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Wang TT, Jiang WR, Xu L, Zhou MY, Huang YS. Effect of blockage of Trem1 on the M1 polarization of macrophages in the regulation dental pulp inflammation. Eur J Oral Sci 2024; 132:e13018. [PMID: 39267299 DOI: 10.1111/eos.13018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 08/22/2024] [Indexed: 09/17/2024]
Abstract
Dental pulp inflammation is a common and significant factor related to poor dental prognosis. Current treatment strategies primarily concentrate on managing the inflammatory response, with specific targets for intervention still under investigation. Triggering receptors expressed on myeloid cells (TREMs) are a group of receptor molecules extensively present on myeloid cell surfaces, crucial in the regulation of inflammatory process. Our analysis of transcriptomic sequencing data from clinical pulp samples of dataset GSE77459 and animal models revealed up-regulation of Trem1 during pulpitis. Administration of the Trem1-blocking peptide LP17 led to lower (more than 1-fold) levels of several pro-inflammatory factors and inhibition of M1 macrophage polarization both in vivo and in vitro. This study of the expression patterns and functions of Trem1 in the development of dental pulp inflammation provides novel insights into the therapeutic strategies for clinical pulpitis.
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Affiliation(s)
- Ting-Ting Wang
- Department of Stomatology, The First Affiliated Hospital of Bengbu Medical University, Bengbu, Anhui, China
| | - Wen-Rui Jiang
- Department of Stomatology, The First Affiliated Hospital of Bengbu Medical University, Bengbu, Anhui, China
| | - Li Xu
- Department of Stomatology, The First Affiliated Hospital of Bengbu Medical University, Bengbu, Anhui, China
| | - Mei-Yun Zhou
- Department of Stomatology, The First Affiliated Hospital of Bengbu Medical University, Bengbu, Anhui, China
| | - Yong-Song Huang
- Department of Stomatology, The First Affiliated Hospital of Bengbu Medical University, Bengbu, Anhui, China
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2
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Tindle C, Fonseca AG, Taheri S, Katkar GD, Lee J, Maity P, Sayed IM, Ibeawuchi SR, Vidales E, Pranadinata RF, Fuller M, Stec DL, Anandachar MS, Perry K, Le HN, Ear J, Boland BS, Sandborn WJ, Sahoo D, Das S, Ghosh P. A living organoid biobank of patients with Crohn's disease reveals molecular subtypes for personalized therapeutics. Cell Rep Med 2024:101748. [PMID: 39332415 DOI: 10.1016/j.xcrm.2024.101748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 07/15/2024] [Accepted: 08/31/2024] [Indexed: 09/29/2024]
Abstract
Crohn's disease (CD) is a complex and heterogeneous condition with no perfect preclinical model or cure. To address this, we explore adult stem cell-derived organoids that retain their tissue identity and disease-driving traits. We prospectively create a biobank of CD patient-derived organoid cultures (PDOs) from colonic biopsies of 53 subjects across all clinical subtypes and healthy subjects. Gene expression analyses enabled benchmarking of PDOs as tools for modeling the colonic epithelium in active disease and identified two major molecular subtypes: immune-deficient infectious CD (IDICD) and stress and senescence-induced fibrostenotic CD (S2FCD). Each subtype shows internal consistency in the transcriptome, genome, and phenome. The spectrum of morphometric, phenotypic, and functional changes within the "living biobank" reveals distinct differences between the molecular subtypes. Drug screens reverse subtype-specific phenotypes, suggesting phenotyped-genotyped CD PDOs can bridge basic biology and patient trials by enabling preclinical phase "0" human trials for personalized therapeutics.
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Affiliation(s)
- Courtney Tindle
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; HUMANOID™ Center of Research Excellence (CoRE), University of California, San Diego, La Jolla, CA 92093, USA
| | - Ayden G Fonseca
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; HUMANOID™ Center of Research Excellence (CoRE), University of California, San Diego, La Jolla, CA 92093, USA
| | - Sahar Taheri
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gajanan D Katkar
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jasper Lee
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Priti Maity
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; HUMANOID™ Center of Research Excellence (CoRE), University of California, San Diego, La Jolla, CA 92093, USA
| | - Ibrahim M Sayed
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stella-Rita Ibeawuchi
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eleadah Vidales
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; HUMANOID™ Center of Research Excellence (CoRE), University of California, San Diego, La Jolla, CA 92093, USA
| | - Rama F Pranadinata
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; HUMANOID™ Center of Research Excellence (CoRE), University of California, San Diego, La Jolla, CA 92093, USA
| | - Mackenzie Fuller
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; HUMANOID™ Center of Research Excellence (CoRE), University of California, San Diego, La Jolla, CA 92093, USA
| | - Dominik L Stec
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; HUMANOID™ Center of Research Excellence (CoRE), University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Kevin Perry
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; HUMANOID™ Center of Research Excellence (CoRE), University of California, San Diego, La Jolla, CA 92093, USA
| | - Helen N Le
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jason Ear
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Brigid S Boland
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
| | - William J Sandborn
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Debashis Sahoo
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Soumita Das
- HUMANOID™ Center of Research Excellence (CoRE), University of California, San Diego, La Jolla, CA 92093, USA; Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Pradipta Ghosh
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; HUMANOID™ Center of Research Excellence (CoRE), University of California, San Diego, La Jolla, CA 92093, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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3
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Lin S, Hannon E, Reppell M, Waring JF, Smaoui N, Pivorunas V, Guay H, Chanchlani N, Bewshea C, Bai BYH, Kennedy NA, Goodhand JR, Mill J, Ahmad T. Whole Blood DNA Methylation Changes Are Associated with Anti-TNF Drug Concentration in Patients with Crohn's Disease. J Crohns Colitis 2024; 18:1190-1201. [PMID: 37551994 PMCID: PMC11324340 DOI: 10.1093/ecco-jcc/jjad133] [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: 03/14/2023] [Revised: 06/23/2023] [Accepted: 08/07/2023] [Indexed: 08/09/2023]
Abstract
BACKGROUND AND AIMS Anti-tumour necrosis factor [TNF] treatment failure in patients with inflammatory bowel disease [IBD] is common and frequently related to low drug concentrations. In order to identify patients who may benefit from dose optimisation at the outset of anti-TNF therapy, we sought to define epigenetic biomarkers in whole blood at baseline associated with anti-TNF drug concentrations at week 14. METHODS DNA methylation from 1104 whole blood samples from 385 patients in the Personalised Anti-TNF Therapy in Crohn's disease [PANTS] study were assessed using the Illumina EPIC Beadchip [v1.0] at baseline and weeks 14, 30, and 54. We compared DNA methylation profiles in anti-TNF-treated patients who experienced primary non-response at week 14 if they were assessed at subsequent time points and were not in remission at week 30 or 54 [infliximab n = 99, adalimumab n = 94], with patients who responded at week 14 and when assessed at subsequent time points were in remission at week 30 or 54 [infliximab n = 99, adalimumab n = 93]. RESULTS Overall, between baseline and week 14, we observed 4999 differentially methylated positions [DMPs] annotated to 2376 genes following anti-TNF treatment. Pathway analysis identified 108 significant gene ontology terms enriched in biological processes related to immune system processes and responses. Epigenome-wide association [EWAS] analysis identified 323 DMPs annotated to 210 genes at baseline associated with higher anti-TNF drug concentrations at Week 14. Of these, 125 DMPs demonstrated shared associations with other common traits [proportion of shared CpGs compared with DMPs] including body mass index [23.2%], followed by C-reactive protein [CRP] [11.5%], smoking [7.4%], alcohol consumption per day [7.1%], and IBD type [6.8%]. EWAS of primary non-response to anti-TNF identified 20 DMPs that were associated with both anti-TNF drug concentration and primary non-response to anti-TNF with a strong correlation of the coefficients [Spearman's rho = -0.94, p <0.001]. CONCLUSION Baseline DNA methylation profiles may be used as a predictor for anti-TNF drug concentration at week 14 to identify patients who may benefit from dose optimisation at the outset of anti-TNF therapy.
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Affiliation(s)
- Simeng Lin
- Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Eilis Hannon
- University of Exeter Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Mark Reppell
- Precision Medicine Immunology, AbbVie Inc., Chicago, IL, USA
| | | | - Nizar Smaoui
- Precision Medicine Immunology, AbbVie Inc., Chicago, IL, USA
| | | | - Heath Guay
- Precision Medicine Immunology, AbbVie Inc., Chicago, IL, USA
| | - Neil Chanchlani
- Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Claire Bewshea
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Benjamin Y H Bai
- Genomics of Inflammation and Immunity Group, Wellcome Sanger Institute, Hinxton, UK
- Postgraduate School of Life Sciences, University of Cambridge, Cambridge, UK
| | - Nicholas A Kennedy
- Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - James R Goodhand
- Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Jonathan Mill
- University of Exeter Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Tariq Ahmad
- Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
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4
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Qiu Y, Hu S, Chao K, Huang L, Huang Z, Mao R, Su F, Zhang C, Lin X, Cao Q, Gao X, Chen M. Developing a Machine-Learning Prediction Model for Infliximab Response in Crohn's Disease: Integrating Clinical Characteristics and Longitudinal Laboratory Trends. Inflamm Bowel Dis 2024:izae176. [PMID: 39126463 DOI: 10.1093/ibd/izae176] [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: 03/11/2024] [Indexed: 08/12/2024]
Abstract
BACKGROUND Achieving long-term clinical remission in Crohn's disease (CD) with antitumor necrosis factor α (anti-TNF-α) agents remains challenging. AIMS This study aims to establish a prediction model based on patients' clinical characteristics using a machine-learning approach to predict the long-term efficacy of infliximab (IFX). METHODS Three cohorts comprising 746 patients with CD were included from 3 inflammatory bowel disease (IBD) centers between June 2013 and January 2022. Clinical records were collected from baseline, 14-, 30-, and 52-week post-IFX treatment. Three machine-learning approaches were employed to develop predictive models based on 23 baseline predictors. The SHapley Additive exPlanations (SHAP) algorithm was used to dissect underlying predictors, and latent class mixed model (LCMM) was applied for trajectory analysis of the longitudinal change of blood routine tests along with long-term IFX therapy. RESULTS The XGBoost model exhibited the best discrimination between long-term responders and nonresponders. In the internal training and testing set, the model achieved an AUC of 0.91 (95% CI, 0.86-0.95) and 0.71 (95% CI, 0.66-0.87), respectively. Moreover, it achieved a moderate predictive performance in the independent external cohort, with an AUC of 0.68 (95% CI, 0.59-0.77). The SHAP algorithm revealed disease-relevant laboratory measurements, notably hemoglobin (HB), white blood cells (WBC), erythrocyte sedimentation rate (ESR), albumin (ALB), and platelets (PLT), alongside age at diagnosis and the Montreal classification, as the most influential predictors. Furthermore, 2 distinct patient clusters based on dynamic laboratory tests were identified for monitoring the long-term remission. CONCLUSIONS The established prediction model demonstrated remarkable discriminatory power in distinguishing long-term responders from nonresponders to IFX therapy. The identification of distinct patient clusters further emphasizes the need for tailored therapeutic approaches in CD management.
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Affiliation(s)
- Yun Qiu
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shixian Hu
- The Translational Medicine Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Kang Chao
- Department of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Lingjie Huang
- Department of Gastroenterology, Sir Run Run Shaw Hospital of Zhejiang University, Hangzhou, China
| | - Zicheng Huang
- Department of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Ren Mao
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Fengyuan Su
- The Translational Medicine Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Chuhan Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaoqing Lin
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Qian Cao
- Department of Gastroenterology, Sir Run Run Shaw Hospital of Zhejiang University, Hangzhou, China
| | - Xiang Gao
- Department of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Minhu Chen
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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5
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Verstockt B, Vancamelbeke M, Vermeire S. Increased inflammatory state in IBD multiplex first-degree relatives not developing intestinal disease. Gut 2024; 73:1586-1588. [PMID: 37833054 DOI: 10.1136/gutjnl-2023-330966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023]
Affiliation(s)
- Bram Verstockt
- Department of Gastroenterology and Hepatology, KU Leuven University Hospitals Leuven, Leuven, Flanders, Belgium
- Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Flanders, Belgium
| | - Maaike Vancamelbeke
- Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Flanders, Belgium
| | - Séverine Vermeire
- Department of Gastroenterology and Hepatology, KU Leuven University Hospitals Leuven, Leuven, Flanders, Belgium
- Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Flanders, Belgium
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6
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Minea H, Singeap AM, Minea M, Juncu S, Muzica C, Sfarti CV, Girleanu I, Chiriac S, Miftode ID, Stanciu C, Trifan A. The Contribution of Genetic and Epigenetic Factors: An Emerging Concept in the Assessment and Prognosis of Inflammatory Bowel Diseases. Int J Mol Sci 2024; 25:8420. [PMID: 39125988 PMCID: PMC11313574 DOI: 10.3390/ijms25158420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 07/25/2024] [Accepted: 07/27/2024] [Indexed: 08/12/2024] Open
Abstract
Inflammatory bowel disease (IBD) represents heterogeneous and relapsing intestinal conditions with a severe impact on the quality of life of individuals and a continuously increasing prevalence. In recent years, the development of sequencing technology has provided new means of exploring the complex pathogenesis of IBD. An ideal solution is represented by the approach of precision medicine that investigates multiple cellular and molecular interactions, which are tools that perform a holistic, systematic, and impartial analysis of the genomic, transcriptomic, proteomic, metabolomic, and microbiomics sets. Hence, it has led to the orientation of current research towards the identification of new biomarkers that could be successfully used in the management of IBD patients. Multi-omics explores the dimension of variation in the characteristics of these diseases, offering the advantage of understanding the cellular and molecular mechanisms that affect intestinal homeostasis for a much better prediction of disease development and choice of treatment. This review focuses on the progress made in the field of prognostic and predictive biomarkers, highlighting the limitations, challenges, and also the opportunities associated with the application of genomics and epigenomics technologies in clinical practice.
