/ijms23136966] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/05/2022] [Accepted: 06/06/2022] [Indexed: 02/08/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic immune-mediated inflammation of the gastrointestinal tract with a highly heterogeneous presentation. It has a relapsing and remitting clinical course that necessitates lifelong monitoring and treatment. Although the availability of a variety of effective therapeutic options including immunomodulators and biologics (such as TNF, CAM inhibitors) has led to a paradigm shift in the treatment outcomes and clinical management of IBD patients, some patients still either fail to respond or lose their responsiveness to therapy over time. Therefore, according to the recent Selecting Therapeutic Targets in Inflammatory Bowel Disease (STRIDE-II) recommendations, continuous disease monitoring from symptomatic relief to endoscopic healing along with short- and long-term therapeutic responses are critical for providing IBD patients with a tailored therapy algorithm. Moreover, considering the high unmet need for novel therapeutic approaches for IBD patients, various new modulators of cytokine signaling events (for example, JAK/TYK inhibitors), inhibitors of cytokines (for example IL-12/IL-23, IL-22, IL-36, and IL-6 inhibitors), anti-adhesion and migration strategies (for example, β7 integrin, sphingosine 1-phosphate receptors, and stem cells), as well as microbial-based therapeutics to decolonize the bed buds (for example, fecal microbiota transplantation and bacterial inhibitors) are currently being evaluated in different phases of controlled clinical trials. This review aims to offer a comprehensive overview of available treatment options and emerging therapeutic approaches for IBD patients. Furthermore, predictive biomarkers for monitoring the therapeutic response to different IBD therapies are also discussed.
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Affiliation(s)
- Duaa Ahmed Elhag
- Research Department, Sidra Medicine, Doha 26999, Qatar; (D.A.E.); (M.K.); (M.S.)
| | - Manoj Kumar
- Research Department, Sidra Medicine, Doha 26999, Qatar; (D.A.E.); (M.K.); (M.S.)
| | - Marwa Saadaoui
- Research Department, Sidra Medicine, Doha 26999, Qatar; (D.A.E.); (M.K.); (M.S.)
| | - Anthony K. Akobeng
- Division of Gastroenterology, Hepatology and Nutrition, Sidra Medicine, Doha 26999, Qatar; (A.K.A.); (F.A.-M.); (M.E.)
| | - Fatma Al-Mudahka
- Division of Gastroenterology, Hepatology and Nutrition, Sidra Medicine, Doha 26999, Qatar; (A.K.A.); (F.A.-M.); (M.E.)
| | - Mamoun Elawad
- Division of Gastroenterology, Hepatology and Nutrition, Sidra Medicine, Doha 26999, Qatar; (A.K.A.); (F.A.-M.); (M.E.)
| | - Souhaila Al Khodor
- Research Department, Sidra Medicine, Doha 26999, Qatar; (D.A.E.); (M.K.); (M.S.)
- Correspondence:
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Affiliation(s)
- Ailsa L Hart
- IBD Unit, St Mark's, The National Bowel Hospital, London, United Kingdom
| | - David T Rubin
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago Medicine Inflammatory Bowel Disease Center, Chicago, Illinois
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25
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Sudhakar P, Alsoud D, Wellens J, Verstockt S, Arnauts K, Verstockt B, Vermeire S. Tailoring Multi-omics to Inflammatory Bowel Diseases: All for One and One for All. J Crohns Colitis 2022; 16:1306-1320. [PMID: 35150242 PMCID: PMC9426669 DOI: 10.1093/ecco-jcc/jjac027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 02/02/2022] [Accepted: 02/10/2022] [Indexed: 12/13/2022]
Abstract
Inflammatory bowel disease [IBD] has a multifactorial origin and originates from a complex interplay of environmental factors with the innate immune system at the intestinal epithelial interface in a genetically susceptible individual. All these factors make its aetiology intricate and largely unknown. Multi-omic datasets obtained from IBD patients are required to gain further insights into IBD biology. We here review the landscape of multi-omic data availability in IBD and identify barriers and gaps for future research. We also outline the various technical and non-technical factors that influence the utility and interpretability of multi-omic datasets and thereby the study design of any research project generating such datasets. Coordinated generation of multi-omic datasets and their systemic integration with clinical phenotypes and environmental exposures will not only enhance understanding of the fundamental mechanisms of IBD but also improve therapeutic strategies. Finally, we provide recommendations to enable and facilitate generation of multi-omic datasets.
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Affiliation(s)
- Padhmanand Sudhakar
- Corresponding author: Padhmanand Sudhakar, Translational Research in Gastrointestinal Disorders [TARGID], ON I, Herestraat 49, box 701, 3000 Leuven, Belgium. Tel.: 0032 [0]16 19 49 40;
| | - Dahham Alsoud
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders [TARGID], Leuven, Belgium
| | - Judith Wellens
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders [TARGID], Leuven, Belgium
| | - Sare Verstockt
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders [TARGID], Leuven, Belgium
| | - Kaline Arnauts
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders [TARGID], Leuven, Belgium
| | - Bram Verstockt
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders [TARGID], Leuven, Belgium,Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Severine Vermeire
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders [TARGID], Leuven, Belgium,Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
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