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Affiliation(s)
- Horia Minea
- Department of Gastroenterology, Grigore T. Popa University of Medicine and Pharmacy, 700115 Iasi, Romania; (H.M.); (S.J.); (C.V.S.); (I.G.); (S.C.); (C.S.); (A.T.)
- Institute of Gastroenterology and Hepatology, “St. Spiridon” University Hospital, 700111 Iasi, Romania
| | - Ana-Maria Singeap
- Department of Gastroenterology, Grigore T. Popa University of Medicine and Pharmacy, 700115 Iasi, Romania; (H.M.); (S.J.); (C.V.S.); (I.G.); (S.C.); (C.S.); (A.T.)
- Institute of Gastroenterology and Hepatology, “St. Spiridon” University Hospital, 700111 Iasi, Romania
| | - Manuela Minea
- Department of Microbiology, The National Institute of Public Health, 700464 Iasi, Romania;
| | - Simona Juncu
- Department of Gastroenterology, Grigore T. Popa University of Medicine and Pharmacy, 700115 Iasi, Romania; (H.M.); (S.J.); (C.V.S.); (I.G.); (S.C.); (C.S.); (A.T.)
- Institute of Gastroenterology and Hepatology, “St. Spiridon” University Hospital, 700111 Iasi, Romania
| | - Cristina Muzica
- Department of Gastroenterology, Grigore T. Popa University of Medicine and Pharmacy, 700115 Iasi, Romania; (H.M.); (S.J.); (C.V.S.); (I.G.); (S.C.); (C.S.); (A.T.)
- Institute of Gastroenterology and Hepatology, “St. Spiridon” University Hospital, 700111 Iasi, Romania
| | - Catalin Victor Sfarti
- Department of Gastroenterology, Grigore T. Popa University of Medicine and Pharmacy, 700115 Iasi, Romania; (H.M.); (S.J.); (C.V.S.); (I.G.); (S.C.); (C.S.); (A.T.)
- Institute of Gastroenterology and Hepatology, “St. Spiridon” University Hospital, 700111 Iasi, Romania
| | - Irina Girleanu
- Department of Gastroenterology, Grigore T. Popa University of Medicine and Pharmacy, 700115 Iasi, Romania; (H.M.); (S.J.); (C.V.S.); (I.G.); (S.C.); (C.S.); (A.T.)
- Institute of Gastroenterology and Hepatology, “St. Spiridon” University Hospital, 700111 Iasi, Romania
| | - Stefan Chiriac
- Department of Gastroenterology, Grigore T. Popa University of Medicine and Pharmacy, 700115 Iasi, Romania; (H.M.); (S.J.); (C.V.S.); (I.G.); (S.C.); (C.S.); (A.T.)
- Institute of Gastroenterology and Hepatology, “St. Spiridon” University Hospital, 700111 Iasi, Romania
| | - Ioana Diandra Miftode
- Department of Radiology, Grigore T. Popa University of Medicine and Pharmacy, 700115 Iasi, Romania;
- Department of Radiology, “St. Spiridon” University Hospital, 700111 Iasi, Romania
| | - Carol Stanciu
- Department of Gastroenterology, Grigore T. Popa University of Medicine and Pharmacy, 700115 Iasi, Romania; (H.M.); (S.J.); (C.V.S.); (I.G.); (S.C.); (C.S.); (A.T.)
- Institute of Gastroenterology and Hepatology, “St. Spiridon” University Hospital, 700111 Iasi, Romania
| | - Anca Trifan
- Department of Gastroenterology, Grigore T. Popa University of Medicine and Pharmacy, 700115 Iasi, Romania; (H.M.); (S.J.); (C.V.S.); (I.G.); (S.C.); (C.S.); (A.T.)
- Institute of Gastroenterology and Hepatology, “St. Spiridon” University Hospital, 700111 Iasi, Romania
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7
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Cao S, Nguyen K, Ma K, Du X, Liu X, Antonova AU, Rood RP, Gremida A, Chen CH, Gutierrez A, Rubin DC, Gregory MH, Gergely M, Escudero GO, Huang K, Jaeger N, Cella M, Newberry RD, Davidson NO, Ciorba MA, Deepak P, Colonna M. Mucosal Single-Cell Profiling of Crohn's-Like Disease of the Pouch Reveals Unique Pathogenesis and Therapeutic Targets. Gastroenterology 2024:S0016-5085(24)05284-3. [PMID: 39084267 DOI: 10.1053/j.gastro.2024.07.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 06/11/2024] [Accepted: 07/15/2024] [Indexed: 08/02/2024]
Abstract
BACKGROUND & AIMS The pathophysiology of Crohn's-like disease of the pouch (CDP) in patients with a history of ulcerative colitis (UC) is unknown. We examined mucosal cells from patients with and without CDP using single-cell analyses. METHODS Endoscopic samples were collected from pouch body and prepouch ileum (pouch/ileum) of 50 patients with an ileal pouch-anal anastomosis. Single-cell RNA sequencing was performed on pouch/ileal tissues of patients with normal pouch/ileum and CDP. Mass cytometry was performed on mucosal immune cells from patients with UC with normal pouch/ileum, CDP, pouchitis, and those with familial adenomatous polyposis after pouch formation. Findings were independently validated using immunohistochemistry. RESULTS The cell populations/states in the pouch body differed from those in the prepouch ileum, likely secondary to increased microbial burden. Compared with the familial adenomatous polyposis pouch, the UC pouch was enriched in colitogenic immune cells even without inflammation. CDP was characterized by increases in T helper 17 cells, inflammatory fibroblasts, inflammatory monocytes, TREM1+ monocytes, clonal expansion of effector T cells, and overexpression of T helper 17 cells-inducing cytokine genes such as IL23, IL1B, and IL6 by mononuclear phagocytes. Ligand-receptor analysis further revealed a stromal-mononuclear phagocytes-lymphocyte circuit in CDP. Integrated analysis showed that up-regulated immune mediators in CDP were similar to those in CD and pouchitis, but not UC. Additionally, CDP pouch/ileum exhibited heightened endoplasmic reticulum stress across all major cell compartments. CONCLUSIONS CDP likely represents a distinct entity of inflammatory bowel disease with heightened endoplasmic reticulum stress in both immune and nonimmune cells, which may become a novel diagnostic biomarker and therapeutic target for CDP.
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Affiliation(s)
- Siyan Cao
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri.
| | - Khai Nguyen
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Kaiming Ma
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Xiaotang Du
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Xiuli Liu
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Alina Ulezko Antonova
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Richard P Rood
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Anas Gremida
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Chien-Huan Chen
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Alexandra Gutierrez
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Deborah C Rubin
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Martin H Gregory
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Mate Gergely
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Guadalupe Oliva Escudero
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Katherine Huang
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Natalia Jaeger
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Marina Cella
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Rodney D Newberry
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Nicholas O Davidson
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Matthew A Ciorba
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Parakkal Deepak
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri.
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8
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Atreya R, Neurath MF. Biomarkers for Personalizing IBD Therapy: The Quest Continues. Clin Gastroenterol Hepatol 2024; 22:1353-1364. [PMID: 38320679 DOI: 10.1016/j.cgh.2024.01.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 02/08/2024]
Abstract
Despite recent advances in the understanding of the pathogenesis of inflammatory bowel diseases (IBD) and advent of multiple targeted therapies, approximately one-third of patients are primary non-responders to initiated treatment, and half of patients lose response over time. There is currently a lack of available biomarkers that would prognosticate therapeutic effectiveness of these advanced therapies. This is partly explained by insufficient characterization of the functional roles assumed by the chosen molecular targets during disease treatment. There is a dire need for validated objective biomarkers, which could be indicators of a biological process, that can be applied in clinical practice to assist us in assigning therapies to patients with the highest probability of response. An appropriate molecular and cellular characterization that accounts for the interindividual differences in drug efficacy and potential side effects would help to guide clinicians in the management of patients with IBD and represent a major step to tailor a more personalized approach to treatment. An appropriate combination of complementing biomarkers should ideally incorporate a multimodal analysis in which genetic, microbial, transcriptional, proteomic, metabolic, and immunologic data are combined to enable a truly personalized approach. This would classify patients into disease subgroups according to molecular characteristics, which would enable us to initiate the most appropriate therapeutic substance. Emergence of single-cell technologies to map the intestinal cellular landscape and multiomic approaches have helped to further dissect the pathogenic mechanisms of mucosal inflammation, but the clinical translation of potential biomarkers remains cumbersome, and an ongoing concerted effort by the IBD community is required.
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Affiliation(s)
- Raja Atreya
- First Department of Medicine, Erlangen University Hospital, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany.
| | - Markus F Neurath
- First Department of Medicine, Erlangen University Hospital, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
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9
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Matellan C, Kennedy C, Santiago-Vela MI, Hochegger J, Ní Chathail MB, Wu A, Shannon C, Roche HM, Aceves SS, Godson C, Manresa MC. The TNFSF12/TWEAK Modulates Colonic Inflammatory Fibroblast Differentiation and Promotes Fibroblast-Monocyte Interactions. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1958-1970. [PMID: 38700420 PMCID: PMC11149899 DOI: 10.4049/jimmunol.2300762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/29/2024] [Indexed: 05/05/2024]
Abstract
Fibroblasts acquire a proinflammatory phenotype in inflammatory bowel disease, but the factors driving this process and how fibroblasts contribute to mucosal immune responses are incompletely understood. TNF superfamily member 12 (TNFSF12, or TNF-like weak inducer of apoptosis [TWEAK]) has gained interest as a mediator of chronic inflammation. In this study, we explore its role as a driver of inflammatory responses in fibroblasts and its contribution to fibroblast-monocyte interaction using human primary colonic fibroblasts, THP-1 and primary monocytes. Recombinant human TWEAK induced the expression of cytokines, chemokines, and immune receptors in primary colonic fibroblasts. The TWEAK upregulated transcriptome shared 29% homology with a previously published transcriptional profile of inflammatory fibroblasts from ulcerative colitis. TWEAK elevated surface expression of activated fibroblast markers and adhesion molecules (podoplanin [PDPN], ICAM-1, and VCAM-1) and secretion of IL-6, CCL2, and CXCL10. In coculture, fibroblasts induced monocyte adhesion and secretion of CXCL1 and IL-8, and they promoted a CD14high/ICAM-1high phenotype in THP-1 cells, which was enhanced when fibroblasts were prestimulated with TWEAK. Primary monocytes in coculture with TWEAK-treated fibroblasts had altered surface expression of CD16 and triggering receptor expressed on myeloid cells-1 (TREM-1) as well as increased CXCL1 and CXCL10 secretion. Conversely, inhibition of the noncanonical NF-κB pathway on colonic fibroblasts with a NF-κB-inducing kinase small molecule inhibitor impaired their ability to induce a CD14high phenotype on monocytes. Our results indicate that TWEAK promotes an inflammatory fibroblast-monocyte crosstalk that may be amenable for therapeutic intervention.
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Affiliation(s)
- Carlos Matellan
- School of Biomolecular and Biomedical Sciences, University College Dublin, Belfield, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, Conway Institute of Biomolecular and biomedical Research, University College Dublin, Belfield, Dublin, Ireland
| | - Ciarán Kennedy
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, Conway Institute of Biomolecular and biomedical Research, University College Dublin, Belfield, Dublin, Ireland
- Diabetes Complications Research Centre, University College Dublin, Belfield, Dublin, Ireland
| | - Miren Itxaso Santiago-Vela
- School of Biomolecular and Biomedical Sciences, University College Dublin, Belfield, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
| | - Johanna Hochegger
- School of Biomolecular and Biomedical Sciences, University College Dublin, Belfield, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
| | - Méabh B. Ní Chathail
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
- School of Public Health, Physiotherapy, and Sports Science, University College Dublin, Belfield, Dublin, Ireland
| | - Amanda Wu
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA
| | - Christopher Shannon
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, Conway Institute of Biomolecular and biomedical Research, University College Dublin, Belfield, Dublin, Ireland
| | - Helen M. Roche
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
- School of Public Health, Physiotherapy, and Sports Science, University College Dublin, Belfield, Dublin, Ireland
- Institute for Global Food Security, Queen’s University Belfast, Belfast, U.K
| | - Seema S. Aceves
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA
- Rady Children’s Hospital, San Diego, CA
| | - Catherine Godson
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, Conway Institute of Biomolecular and biomedical Research, University College Dublin, Belfield, Dublin, Ireland
- Diabetes Complications Research Centre, University College Dublin, Belfield, Dublin, Ireland
| | - Mario C. Manresa
- School of Biomolecular and Biomedical Sciences, University College Dublin, Belfield, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
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10
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Wetwittayakhlang P, Kotrri G, Bessissow T, Lakatos PL. How close are we to a success stratification tool for improving biological therapy in ulcerative colitis? Expert Opin Biol Ther 2024; 24:433-441. [PMID: 38903049 DOI: 10.1080/14712598.2024.2371049] [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: 04/01/2024] [Accepted: 06/18/2024] [Indexed: 06/22/2024]
Abstract
INTRODUCTION Biological therapies have become the standard treatment for ulcerative colitis (UC). However, clinical remission rates post-induction therapy remain modest at 40-50%, with many initial responders losing response over time. Current treatment strategies frequently rely on a 'trial and error' approach, leading to prolonged periods of ineffective and costly therapies for patients, accompanied by associated treatment complications. AREA COVERED This review discusses current evidence on risk stratification tools for predicting therapeutic efficacy and minimizing adverse events in UC management. Recent studies have identified predictive factors for biologic therapy response. In the context of personalized medicine, the goal is to identify patients at high risk of progression and complications, as well as those likely to respond to specific therapies. Essential risk stratification tools include clinical decision-making aids, biomarkers, genomics, multi-omics factors, endoscopic, imaging, and histological assessments. EXPERT OPINION Employing risk stratification tools to predict therapeutic response and prevent treatment-related complications is essential for precision medicine in the biological management of UC. These tools are necessary to select the most suitable treatment for each individual patient, thereby enhancing efficacy and safety.
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Affiliation(s)
- Panu Wetwittayakhlang
- Gastroenterology and Hepatology Unit, Division of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
- Division of Gastroenterology and Hepatology, McGill University Health Center, Montreal, QC, Canada
| | - Gynter Kotrri
- Division of Gastroenterology and Hepatology, McGill University Health Center, Montreal, QC, Canada
| | - Talat Bessissow
- Division of Gastroenterology and Hepatology, McGill University Health Center, Montreal, QC, Canada
| | - Peter L Lakatos
- Division of Gastroenterology and Hepatology, McGill University Health Center, Montreal, QC, Canada
- Department of Oncology and Medicine, Semmelweis University, Budapest, Hungary
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11
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Zhong T, Cheng X, Gu Q, Fu G, Wang Y, Jiang Y, Xu J, Jiang Z. Integrated analyses reveal the diagnostic and predictive values of COL5A2 and association with immune environment in Crohn's disease. Genes Immun 2024; 25:209-218. [PMID: 38789829 PMCID: PMC11178494 DOI: 10.1038/s41435-024-00276-5] [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: 09/18/2023] [Revised: 05/03/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024]
Abstract
The pathogenesis of Crohn's disease (CD) involves abnormal immune cell infiltration and dysregulated immune response. Therefore, thorough research on immune cell abnormalities in CD is crucial for improved treatment of this disease. Single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data of CD were obtained from the Gene Expression Omnibus (GEO) database. Cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT), weighted gene co-expression network analysis (WGCNA), protein-protein interaction (PPI) networks evaluated the proportion of immune infiltrating cells, constructed co-expression network and identified key genes, respectively. Based on the dataset (GSE134809), 15 cell clusters were defined and labeled as different cell types. Among the 11 modules, the yellow module had the closest relationship with plasma cells (cluster 5). Confirmed using RNA sequencing and IHC assay, the expression of COL5A2 in CD samples was higher than that in control samples. Furthermore, the COL5A2 protein expression remarkably decreased in the group of patients who responded to anti-tumor necrosis factor (TNF) treatments, compared to the non-response group. The comprehensive analyses described here provided novel insight into the landscape of CD-associated immune environment. In addition, COL5A2 were identified as potential diagnostic indicators for CD, as well as promising predictive markers for CD patients.
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Affiliation(s)
- Tingting Zhong
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoqing Cheng
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qianru Gu
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Guoxiang Fu
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yihong Wang
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yujie Jiang
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiaqi Xu
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Zhinong Jiang
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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12
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Syed S, Boland BS, Bourke LT, Chen LA, Churchill L, Dobes A, Greene A, Heller C, Jayson C, Kostiuk B, Moss A, Najdawi F, Plung L, Rioux JD, Rosen MJ, Torres J, Zulqarnain F, Satsangi J. Challenges in IBD Research 2024: Precision Medicine. Inflamm Bowel Dis 2024; 30:S39-S54. [PMID: 38778628 DOI: 10.1093/ibd/izae084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Indexed: 05/25/2024]
Abstract
Precision medicine is part of 5 focus areas of the Challenges in IBD Research 2024 research document, which also includes preclinical human IBD mechanisms, environmental triggers, novel technologies, and pragmatic clinical research. Building on Challenges in IBD Research 2019, the current Challenges aims to provide a comprehensive overview of current gaps in inflammatory bowel diseases (IBDs) research and deliver actionable approaches to address them with a focus on how these gaps can lead to advancements in interception, remission, and restoration for these diseases. The document is the result of multidisciplinary input from scientists, clinicians, patients, and funders, and represents a valuable resource for patient-centric research prioritization. In particular, the precision medicine section is focused on the main research gaps in elucidating how to bring the best care to the individual patient in IBD. Research gaps were identified in biomarker discovery and validation for predicting disease progression and choosing the most appropriate treatment for each patient. Other gaps were identified in making the best use of existing patient biosamples and clinical data, developing new technologies to analyze large datasets, and overcoming regulatory and payer hurdles to enable clinical use of biomarkers. To address these gaps, the Workgroup suggests focusing on thoroughly validating existing candidate biomarkers, using best-in-class data generation and analysis tools, and establishing cross-disciplinary teams to tackle regulatory hurdles as early as possible. Altogether, the precision medicine group recognizes the importance of bringing basic scientific biomarker discovery and translating it into the clinic to help improve the lives of IBD patients.
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Affiliation(s)
- Sana Syed
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
- Patient representative for Crohn's & Colitis Foundation, New York, NY, USA
| | - Brigid S Boland
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lauren T Bourke
- Precision Medicine Drug Development, Early Respiratory and Immunology, AstraZeneca, Boston, MA, USA
| | - Lea Ann Chen
- Division of Gastroenterology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Laurie Churchill
- Leona M. and Harry B. Helmsley Charitable Trust, New York, NY, USA
| | | | - Adam Greene
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | | | | | | | - Alan Moss
- Crohn's & Colitis Foundation, New York, NY, USA
| | | | - Lori Plung
- Patient representative for Crohn's & Colitis Foundation, New York, NY, USA
| | - John D Rioux
- Research Center, Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | - Michael J Rosen
- Division of Pediatric Gastroenterology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Joana Torres
- Division of Gastroenterology, Hospital Beatriz Ângelo, Hospital da Luz, Lisbon, Portugal
- Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Fatima Zulqarnain
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | - Jack Satsangi
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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13
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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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14
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Verstockt B, Pivorunas V, Al Mahi N, Smaoui N, Guay H, Kennedy NA, Goodhand JR, Lin S, Bai BYH, Hanauer SB, Ferrante M, Panés J, Vermeire S. Baseline TREM-1 Whole Blood Gene Expression Does Not Predict Response to Adalimumab Treatment in Patients with Ulcerative Colitis or Crohn's Disease in the SERENE Studies. J Crohns Colitis 2024; 18:493-505. [PMID: 37801628 PMCID: PMC11037103 DOI: 10.1093/ecco-jcc/jjad170] [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: 03/31/2023] [Indexed: 10/08/2023]
Abstract
BACKGROUND AND AIMS This study assessed whether baseline triggering receptor expressed on myeloid cells [TREM-1] whole blood gene expression predicts response to anti-tumour necrosis factor [anti-TNF] therapy in patients with ulcerative colitis [UC] or Crohn's disease [CD]. METHODS TREM-1 whole blood gene expression was analysed by RNA sequencing in patients with moderately to severely active UC or CD treated with adalimumab in the Phase 3 SERENE-UC and SERENE-CD clinical trials. The predictive value of baseline TREM-1 expression was evaluated and compared according to endoscopic and clinical response vs non-response, and remission vs non-remission, at Weeks 8 and 52 [SERENE-UC], and Weeks 12 and 56 [SERENE-CD]. RESULTS TREM-1 expression was analysed in 95 and 106 patients with UC and CD, respectively, receiving standard-dose adalimumab induction treatment. In SERENE-UC, baseline TREM-1 expression was not predictive of endoscopic response [p = 0.48], endoscopic remission [p = 0.53], clinical response [p = 0.58], or clinical remission [p = 0.79] at Week 8, or clinical response [p = 0.60] at Week 52. However, an association was observed with endoscopic response [p = 0.01], endoscopic remission [p = 0.048], and clinical remission [p = 0.04997] at Week 52. For SERENE-CD, baseline TREM-1 expression was not predictive of endoscopic response [p = 0.56], endoscopic remission [p = 0.33], clinical response [p = 0.07], or clinical remission [p = 0.65] at Week 12, or endoscopic response [p = 0.61], endoscopic remission [p = 0.51], clinical response [p = 0.62], or clinical remission [p = 0.97] at Week 56. CONCLUSIONS Baseline TREM-1 gene expression did not uniformly predict adalimumab response in SERENE clinical trials. Further research is needed to identify potential blood-based biomarkers predictive of response to anti-TNF therapy in patients with inflammatory bowel disease. CLINICALTRIALS.GOV IDENTIFIERS NCT02065622; NCT02065570.
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Affiliation(s)
- Bram Verstockt
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
- Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Valerie Pivorunas
- Precision Medicine Immunology, AbbVie Bioresearch Centre, Worcester, MA, USA
| | - Naim Al Mahi
- Genomic Research Center, AbbVie, North Chicago, IL, USA
| | - Nizar Smaoui
- Genomic Research Center, AbbVie, North Chicago, IL, USA
| | - Heath Guay
- Precision Medicine Immunology, AbbVie Bioresearch Centre, Worcester, MA, USA
| | - Nicholas A Kennedy
- Department of Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - James R Goodhand
- Department of Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Simeng Lin
- Department of Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Benjamin Y H Bai
- Genomics of Inflammation and Immunity Group, Wellcome Sanger Institute, Hinxton, UK
| | - Stephen B Hanauer
- Department of Medicine, Northwestern University Feinberg School of Medicine, Evanston, IL, USA
| | - Marc Ferrante
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
- Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Julian Panés
- Hospital Clinic de Barcelona, IDIBAPS, CIBERehd, Barcelona, Catalonia, Spain
| | - Séverine Vermeire
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
- Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
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15
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Salvador-Martín S, Rubbini G, Vellosillo P, Zapata-Cobo P, Velasco M, Palomino LM, Clemente S, Segarra O, Moreno-Álvarez A, Fernández-Lorenzo A, Pérez-Moneo B, Montraveta M, Sánchez C, Tolín M, Loverdos I, Fobelo MJ, Navas-López VM, Magallares L, García-Romero R, Torres-Peral R, Rodríguez A, Bossacoma F, Merino-Bohórquez V, Salcedo E, Álvarez R, Dopazo A, Sanjurjo-Sáez M, López-Fernández LA. Blood gene expression biomarkers of response to anti-TNF drugs in pediatric inflammatory bowel diseases before initiation of treatment. Biomed Pharmacother 2024; 173:116299. [PMID: 38401525 DOI: 10.1016/j.biopha.2024.116299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 02/06/2024] [Accepted: 02/17/2024] [Indexed: 02/26/2024] Open
Abstract
BACKGROUND/AIMS Changes in gene expression profiles among individuals with inflammatory bowel diseases (IBDs) could potentially influence the responsiveness to anti-TNF treatment. The aim of this study was to identify genes that could serve as predictors of early response to anti-TNF therapies in pediatric IBD patients prior to the initiation of treatment. METHODS We conducted a prospective, longitudinal, and multicenter study, enrolling 24 pediatric IBD patients aged less than 18 years who were initiating treatment with either infliximab or adalimumab. RNA-seq from blood samples was analyzed using the DESeq2 library by comparing responders and non-responders to anti-TNF drugs. RESULTS Bioinformatic analyses unveiled 102 differentially expressed genes, with 99 genes exhibiting higher expression in responders compared to non-responders prior to the initiation of anti-TNF therapy. Functional enrichment analyses highlighted defense response to Gram-negative bacteria (FDR = 2.3 ×10-7) as the most significant biological processes, and hemoglobin binding (FDR = 0.002), as the most significant molecular function. Gene Set Enrichment Analysis (GSEA) revealed notable enrichment in transcriptional misregulation in cancer (FDR = 0.016). Notably, 13 genes (CEACAM8, CEACAM6, CILP2, COL17A1, OLFM4, INHBA, LCN2, LTF, MMP8, DEFA4, PRTN3, AZU1, and ELANE) were selected for validation, and a consistent trend of increased expression in responders prior to drug administration was observed for most of these genes, with findings for 4 of them being statistically significant (CEACAM8, LCN2, LTF2, and PRTN3). CONCLUSIONS We identified 102 differentially expressed genes involved in the response to anti-TNF drugs in children with IBDs and validated CEACAM8, LCN2, LTF2, and PRTN3. Genes participating in defense response to Gram-negative bacterium, serine-type endopeptidase activity, and transcriptional misregulation in cancer are good candidates for anticipating the response to anti-TNF drugs in children with IBDs.
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Affiliation(s)
- Sara Salvador-Martín
- Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain.
| | - Gianluca Rubbini
- Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain.
| | - Perceval Vellosillo
- Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Unidad de Investigación Materno Infantil Fundación Familia Alonso (UDIMIFFA), Spain.
| | - Paula Zapata-Cobo
- Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain.
| | - Marta Velasco
- Hospital Universitario Infantil Niño Jesús, Madrid, Spain.
| | | | | | | | | | | | | | | | - Cesar Sánchez
- Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain.
| | - Mar Tolín
- Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain.
| | | | - María José Fobelo
- Hospital Universitario Virgen de Valme, Universidad de Sevilla, Sevilla, Spain.
| | | | | | | | | | | | - Ferrán Bossacoma
- Servicio de Gastroenterología, Hepatología y Nutrición Pediátrica, Hospital Sant Joan de Dèu, Barcelona, Spain.
| | | | | | - Rebeca Álvarez
- Genomics Unit, Spanish National Center for Cardiovascular Disease (CNIC), Madrid 28029, Spain.
| | - Ana Dopazo
- Genomics Unit, Spanish National Center for Cardiovascular Disease (CNIC), Madrid 28029, Spain.
| | - María Sanjurjo-Sáez
- Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain.
| | - Luis A López-Fernández
- Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain.
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16
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Dolinger M, Torres J, Vermeire S. Crohn's disease. Lancet 2024; 403:1177-1191. [PMID: 38437854 DOI: 10.1016/s0140-6736(23)02586-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/25/2023] [Accepted: 11/17/2023] [Indexed: 03/06/2024]
Abstract
Crohn's disease is a chronic inflammatory disease of the gastrointestinal tract that might lead to progressive bowel damage and disability. The exact cause of Crohn's disease is unknown, but evidence points towards multifactorial events causing dysregulation of the innate immune system in genetically susceptible people. Commonly affecting the terminal ileum and proximal colon, Crohn's disease inflammation is often discontinuous and patchy, segmental, and transmural. Identification of characteristic findings on ileocolonoscopy and histology remains the diagnostic gold standard, but complete assessment involves laboratory abnormalities, including micronutrient deficiencies, cross-sectional imaging to identify transmural disease extent, severity and complications, and a psychosocial assessment. Treatment strategies for patients with Crohn's disease now go beyond achieving clinical remission to include deeper targets of endoscopic healing and consideration of adjunctive histological and transmural targets to alter disease progression potentially further. The use of early effective advanced therapies and development of therapies targeting alternative novel pathways with improved safety profiles have resulted in a new era of healing in Crohn's disease management. Future combination of advanced therapies with diet or other biological drugs and small molecules, together with improvements in tight control monitoring tools and predictive biomarkers might continue to improve outcomes for patients with Crohn's disease.
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Affiliation(s)
- Michael Dolinger
- Division of Paediatric Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Joana Torres
- Division of Gastroenterology, Hospital da Luz, Lisbon, Portugal; Hospital Beatriz Ângelo, Loures, Portugal; Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Severine Vermeire
- Department of Gastroenterology and Hepatology, University Hospitals Leuven and KU Leuven, Leuven, Belgium.
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Krauthammer A, Cozacov T, Fried S, Har-Zahav A, Shamir R, Assa A, Waisbourd-Zinman O. Tissue markers may predict treatment response to antitumor necrosis factor-α agents in children with Crohn's disease. J Pediatr Gastroenterol Nutr 2024; 78:662-669. [PMID: 38299301 DOI: 10.1002/jpn3.12146] [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: 10/23/2023] [Revised: 01/15/2024] [Accepted: 01/20/2024] [Indexed: 02/02/2024]
Abstract
OBJECTIVES Patients with moderate-severe Crohn's disease (CD) who are treated with antitumor necrosis factor alpha (TNF-α) agents may be subjected to primary nonresponse or partial response. We aimed to identify tissue markers that may predict response to these agents. METHODS Pediatric patients (6-18 years) with either ileal or ileo-colonic CD who were treated with anti-TNF-α were stratified into three different groups based on their overall response to therapy at the end of induction including clinical and laboratory parameters (group 1-full responders [FR], group 2-partial responders [PR], group 3-nonresponders [NR]). Seven tissue markers (fibronectin, interleukin [IL]-23R, IL-23, TNF-α, collagen-III, IL-13R, and hypoxia-inducible factors [HIF]-1α) were evaluated. Immunofluorescence (IF) analyses were performed on biopsies from the terminal ileum, which were retrieved up to 6 months before treatment initiation. RESULTS Twenty-six CD patients (16 [61.5%] males; age 13.9 ± 2.9 years), including 8 (30.8%) with ileal disease and 18 (69.2%) with ileo-colonic disease, were enrolled. Terminal ileum biopsies from nine patients from group 1, nine from group 2, and eight from group 3 were evaluated. Three antibodies were found to be significantly different between NR and FR groups; Collagen III and fibronectin stains were significantly more prominent in NR patients, while TNF-α stain was significantly more pronounced in FR, p < 0.05 for each. PR could not have been predicted with neither of markers. CONCLUSIONS Decreased tissue IF intensity of fibronectin and collagen III and increased intensity of TNF-α may predict response to anti-TNF-α treatment.
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Affiliation(s)
- Alexander Krauthammer
- Schneider Children's Medical Center of Israel, Institute of Gastroenterology, Nutrition and Liver Diseases, Petah Tikva, Israel
- Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Tal Cozacov
- Schneider Children's Medical Center of Israel, Institute of Gastroenterology, Nutrition and Liver Diseases, Petah Tikva, Israel
- Felsenstein Medical Research Center, Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Sophia Fried
- Schneider Children's Medical Center of Israel, Institute of Gastroenterology, Nutrition and Liver Diseases, Petah Tikva, Israel
- Felsenstein Medical Research Center, Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Adi Har-Zahav
- Schneider Children's Medical Center of Israel, Institute of Gastroenterology, Nutrition and Liver Diseases, Petah Tikva, Israel
- Felsenstein Medical Research Center, Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Raanan Shamir
- Schneider Children's Medical Center of Israel, Institute of Gastroenterology, Nutrition and Liver Diseases, Petah Tikva, Israel
- Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Amit Assa
- The Juliet Keidan Institute of Pediatric Gastroenterology and Nutrition, Shaare Zedek Medical Center, The Hebrew University, Jerusalem, Israel
| | - Orith Waisbourd-Zinman
- Schneider Children's Medical Center of Israel, Institute of Gastroenterology, Nutrition and Liver Diseases, Petah Tikva, Israel
- Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Felsenstein Medical Research Center, Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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18
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Bai BYH, Reppell M, Smaoui N, Waring JF, Pivorunas V, Guay H, Lin S, Chanchlani N, Bewshea C, Goodhand JR, Kennedy NA, Ahmad T, Anderson CA. Baseline Expression of Immune Gene Modules in Blood is Associated With Primary Response to Anti-TNF Therapy in Crohn's Disease Patients. J Crohns Colitis 2024; 18:431-445. [PMID: 37776235 PMCID: PMC10906954 DOI: 10.1093/ecco-jcc/jjad166] [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: 06/06/2023] [Revised: 08/22/2023] [Accepted: 09/28/2023] [Indexed: 10/02/2023]
Abstract
BACKGROUND AND AIMS Anti-tumour necrosis factor [anti-TNF] therapy is widely used for the treatment of inflammatory bowel disease, yet many patients are primary non-responders, failing to respond to induction therapy. We aimed to identify blood gene expression differences between primary responders and primary non-responders to anti-TNF monoclonal antibodies [infliximab and adalimumab], and to predict response status from blood gene expression and clinical data. METHODS The Personalised Anti-TNF Therapy in Crohn's Disease [PANTS] study is a UK-wide prospective observational cohort study of anti-TNF therapy outcome in anti-TNF-naive Crohn's disease patients [ClinicalTrials.gov identifier: NCT03088449]. Blood gene expression in 324 unique patients was measured by RNA-sequencing at baseline [week 0], and at weeks 14, 30, and 54 after treatment initiation [total sample size = 814]. RESULTS After adjusting for clinical covariates and estimated blood cell composition, baseline expression of major histocompatibility complex, antigen presentation, myeloid cell enriched receptor, and other innate immune gene modules was significantly higher in anti-TNF responders vs non-responders. Expression changes from baseline to week 14 were generally of consistent direction but greater magnitude [i.e. amplified] in responders, but interferon-related genes were upregulated uniquely in non-responders. Expression differences between responders and non-responders observed at week 14 were maintained at weeks 30 and 54. Prediction of response status from baseline clinical data, cell composition, and module expression was poor. CONCLUSIONS Baseline gene module expression was associated with primary response to anti-TNF therapy in PANTS patients. However, these baseline expression differences did not predict response with sufficient sensitivity for clinical use.
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Affiliation(s)
- Benjamin Y H Bai
- Genomics of Inflammation and Immunity Group, Wellcome Sanger Institute, Hinxton, UK
- Postgraduate School of Life Sciences, University of Cambridge, Cambridge, UK
| | | | | | | | | | | | - Simeng Lin
- Department of Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Neil Chanchlani
- Department of Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Claire Bewshea
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - James R Goodhand
- Department of Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Nicholas A Kennedy
- Department of Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Tariq Ahmad
- Department of Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Carl A Anderson
- Genomics of Inflammation and Immunity Group, Wellcome Sanger Institute, Hinxton, UK
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19
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Arosa L, Camba-Gómez M, Golubnitschaja O, Conde-Aranda J. Predictive, preventive and personalised approach as a conceptual and technological innovation in primary and secondary care of inflammatory bowel disease benefiting affected individuals and populations. EPMA J 2024; 15:111-123. [PMID: 38463620 PMCID: PMC10923750 DOI: 10.1007/s13167-024-00351-x] [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: 01/16/2024] [Accepted: 01/25/2024] [Indexed: 03/12/2024]
Abstract
Inflammatory bowel disease (IBD) is a global health burden which carries lifelong morbidity affecting all age groups in populations with the disease-specific peak of the age groups ranging between 15 and 35 years, which are of great economic importance for the society. An accelerating incidence of IBD is reported for newly industrialised countries, whereas stabilising incidence but increasing prevalence is typical for countries with a Westernised lifestyle, such as the European area and the USA. Although the aetiology of IBD is largely unknown, the interplay between the genetic, environmental, immunological, and microbial components is decisive for the disease manifestation, course, severity and individual outcomes. Contextually, the creation of an individualised patient profile is crucial for the cost-effective disease management in primary and secondary care of IBD. The proposed pathomechanisms include intestinal pathoflora and dysbiosis, chronic inflammation and mitochondrial impairments, amongst others, which collectively may reveal individual molecular signatures defining IBD subtypes and leading to clinical phenotypes, patient stratification and cost-effective protection against health-to-disease transition and treatments tailored to individualised patient profiles-all the pillars of an advanced 3PM approach. The paradigm change from reactive medical services to predictive diagnostics, cost-effective targeted prevention and treatments tailored to individualised patient profiles in overall IBD management holds a promise to meet patient needs in primary and secondary care, to increase the life-quality of affected individuals and to improve health economy in the area of IBD management. This article analyses current achievements and provides the roadmap for future developments in the area in the context of 3P medicine benefiting society at large.
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Affiliation(s)
- Laura Arosa
- Molecular and Cellular Gastroenterology, Health Research Institute of Santiago de Compostela (IDIS), Laboratory 15, Trav. Choupana S/N, Building C, Level -2, 15706 Santiago de Compostela, Spain
| | - Miguel Camba-Gómez
- Molecular and Cellular Gastroenterology, Health Research Institute of Santiago de Compostela (IDIS), Laboratory 15, Trav. Choupana S/N, Building C, Level -2, 15706 Santiago de Compostela, Spain
| | - Olga Golubnitschaja
- 3P Medicine Research Unit, University Hospital, Rheinische Friedrich-Wilhelms Universität Bonn, 53127 Bonn, Germany
| | - Javier Conde-Aranda
- Molecular and Cellular Gastroenterology, Health Research Institute of Santiago de Compostela (IDIS), Laboratory 15, Trav. Choupana S/N, Building C, Level -2, 15706 Santiago de Compostela, Spain
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20
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Puca P, Capobianco I, Coppola G, Di Vincenzo F, Trapani V, Petito V, Laterza L, Pugliese D, Lopetuso LR, Scaldaferri F. Cellular and Molecular Determinants of Biologic Drugs Resistance and Therapeutic Failure in Inflammatory Bowel Disease. Int J Mol Sci 2024; 25:2789. [PMID: 38474034 DOI: 10.3390/ijms25052789] [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: 02/06/2024] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
The advent of biologic drugs has revolutionized the treatment of Inflammatory Bowel Disease, increasing rates of response and mucosal healing in comparison to conventional therapies by allowing the treatment of corticosteroid-refractory cases and reducing corticosteroid-related side effects. However, biologic therapies (anti-TNFα inhibitors, anti-α4β7 integrin and anti-IL12/23) are still burdened by rates of response that hover around 40% (in biologic-naïve patients) or lower (for biologic-experienced patients). Moreover, knowledge of the mechanisms underlying drug resistance or loss of response is still scarce. Several cellular and molecular determinants are implied in therapeutic failure; genetic predispositions, in the form of single nucleotide polymorphisms in the sequence of cytokines or Human Leukocyte Antigen, or an altered expression of cytokines and other molecules involved in the inflammation cascade, play the most important role. Accessory mechanisms include gut microbiota dysregulation. In this narrative review of the current and most recent literature, we shed light on the mentioned determinants of therapeutic failure in order to pave the way for a more personalized approach that could help avoid unnecessary treatments and toxicities.
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Affiliation(s)
- Pierluigi Puca
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Ivan Capobianco
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Gaetano Coppola
- IBD Unit, UOC CEMAD Centro Malattie dell'Apparato Digerente, Dipartimento di Scienze Mediche e Chirurgiche Addominali ed Endocrino Metaboliche, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Federica Di Vincenzo
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Valentina Trapani
- Alleanza Contro il Cancro, Istituto Superiore di Sanità, 00144 Rome, Italy
| | - Valentina Petito
- IBD Unit, UOC CEMAD Centro Malattie dell'Apparato Digerente, Dipartimento di Scienze Mediche e Chirurgiche Addominali ed Endocrino Metaboliche, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Lucrezia Laterza
- IBD Unit, UOC CEMAD Centro Malattie dell'Apparato Digerente, Dipartimento di Scienze Mediche e Chirurgiche Addominali ed Endocrino Metaboliche, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Daniela Pugliese
- IBD Unit, UOC CEMAD Centro Malattie dell'Apparato Digerente, Dipartimento di Scienze Mediche e Chirurgiche Addominali ed Endocrino Metaboliche, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Loris Riccardo Lopetuso
- IBD Unit, UOC CEMAD Centro Malattie dell'Apparato Digerente, Dipartimento di Scienze Mediche e Chirurgiche Addominali ed Endocrino Metaboliche, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
- Department of Medicine and Ageing Sciences, "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
| | - Franco Scaldaferri
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
- IBD Unit, UOC CEMAD Centro Malattie dell'Apparato Digerente, Dipartimento di Scienze Mediche e Chirurgiche Addominali ed Endocrino Metaboliche, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
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21
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Gerasimidis K, Russell RK, Giachero F, Gkikas K, Tel B, Assa A, Bronsky J, de Ridder L, Hojsak I, Jenke A, Norsa L, Sigall-Boneh R, Sila S, Wine E, Zilbauer M, Strisciuglio C, Gasparetto M. Precision nutrition in pediatric IBD: A position paper from the ESPGHAN special interest group for basic science and translational research, the IBD Porto group, and allied health professionals. J Pediatr Gastroenterol Nutr 2024; 78:428-445. [PMID: 38374554 DOI: 10.1002/jpn3.12096] [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: 07/25/2023] [Revised: 10/24/2023] [Accepted: 11/30/2023] [Indexed: 02/21/2024]
Abstract
Stratified and precision nutrition refers to disease management or prevention of disease onset, based on dietary interventions tailored to a person's characteristics, biology, gut microbiome, and environmental exposures. Such treatment models may lead to more effective management of inflammatory bowel disease (IBD) and reduce risk of disease development. This societal position paper aimed to report advances made in stratified and precision nutritional therapy in IBD. Following a structured literature search, limited to human studies, we identified four relevant themes: (a) nutritional epidemiology for risk prediction of IBD development, (b) food-based dietary interventions in IBD, (c) exclusive enteral nutrition (EEN) for Crohn's disease (CD) management, and (d) pre- and probiotics for IBD management. There is scarce literature upon which we can make recommendations for precision or stratified dietary therapy for IBD, both for risk of disease development and disease management. Certain single-nucleotide polymorphisms related to polyunsaturated fatty acid (PUFA) metabolism may modify the effect dietary PUFA have in increasing the risk of IBD development. Non-colonic CD, mild-to-moderate CD, and high microbiota richness may predict success of EEN and may be used both for prediction of treatment continuation, but also for early cessation in nonresponders. There is currently insufficient evidence to make recommendations for precision or stratified dietary therapy for patients with established IBD. Despite the great interest in stratified and precision nutrition, we currently lack data to support conclusive recommendations. Replication of early findings by independent research groups and within structured clinical interventions is required.
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Affiliation(s)
| | - Richard K Russell
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Royal Hospital for Children and Young People, Edinburgh, UK
| | - Federica Giachero
- Department of Paediatric Gastroenterology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Trust, Cambridge, UK
| | - Konstantinos Gkikas
- Department of Human Nutrition, School of Medicine, University of Glasgow, Glasgow, UK
| | - Balint Tel
- Pediatric Center, MTA Center of Excellence, Semmelweis University, Budapest, Hungary
| | - Amit Assa
- The Juliet Keidan Institute of Pediatric Gastroenterology Hepatology and Nutrition, Shaare Zedek Medical Center, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jiri Bronsky
- Department of Paediatrics, University Hospital Motol, Prague, Czech Republic
| | - Lissy de Ridder
- Sophia Children's Hospital, Erasmus MC University, Rotterdam, The Netherlands
| | - Iva Hojsak
- Children's Hospital Zagreb, University of Zagreb Medical School, Zagreb, Croatia
| | - Andreas Jenke
- Children's Hospital Kassel, University of Witten/Herdecke, Witten, Germany
| | - Lorenzo Norsa
- Pediatric Hepatology, Gastroenterology and Transplantation ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Rotem Sigall-Boneh
- Israel Pediatric Gastroenterology and Nutrition Unit, The E. Wolfson Medical Center, Holon, Israel
- Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Sara Sila
- Referral Center for Pediatric Gastroenterology and Nutrition, Children's Hospital Zagreb, Zagreb, Croatia
| | - Eytan Wine
- Department of Pediatrics, Division of Pediatric Gastroenterology, University of Alberta, Edmonton, Alberta, Canada
| | - Matthias Zilbauer
- Wellcome MRC Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Caterina Strisciuglio
- Department of Woman, Child and General and Specialist Surgery, University of Campania "Vanvitelli", Napoli, Italy
| | - Marco Gasparetto
- Department of Paediatric Gastroenterology, Jenny Lind Children's Hospital, Norfolk and Norwich University Hospitals, Norwich, UK
- Norwich Medical School, Faculty of Medicine and Health Science, University of East Anglia (UEA), Norwich, UK
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22
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Yang Y, Fu KZ, Pan G. Role of Oncostatin M in the prognosis of inflammatory bowel disease: A meta-analysis. World J Gastrointest Surg 2024; 16:228-238. [PMID: 38328320 PMCID: PMC10845284 DOI: 10.4240/wjgs.v16.i1.228] [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: 11/14/2023] [Revised: 12/19/2023] [Accepted: 12/29/2023] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND Oncostatin M (OSM) is a pleiotropic cytokine which is implicated in the pathogenesis of inflammatory bowel disease (IBD). AIM To evaluate the prognostic role of OSM in IBD patients. METHODS Literature search was conducted in electronic databases (Google Scholar, Embase, PubMed, Science Direct, Springer, and Wiley). Studies were selected if they reported prognostic information about OSM in IBD patients. Outcome data were synthesized, and meta-analyses were performed to estimate standardized mean differences (SMDs) in OSM levels between treatment responders and non-responders and to seek overall correlations of OSM with other inflammatory biomarkers. RESULTS Sixteen studies (818 Crohn's disease and 686 ulcerative colitis patients treated with anti-tumor necrosis factor-based therapies) were included. OSM levels were associated with IBD severity. A meta-analysis found significantly higher OSM levels in non-responders than in responders to therapy [SMD 0.80 (0.33, 1.27); P = 0.001], in non-remitters than in remitters [SMD 0.75 (95%CI: 0.35 to 1.16); P < 0.0001] and in patients with no mucosal healing than in those with mucosal healing [SMD 0.63 (0.30, 0.95); P < 0.0001]. Area under receiver operator curve values showed considerable variability between studies but in general higher OSM levels were associated with poor prognosis. OSM had significant correlations with Simple Endoscopic Score of Crohn's disease [r = 0.47 (95%CI: 0.25 to 0.64); P < 0.0001], Mayo Endoscopic Score [r = 0.35 (95%CI: 0.28 to 0.41); P < 0.0001], fecal calprotectin [r = 0.19 (95%CI: 0.08 to 0.3); P = 0.001], C-reactive protein [r = 0.25 (95%CI: 0.11 to 0.39); P < 0.0001], and platelet count [r = 0.28 (95%CI: 0.17 to 0.39); P < 0.0001]. CONCLUSION OSM is a potential candidate for determining the severity of disease and predicting the outcomes of anti-tumor necrosis factor-based therapies in IBD patients.
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Affiliation(s)
- Yue Yang
- Department of Gastroenterology III, Heilongjiang Provincial Hospital, Harbin 150036, Heilongjiang Province, China
| | - Kan-Zuo Fu
- Department of Nursing, The Second Hospital of Harbin, Harbin 150056, Heilongjiang Province, China
| | - Gu Pan
- Department of Gastroenterology III, Heilongjiang Provincial Hospital, Harbin 150036, Heilongjiang Province, China
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23
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Ananthakrishnan AN. Precision medicine in inflammatory bowel diseases. Intest Res 2024; 22:8-14. [PMID: 37939722 PMCID: PMC10850693 DOI: 10.5217/ir.2023.00087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/16/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023] Open
Abstract
Inflammatory bowel diseases comprising Crohn's disease and ulcerative colitis have emerged as global diseases. Multiple distinct therapeutic mechanisms have allowed us to increase our rates of achieving remission and reducing permanent disease-related morbidity. However, there is limited data to inform relative positioning of different therapies. This review will summarize existing literature on use of clinical decision models to inform relative efficacy of one therapeutic mechanism compared to the other given individual patient characteristics. It will also demonstrate the value of serologic, transcriptomic (from biopsies), and microbiome-based biomarkers in identifying which therapy is most likely to work for a given patient. We will review the existing gaps in the literature in this field and suggest a path forward for future studies to better inform patient care, incorporating the principles of precision medicine in the management of inflammatory bowel disease.
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Affiliation(s)
- Ashwin N. Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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24
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Clinton JW, Cross RK. Personalized Treatment for Crohn's Disease: Current Approaches and Future Directions. Clin Exp Gastroenterol 2023; 16:249-276. [PMID: 38111516 PMCID: PMC10726957 DOI: 10.2147/ceg.s360248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 12/04/2023] [Indexed: 12/20/2023] Open
Abstract
Crohn's disease is a complex, relapsing and remitting inflammatory disorder of the gastrointestinal tract with a variable disease course. While the treatment options for Crohn's disease have dramatically increased over the past two decades, predicting individual patient response to treatment remains a challenge. As a result, patients often cycle through multiple different therapies before finding an effective treatment which can lead to disease complications, increased costs, and decreased quality of life. Recently, there has been increased emphasis on personalized medicine in Crohn's disease to identify individual patients who require early advanced therapy to prevent complications of their disease. In this review, we summarize our current approach to management of Crohn's disease by identifying risk factors for severe or disabling disease and tailoring individual treatments to patient-specific goals. Lastly, we outline our knowledge gaps in implementing personalized Crohn's disease treatment and describe the future directions in precision medicine.
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Affiliation(s)
- Joseph William Clinton
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Raymond Keith Cross
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Maryland School of Medicine, Baltimore, MD, USA
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25
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Granot M, Braun T, Efroni G, Picard O, Fudim E, Yavzori M, Haj O, Weiss B, Ben-Horin S, Kopylov U, Haberman Y. Baseline Peripheral Blood Mononuclear Cell Transcriptomics Before Ustekinumab Treatment Is Linked With Crohn's Disease Clinical Response at 1 Year. Clin Transl Gastroenterol 2023; 14:e00635. [PMID: 37655708 PMCID: PMC10749706 DOI: 10.14309/ctg.0000000000000635] [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: 05/14/2023] [Accepted: 08/24/2023] [Indexed: 09/02/2023] Open
Abstract
INTRODUCTION Ustekinumab, a monoclonal antibody to the p40 subunit of interleukin (IL)-12 and IL-23, is used for Crohn's disease (CD), and the documented clinical remission rate after 1 year was observed in approximately 50% of patients. We aimed to identify predictors for a clinical response using peripheral blood obtained from patients with CD just before ustekinumab treatment initiation. METHODS RNA extraction from peripheral blood mononuclear cells was followed by mRNA paired-end sequencing. Differential gene expression was performed using DESeq2. RESULTS We processed samples from 36 adults with CD (13 men, 36%) obtained at baseline before starting ustekinumab treatment. Twenty-two of 36 (61%) were defined as responders and 14/36 (39%) as nonresponders after 1 year based on Physician Global Assessment. Differential gene expression between responders (n = 22) and nonresponders (n = 14) did not show a gene expression signature that passed false discovery rate (FDR) correction. However, the analyses identified 68 genes, including CXCL1/2/3, which were induced in nonresponders vs responders with P < 0.05 and fold change above 1.5. Functional annotation enrichments of these 68 genes using ToppGene indicated enrichment for cytokine activity (FDR = 1.98E-05), CXCR chemokine receptor binding (FDR = 2.11E-05), IL-10 signaling (FDR = 5.03E-07), genes encoding secreted soluble factors (FDR = 1.73E-05), and myeloid dendritic cells (FDR = 1.80E-08). DISCUSSION No substantial differences were found in peripheral blood mononuclear cell transcriptomics between responders and nonresponders. However, among the nonresponders, we noted an increased inflammatory response enriched for pathways linked with cytokine activity and chemokine receptor binding and innate myeloid signature. A larger cohort is required to validate and further explore these findings.
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Affiliation(s)
- Maya Granot
- Pediatric Gastroenterology and Nutrition Unit, Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Tel-Aviv, Israel
| | - Tzipi Braun
- Pediatric Gastroenterology and Nutrition Unit, Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Tel-Aviv, Israel
| | - Gilat Efroni
- Pediatric Gastroenterology and Nutrition Unit, Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Tel-Aviv, Israel
| | - Orit Picard
- Department of Gastroenterology, Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Tel-Aviv, Israel
| | - Ella Fudim
- Department of Gastroenterology, Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Tel-Aviv, Israel
| | - Miri Yavzori
- Department of Gastroenterology, Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Tel-Aviv, Israel
| | - Ola Haj
- Department of Gastroenterology, Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Tel-Aviv, Israel
| | - Batia Weiss
- Pediatric Gastroenterology and Nutrition Unit, Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Tel-Aviv, Israel
| | - Shomron Ben-Horin
- Department of Gastroenterology, Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Tel-Aviv, Israel
| | - Uri Kopylov
- Department of Gastroenterology, Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Tel-Aviv, Israel
| | - Yael Haberman
- Pediatric Gastroenterology and Nutrition Unit, Sheba Medical Center, Tel-HaShomer, affiliated with the Tel-Aviv University, Tel-Aviv, Israel
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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26
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Rimmer P, Iqbal T. Prognostic modelling in IBD. Best Pract Res Clin Gastroenterol 2023; 67:101877. [PMID: 38103929 DOI: 10.1016/j.bpg.2023.101877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 11/24/2023] [Indexed: 12/19/2023]
Abstract
In the ideal world prognostication or predicting disease course in any chronic condition would allow the clinician to anticipate disease behaviour, providing crucial information for the patient and data regarding best use of resources. Prognostication also allows an understanding of likely response to treatment and the risk of adverse effects of a treatment leading to withdrawal in any individual patient. Therefore, the ability to predict outcomes from the onset of disease is the key step to developing precision personalised medicine, which is the design of medical care to optimise efficiency or therapeutic benefit based on careful profiling of patients. An important corollary is to prevent unnecessary healthcare costs. This paper outlines currently available predictors of disease outcome in IBD and looks to the future which will involve the use of artificial intelligence to interrogate big data derived from various important 'omes' to tease out a more holistic approach to IBD.
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Affiliation(s)
- Peter Rimmer
- Queen Elizabeth Hospital Birmingham, B15 2TH, UK; University of Birmingham, College of Medical and Dental Science, UK.
| | - Tariq Iqbal
- Queen Elizabeth Hospital Birmingham, B15 2TH, UK; University of Birmingham, College of Medical and Dental Science, UK.
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Derakhshan Nazari MH, Shahrokh S, Ghanbari-Maman L, Maleknia S, Ghorbaninejad M, Meyfour A. Prediction of anti-TNF therapy failure in ulcerative colitis patients by ensemble machine learning: A prospective study. Heliyon 2023; 9:e21154. [PMID: 37928018 PMCID: PMC10623293 DOI: 10.1016/j.heliyon.2023.e21154] [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: 07/12/2023] [Revised: 09/05/2023] [Accepted: 10/17/2023] [Indexed: 11/07/2023] Open
Abstract
Nowadays, anti-TNF therapy remarkably improves the medical management of ulcerative colitis (UC), but approximately 40 % of patients do not respond to this treatment. In this study, we used 79 anti-TNF-naive patients with moderate-to-severe UC from four cohorts to discover alternative therapeutic targets and develop a personalized medicine approach that can diagnose UC non-responders (UCN) prior to receiving anti-TNF therapy. To this end, two microarray data series were integrated to create a discovery cohort with 35 UC samples. A comprehensive gene expression and functional analysis was performed and identified 313 significantly altered genes, among which IL6 and INHBA were highlighted as overexpressed genes in the baseline mucosal biopsies of UCN, whose cooperation may lead to a decrease in the Tregs population. Besides, screening the abundances of immune cell subpopulations showed neutrophils' accumulation increasing the inflammation. Furthermore, the correlation of KRAS signaling activation with unresponsiveness to anti-TNF mAb was observed using network analysis. Using 50x repeated 10-fold cross-validation LASSO feature selection and a stack ensemble machine learning algorithm, a five-mRNA prognostic panel including IL13RA2, HCAR3, CSF3, INHBA, and MMP1 was introduced that could predict the response of UC patients to anti-TNF antibodies with an average accuracy of 95.3 %. The predictive capacity of the introduced biomarker panel was also validated in two independent cohorts (44 UC patients). Moreover, we presented a distinct immune cell landscape and gene signature for UCN to anti-TNF drugs and further studies should be considered to make this predictive biomarker panel and therapeutic targets applicable in the clinical setting.
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Affiliation(s)
- Mohammad Hossein Derakhshan Nazari
- Basic and Molecular Epidemiology of Gastrointestinal Disorders, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shabnam Shahrokh
- Research Center for Gastroenterology and Liver Diseases, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Leila Ghanbari-Maman
- Basic and Molecular Epidemiology of Gastrointestinal Disorders, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Computer Science, Faculty of Mathematical Sciences, University of Kashan, Kashan, Iran
| | - Samaneh Maleknia
- Basic and Molecular Epidemiology of Gastrointestinal Disorders, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahsa Ghorbaninejad
- Basic and Molecular Epidemiology of Gastrointestinal Disorders, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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28
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Yang X, Shi J, Wang G, Chen H, Ye Y, Zhong J, Wang Z. Novel mRNA Signature for Anti-TNF-α Therapy Primary Response in Patients With Ulcerative Colitis. Inflamm Bowel Dis 2023; 29:1458-1469. [PMID: 37080716 DOI: 10.1093/ibd/izad060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Indexed: 04/22/2023]
Abstract
BACKGROUND Ulcerative colitis (UC), an idiopathic, chronic inflammatory disorder of the colonic mucosa, is commonly treated with antitumor necrosis factor α (anti-TNF-α) agents. However, only approximately two-thirds have an initial response to these therapies. METHODS We integrated gene expression profiling from 3 independent data sets of 79 UC patients before they began anti-TNF-α therapy and calculated the differentially expressed genes between patient response and nonresponse to anti-TNF-α therapy and developed a de novo response-associated transcription signature score (logOR_Score) to demonstrate the predictive capability of anti-TNF-α therapy for therapeutic efficacy. Furthermore, we performed association analysis of the logOR_Score and clinical features, such as disease activity and immune microenvironment. RESULTS A total of 2522 responsive and 1824 nonresponsive genes were identified from the integrated data set. Responsive genes were significantly enriched in metabolism-related pathways, whereas nonresponsive ones were associated with immune response-related pathways. The logOR_Score enabled the accurate prediction of the therapeutic efficacy of anti-TNF-α in 4 independent patient cohorts and outperformed the predictions made based on 6 transcriptome-based signatures. In terms of clinical features, the logOR_Score correlated highly with the activity of UC. From an immune microenvironment perspective, logOR_Scores of CD8+IL-17+ T cells, follicular B cells, and innate lymphoid cells significantly decreased in inflamed UC tissue. CONCLUSIONS The de novo response-associated transcription signature may provide novel insights into the personalized treatment of patients with UC. Comprehensive analyses of the response-related subtypes and the association between logOR_Score and clinical features and immune microenvironment may provide insights into the underlying UC pathogenesis.
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Affiliation(s)
- Xinhui Yang
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
| | - Jintong Shi
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P.R. China
| | - Gaoyang Wang
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P.R. China
| | - Huifang Chen
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P.R. China
| | - Youqiong Ye
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P.R. China
| | - Jie Zhong
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
| | - Zhengting Wang
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
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Zapata-Cobo P, Salvador-Martín S, Velasco M, Palomino LM, Clemente S, Segarra O, Moreno-Álvarez A, Fernández-Lorenzo A, Pérez-Moneo B, Montraveta M, Sánchez C, Tolín M, Loverdos I, Fobelo MJ, Navas-López VM, Magallares L, García-Romero R, Sánchez-Hernández JG, Rodríguez A, Bossacoma F, Balboa MJ, Salcedo E, Sanjurjo-Sáez M, López-Fernández LA. Polymorphisms indicating risk of inflammatory bowel disease or antigenicity to anti-TNF drugs as biomarkers of response in children. Pharmacol Res 2023; 194:106859. [PMID: 37473877 DOI: 10.1016/j.phrs.2023.106859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/17/2023] [Accepted: 07/17/2023] [Indexed: 07/22/2023]
Abstract
Few genetic polymorphisms predict early response to anti-TNF drugs in inflammatory bowel disease (IBD), and even fewer have been identified in the pediatric population. However, it would be of considerable clinical interest to identify and validate genetic biomarkers of long-term response. Therefore, the aim of the study was to analyze the usefulness of biomarkers of response to anti-TNFs in pediatric IBD (pIBD) as long-term biomarkers and to find differences by type of IBD and type of anti-TNF drug. The study population comprised 340 children diagnosed with IBD who were treated with infliximab or adalimumab. Genotyping of 9 selected SNPs for their association with early response and/or immunogenicity to anti-TNFs was performed using real-time PCR. Variants C rs10508884 (CXCL12), A rs2241880 (ATG16L1), and T rs6100556 (PHACTR3) (p value 0.049; p value 0.03; p value 0.031) were associated with worse long-term response to anti-TNFs in pIBD. DNA variants specific to disease type and anti-TNF type were identified in the pediatric population. Genotyping of these genetic variants before initiation of anti-TNFs would enable, if validated in a prospective cohort, the identification of pediatric patients who are long-term responders to this therapy.
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Affiliation(s)
- Paula Zapata-Cobo
- Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Sara Salvador-Martín
- Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Marta Velasco
- Hospital Universitario Infantil Niño Jesús, Madrid, Spain
| | | | | | | | | | | | | | | | - Cesar Sánchez
- Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Mar Tolín
- Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | | | - María Jesús Fobelo
- Hospital Universitario Virgen de Valme, Universidad de Sevilla, Sevilla, Spain
| | | | | | | | | | | | - Ferrán Bossacoma
- Servicio de Gastroenterología, Hepatología y Nutrición Pediátrica, Hospital Sant Joan de Dèu, Barcelona, Spain
| | | | | | - María Sanjurjo-Sáez
- Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Luis A López-Fernández
- Instituto de Investigación Sanitaria Gregorio Marañón, Hospital General Universitario Gregorio Marañón, Madrid, Spain.
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30
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Kellerman R, Bleiweiss A, Samuel S, Margalit-Yehuda R, Aflalo E, Barzilay O, Ben-Horin S, Eliakim R, Zimlichman E, Soffer S, Klang E, Kopylov U. Spatiotemporal analysis of small bowel capsule endoscopy videos for outcomes prediction in Crohn's disease. Therap Adv Gastroenterol 2023; 16:17562848231172556. [PMID: 37440929 PMCID: PMC10333642 DOI: 10.1177/17562848231172556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/12/2023] [Indexed: 07/15/2023] Open
Abstract
Background Deep learning techniques can accurately detect and grade inflammatory findings on images from capsule endoscopy (CE) in Crohn's disease (CD). However, the predictive utility of deep learning of CE in CD for disease outcomes has not been examined. Objectives We aimed to develop a deep learning model that can predict the need for biological therapy based on complete CE videos of newly-diagnosed CD patients. Design This was a retrospective cohort study. The study cohort included treatment-naïve CD patients that have performed CE (SB3, Medtronic) within 6 months of diagnosis. Complete small bowel videos were extracted using the RAPID Reader software. Methods CE videos were scored using the Lewis score (LS). Clinical, endoscopic, and laboratory data were extracted from electronic medical records. Machine learning analysis was performed using the TimeSformer computer vision algorithm developed to capture spatiotemporal characteristics for video analysis. Results The patient cohort included 101 patients. The median duration of follow-up was 902 (354-1626) days. Biological therapy was initiated by 37 (36.6%) out of 101 patients. TimeSformer algorithm achieved training and testing accuracy of 82% and 81%, respectively, with an Area under the ROC Curve (AUC) of 0.86 to predict the need for biological therapy. In comparison, the AUC for LS was 0.70 and for fecal calprotectin 0.74. Conclusion Spatiotemporal analysis of complete CE videos of newly-diagnosed CD patients achieved accurate prediction of the need for biological therapy. The accuracy was superior to that of the human reader index or fecal calprotectin. Following future validation studies, this approach will allow for fast and accurate personalization of treatment decisions in CD.
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Affiliation(s)
| | | | | | - Reuma Margalit-Yehuda
- Department of Gastroenterology, Sheba Medical
Center, Tel Hashomer, Israel and Tel Aviv University, Tel Aviv, Israel
| | | | - Oranit Barzilay
- Department of Internal Medicine F, Sheba
Medical Center, Tel Hashomer, Israel and Tel Aviv University, Tel Aviv,
Israel
| | - Shomron Ben-Horin
- Department of Gastroenterology, Sheba Medical
Center, Tel Hashomer, Israel and Tel Aviv University, Tel Aviv, Israel
| | - Rami Eliakim
- Department of Gastroenterology, Sheba Medical
Center, Tel Hashomer, Israel and Tel Aviv University, Tel Aviv, Israel
| | - Eyal Zimlichman
- Sheba ARC and Hospital Management, Sheba
Medical Center, Tel Hashomer, Israel and Tel Aviv University, Tel Aviv,
Israel
| | - Shelly Soffer
- Department of Internal Medicine B, Assuta
Medical Center, 7747629, Ashdod, Israel
- Ben-Gurion University of the Negev, Be’er
Sheva, Israel
| | - Eyal Klang
- Sheba ARC, Sheba Medical Center, Tel Hashomer,
Israel and Tel Aviv University, Tel Aviv, Israel
| | - Uri Kopylov
- Department of Gastroenterology, Sheba Medical
Center, Tel Hashomer, Israel and Tel Aviv University, Tel Aviv, Israel
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31
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Hasselblatt P, Reindl W, Gauss A, Neeff H, Fusco S, Klaus J. Questions to consider when caring for patients with ulcerative colitis. ZEITSCHRIFT FUR GASTROENTEROLOGIE 2023; 61:690-700. [PMID: 36257329 DOI: 10.1055/a-1890-6015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Although the management of patients with ulcerative colitis (UC) is well defined by national and international guidelines, there are many debates and open questions related to daily care of UC patients. Here, we aimed to review topics with high clinical relevance including therapy algorithms, potential biomarkers for disease prognosis and response to therapy, the role of interventions targeting the gut microbiota, insights from head-to-head trials, novel UC medications, exit strategies, the impact of COVID19 on UC, care of patients with acute severe disease, cancer screening, and the role of surgery.
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Affiliation(s)
- Peter Hasselblatt
- Department of Medicine II, University Hospital Freiburg, Freiburg, Germany
| | - Wolfgang Reindl
- Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Annika Gauss
- University Hospital Heidelberg, Heidelberg, Germany
| | - Hannes Neeff
- Dept. of General and Visceral Surgery, Medical Center - University of Freiburg, Freiburg, Germany
| | - Stefano Fusco
- Department of Gastroenterology, Eberhard-Karls-Universität Tübingen Medizinische Fakultät, Tübingen, Germany
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32
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Lenti MV, Scribano ML, Biancone L, Ciccocioppo R, Pugliese D, Pastorelli L, Fiorino G, Savarino E, Caprioli FA, Ardizzone S, Fantini MC, Tontini GE, Orlando A, Sampietro GM, Sturniolo GC, Monteleone G, Vecchi M, Kohn A, Daperno M, D’Incà R, Corazza GR, Di Sabatino A. Personalize, participate, predict, and prevent: 4Ps in inflammatory bowel disease. Front Med (Lausanne) 2023; 10:1031998. [PMID: 37113615 PMCID: PMC10126747 DOI: 10.3389/fmed.2023.1031998] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 03/14/2023] [Indexed: 04/29/2023] Open
Abstract
Inflammatory bowel disease (IBD), which includes Crohn's disease (CD) and ulcerative colitis (UC), is a complex, immune-mediated, disorder which leads to several gastrointestinal and systemic manifestations determining a poor quality of life, disability, and other negative health outcomes. Our knowledge of this condition has greatly improved over the last few decades, and a comprehensive management should take into account both biological (i.e., disease-related, patient-related) and non-biological (i.e., socioeconomic, cultural, environmental, behavioral) factors which contribute to the disease phenotype. From this point of view, the so called 4P medicine framework, including personalization, prediction, prevention, and participation could be useful for tailoring ad hoc interventions in IBD patients. In this review, we discuss the cutting-edge issues regarding personalization in special settings (i.e., pregnancy, oncology, infectious diseases), patient participation (i.e., how to communicate, disability, tackling stigma and resilience, quality of care), disease prediction (i.e., faecal markers, response to treatments), and prevention (i.e., dysplasia through endoscopy, infections through vaccinations, and post-surgical recurrence). Finally, we provide an outlook discussing the unmet needs for implementing this conceptual framework in clinical practice.
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Affiliation(s)
- Marco Vincenzo Lenti
- Department of Internal Medicine and Medical Therapeutics, University of Pavia, Pavia, Italy
- Department of Internal Medicine, San Matteo Hospital Foundation, Pavia, Italy
| | | | - Livia Biancone
- Unit of Gastroenterology, Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Rachele Ciccocioppo
- Gastroenterology Unit, Department of Medicine, A.O.U.I. Policlinico G.B. Rossi and University of Verona, Verona, Italy
| | - Daniela Pugliese
- CEMAD Digestive Disease Center, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Luca Pastorelli
- Liver and Gastroenterology Unit, ASST Santi Paolo e Carlo, Milan, Italy
- Department of Health Sciences, University of Milan, Milan, Italy
| | - Gionata Fiorino
- IBD Unit, Ospedale San Camillo-Forlanini, Rome, Italy
- Department of Gastroenterology, San Raffaele Hospital and Vita-Salute San Raffaele University,, Milan, Italy
| | - Edoardo Savarino
- Gastroenterology Unit, Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy
| | - Flavio Andrea Caprioli
- Gastroenterology and Endoscopy Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Cà Granda, Ospedale Maggiore Policlinico and Università degli Studi di Milano, Milan, Italy
| | - Sandro Ardizzone
- Gastroenterology and Digestive Endoscopy Unit, ASST Fatebenefratelli Sacco, Milan, Italy
| | - Massimo Claudio Fantini
- Department of Medical Science and Public Health, University of Cagliari, Cagliari, Italy
- Gastroenterology Unit, Azienda Ospedaliero-Universitaria (AOU) di Cagliari, Cagliari, Italy
| | - Gian Eugenio Tontini
- Department of Pathophysiology and Transplantation, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milano, Italy
| | - Ambrogio Orlando
- Inflammatory Bowel Disease Unit, Azienda Ospedaliera Ospedali Riuniti "Villa Sofia-Cervello" Palermo, Palermo, Italy
| | | | - Giacomo Carlo Sturniolo
- Gastroenterology Unit, Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy
| | - Giovanni Monteleone
- Unit of Gastroenterology, Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Maurizio Vecchi
- Gastroenterology and Endoscopy Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Cà Granda, Ospedale Maggiore Policlinico and Università degli Studi di Milano, Milan, Italy
| | - Anna Kohn
- Gastroenterology Operative Unit, Azienda Ospedaliera San Camillo-Forlanini FR, Rome, Italy
| | - Marco Daperno
- Division of Gastroenterology, Ospedale Ordine Mauriziano di Torino, Turin, Italy
| | - Renata D’Incà
- Department of Gastroenterology, San Raffaele Hospital and Vita-Salute San Raffaele University,, Milan, Italy
| | - Gino Roberto Corazza
- Department of Internal Medicine and Medical Therapeutics, University of Pavia, Pavia, Italy
- Department of Internal Medicine, San Matteo Hospital Foundation, Pavia, Italy
| | - Antonio Di Sabatino
- Department of Internal Medicine and Medical Therapeutics, University of Pavia, Pavia, Italy
- Department of Internal Medicine, San Matteo Hospital Foundation, Pavia, Italy
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Kalla R, Adams AT, Nowak JK, Bergemalm D, Vatn S, Ventham NT, Kennedy NA, Ricanek P, Lindstrom J, Söderholm J, Pierik M, D’Amato M, Gomollón F, Olbjørn C, Richmond R, Relton C, Jahnsen J, Vatn MH, Halfvarson J, Satsangi J. Analysis of Systemic Epigenetic Alterations in Inflammatory Bowel Disease: Defining Geographical, Genetic and Immune-Inflammatory influences on the Circulating Methylome. J Crohns Colitis 2023; 17:170-184. [PMID: 36029471 PMCID: PMC10024547 DOI: 10.1093/ecco-jcc/jjac127] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND Epigenetic alterations may provide valuable insights into gene-environment interactions in the pathogenesis of inflammatory bowel disease [IBD]. METHODS Genome-wide methylation was measured from peripheral blood using the Illumina 450k platform in a case-control study in an inception cohort (295 controls, 154 Crohn's disease [CD], 161 ulcerative colitis [UC], 28 IBD unclassified [IBD-U)] with covariates of age, sex and cell counts, deconvoluted by the Houseman method. Genotyping was performed using Illumina HumanOmniExpressExome-8 BeadChips and gene expression using the Ion AmpliSeq Human Gene Expression Core Panel. Treatment escalation was characterized by the need for biological agents or surgery after initial disease remission. RESULTS A total of 137 differentially methylated positions [DMPs] were identified in IBD, including VMP1/MIR21 [p = 9.11 × 10-15] and RPS6KA2 [6.43 × 10-13], with consistency seen across Scandinavia and the UK. Dysregulated loci demonstrate strong genetic influence, notably VMP1 [p = 1.53 × 10-15]. Age acceleration is seen in IBD [coefficient 0.94, p < 2.2 × 10-16]. Several immuno-active genes demonstrated highly significant correlations between methylation and gene expression in IBD, in particular OSM: IBD r = -0.32, p = 3.64 × 10-7 vs non-IBD r = -0.14, p = 0.77]. Multi-omic integration of the methylome, genome and transcriptome also implicated specific pathways that associate with immune activation, response and regulation at disease inception. At follow-up, a signature of three DMPs [TAP1, TESPA1, RPTOR] were associated with treatment escalation to biological agents or surgery (hazard ratio of 5.19 [CI: 2.14-12.56], logrank p = 9.70 × 10-4). CONCLUSION These data demonstrate consistent epigenetic alterations at diagnosis in European patients with IBD, providing insights into the pathogenetic importance and translational potential of epigenetic mapping in complex disease.
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Affiliation(s)
- Rahul Kalla
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- MRC Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Alex T Adams
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Jan K Nowak
- Department of Paediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Daniel Bergemalm
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Simen Vatn
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
| | - Nicholas T Ventham
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Nicholas A Kennedy
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Exeter IBD and Pharmacogenetics group, University of Exeter, Exeter, UK
| | - Petr Ricanek
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - Jonas Lindstrom
- Health Services Research Unit, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - Johan Söderholm
- Department of Surgery and Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Marie Pierik
- Maastricht University Medical Centre (MUMC), Department of Gastroenterology and Hepatology, Maastricht, Netherlands
| | - Mauro D’Amato
- CIC bioGUNE – BRTA, Derio, SpainIKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | | | - Christine Olbjørn
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - Rebecca Richmond
- Medical Research Council Integrative Epidemiology Unit (MRC IEU), School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Caroline Relton
- Medical Research Council Integrative Epidemiology Unit (MRC IEU), School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Jørgen Jahnsen
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - Morten H Vatn
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Jack Satsangi
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, UK
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Cheah E, Huang JG. Precision medicine in inflammatory bowel disease: Individualizing the use of biologics and small molecule therapies. World J Gastroenterol 2023; 29:1539-1550. [PMID: 36970587 PMCID: PMC10037250 DOI: 10.3748/wjg.v29.i10.1539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/17/2023] [Accepted: 02/22/2023] [Indexed: 03/14/2023] Open
Abstract
The advent of biologics and small molecules in inflammatory bowel disease (IBD) has marked a significant turning point in the prognosis of IBD, decreasing the rates of corticosteroid dependence, hospitalizations and improving overall quality of life. The introduction of biosimilars has also increased affordability and enhanced access to these otherwise costly targeted therapies. Biologics do not yet represent a complete panacea: A subset of patients do not respond to first-line anti-tumor necrosis factor (TNF)-alpha agents or may subsequently demonstrate a secondary loss of response. Patients who fail to respond to anti-TNF agents typically have a poorer response rate to second-line biologics. It is uncertain which patient would benefit from a different sequencing of biologics or even a combination of biologic agents. The introduction of newer classes of biologics and small molecules may provide alternative therapeutic targets for patients with refractory disease. This review examines the therapeutic ceiling in current treatment strategies of IBD and the potential paradigm shifts in the future.
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Affiliation(s)
- Eric Cheah
- Department of Gastroenterology and Clinical Nutrition, The Royal Children's Hospital Melbourne, Parkville, VIC 3052, Australia
| | - James Guoxian Huang
- Department of Paediatrics, Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore 119228, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
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Cheah E, Huang JG. Precision medicine in inflammatory bowel disease: Individualizing the use of biologics and small molecule therapies. World J Gastroenterol 2023; 29:1395-1406. [DOI: 10.3748/wjg.v29.i10.1395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/10/2023] Open
Abstract
The advent of biologics and small molecules in inflammatory bowel disease (IBD) has marked a significant turning point in the prognosis of IBD, decreasing the rates of corticosteroid dependence, hospitalizations and improving overall quality of life. The introduction of biosimilars has also increased affordability and enhanced access to these otherwise costly targeted therapies. Biologics do not yet represent a complete panacea: A subset of patients do not respond to first-line anti-tumor necrosis factor (TNF)-alpha agents or may subsequently demonstrate a secondary loss of response. Patients who fail to respond to anti-TNF agents typically have a poorer response rate to second-line biologics. It is uncertain which patient would benefit from a different sequencing of biologics or even a combination of biologic agents. The introduction of newer classes of biologics and small molecules may provide alternative therapeutic targets for patients with refractory disease. This review examines the therapeutic ceiling in current treatment strategies of IBD and the potential paradigm shifts in the future.
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Affiliation(s)
- Eric Cheah
- Department of Gastroenterology and Clinical Nutrition, The Royal Children's Hospital Melbourne, Parkville, VIC 3052, Australia
| | - James Guoxian Huang
- Department of Paediatrics, Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore 119228, Singapore,Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
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Identification of Specific Biomarkers and Pathways in the Treatment Response of Infliximab for Inflammatory Bowel Disease: In-Silico Analysis. Life (Basel) 2023; 13:life13030680. [PMID: 36983834 PMCID: PMC10057676 DOI: 10.3390/life13030680] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/19/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Background: Inflammatory bowel disease (IBD) is characterized by chronic inflammation of the gastrointestinal tract. In biological therapy, infliximab became the first anti-tumor necrosis factor (TNF) agent approved for IBD. Despite this success, infliximab is expensive, often ineffective, and associated with adverse events. Prediction of infliximab resistance would improve overall potential outcomes. Therefore, there is a pressing need to widen the scope of investigating the role of genetics in IBD to their association with therapy response. Methods: In the current study, an in-silico analysis of publicly available IBD patient transcriptomics datasets from Gene Expression Omnibus (GEO) are used to identify subsets of differentially expressed genes (DEGs) involved in the pathogenesis of IBD and may serve as potential biomarkers for Infliximab response. Five datasets were found that met the inclusion criteria. The DEGs for datasets were identified using limma R packages through the GEOR2 tool. The probes’ annotated genes in each dataset intersected with DGEs from all other datasets. Enriched gene Ontology Clustering for the identified genes was performed using Metascape to explore the possible connections or interactions between the genes. Results: 174 DEGs between IBD and healthy controls were found from analyzing two datasets (GSE14580 and GSE73661), indicating a possible role in the pathogenesis of IBD. Of the 174 DEGs, five genes (SELE, TREM1, AQP9, FPR2, and HCAR3) were shared between all five datasets. Moreover, these five genes were identified as downregulated in the infliximab responder group compared to the non-responder group. Conclusions: We hypothesize that alteration in the expression of these genes leads to an impaired response to infliximab in IBD patients. Thus, these genes can serve as potential biomarkers for the early detection of compromised infliximab response in IBD patients.
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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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Liu XY, Tang H, Zhou QY, Zeng YL, Chen D, Xu H, Li Y, Tan B, Qian JM. Advancing the precision management of inflammatory bowel disease in the era of omics approaches and new technology. World J Gastroenterol 2023; 29:272-285. [PMID: 36687128 PMCID: PMC9846940 DOI: 10.3748/wjg.v29.i2.272] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/01/2022] [Accepted: 12/21/2022] [Indexed: 01/06/2023] Open
Abstract
There is great heterogeneity among inflammatory bowel disease (IBD) patients in terms of pathogenesis, clinical manifestation, response to treatment, and prognosis, which requires the individualized and precision management of patients. Many studies have focused on prediction biomarkers and models for assessing IBD disease type, activity, severity, and prognosis. During the era of biologics, how to predict the response and side effects of patients to different treatments and how to quickly recognize the loss of response have also become important topics. Multiomics is a promising area for investigating the complex network of IBD pathogenesis. Integrating numerous amounts of data requires the use of artificial intelligence.
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Affiliation(s)
- Xin-Yu Liu
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
- Eight-year Medical Doctor Program, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
| | - Hao Tang
- Department of Internal Medicine, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
| | - Qing-Yang Zhou
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
| | - Yan-Lin Zeng
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Dan Chen
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing 100730, China
| | - Hui Xu
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
| | - Yue Li
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
| | - Bei Tan
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
| | - Jia-Ming Qian
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
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Vieujean S, Louis E. Precision medicine and drug optimization in adult inflammatory bowel disease patients. Therap Adv Gastroenterol 2023; 16:17562848231173331. [PMID: 37197397 PMCID: PMC10184262 DOI: 10.1177/17562848231173331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/16/2023] [Indexed: 05/19/2023] Open
Abstract
Inflammatory bowel diseases (IBD) encompass two main entities including ulcerative colitis and Crohn's disease. Although having a common global pathophysiological mechanism, IBD patients are characterized by a significant interindividual heterogeneity and may differ by their disease type, disease locations, disease behaviours, disease manifestations, disease course as well as treatment needs. Indeed, although the therapeutic armamentarium for these diseases has expanded rapidly in recent years, a proportion of patients remains with a suboptimal response to medical treatment due to primary non-response, secondary loss of response or intolerance to currently available drugs. Identifying, prior to treatment initiation, which patients are likely to respond to a specific drug would improve the disease management, avoid unnecessary side effects and reduce the healthcare expenses. Precision medicine classifies individuals into subpopulations according to clinical and molecular characteristics with the objective to tailor preventative and therapeutic interventions to the characteristics of each patient. Interventions would thus be performed only on those who will benefit, sparing side effects and expense for those who will not. This review aims to summarize clinical factors, biomarkers (genetic, transcriptomic, proteomic, metabolic, radiomic or from the microbiota) and tools that could predict disease progression to guide towards a step-up or top-down strategy. Predictive factors of response or non-response to treatment will then be reviewed, followed by a discussion about the optimal dose of drug required for patients. The time at which these treatments should be administered (or rather can be stopped in case of a deep remission or in the aftermath of a surgery) will also be addressed. IBD remain biologically complex, with multifactorial etiopathology, clinical heterogeneity as well as temporal and therapeutic variabilities, which makes precision medicine especially challenging in this area. Although applied for many years in oncology, it remains an unmet medical need in IBD.
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Affiliation(s)
- Sophie Vieujean
- Hepato-Gastroenterology and Digestive Oncology, University Hospital CHU of Liège, Liège, Belgium
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Magalhaes D, Peyrin-Biroulet L, Estevinho MM, Danese S, Magro F. Pursuing neutrophils: systematic scoping review on blood-based biomarkers as predictors of treatment outcomes in inflammatory bowel disease. Therap Adv Gastroenterol 2023; 16:17562848231155987. [PMID: 36923488 PMCID: PMC10009059 DOI: 10.1177/17562848231155987] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 01/23/2023] [Indexed: 03/14/2023] Open
Abstract
Background Long-term management of inflammatory bowel diseases (IBD) is challenging and the identification of reliable predictors for treatment outcomes is an unmet need. Neutrophil-related biomarkers have been mainly studied in the feces, but blood analyses have inherent advantages. Objective To review the recent learnings on the ability of blood-based neutrophil-expressed biomarkers to predict treatment outcomes in IBD. Design Systematic scoping review. Data sources and methods We performed a literature search in Pubmed, EMBASE, SCOPUS, Web of Science, ScienceDirect, and Cochrane Central Register of Controlled Trials from inception until May 2022 according to Preferred Reporting Items for Systematic reviews and Meta-Analyses guidelines. All human studies associating blood-based neutrophil-related compounds with the prediction of disease progression, complication onset, or treatment outcomes were included. Results From 1032 retrieved entries, 34 studies were selected, 32 published in 2013 or later. In all, 17 biomarkers from granules, cytoplasm, plasmatic membrane, and plasma were explored. In total, 1850 Crohn's disease (CD) and 1122 ulcerative colitis non-duplicated patients were included. The most mentioned biomarkers were nCD64, serum calprotectin (SC), oncostatin M (OSM), neutrophil elastase-generated calprotectin fragment (CPa9-HNE), and triggering receptor expressed on myeloid cells 1 (TREM1). Six biomarkers showed promising results: OSM, SC, eNAMPT, nCD64, TREM1, and CPa9-HNE. Variable positive signals were found for human neutrophil peptide 1-3, LL-37, S100A12, and neutrophil gelatinase-associated lipocalin. No predictive ability was found for the remaining markers. Sharing a neutrophil compartment did not indicate similar behavior. Conclusion Advances in the last decade began to unveil the untapped potential of the readily accessible blood neutrophil-expressed biomarkers, especially nCD64, TREM1, and CPa9-HNE. Current evidence suggests that future research should focus on well-defined subpopulations instead of a one-size-fits-all biomarker. Registration https://osf.io/kes9a.
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Affiliation(s)
- Diogo Magalhaes
- Department of Biomedicine, Unit of Pharmacology and Therapeutics, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Laurent Peyrin-Biroulet
- Department of Gastroenterology and Inserm NGERE U1256, University Hospital of Nancy, University of Lorraine, Vandoeuvre-lès-Nancy, France
| | - Maria Manuela Estevinho
- Department of Biomedicine, Unit of Pharmacology and Therapeutics, Faculty of Medicine, University of Porto, Porto, Portugal.,Department of Gastroenterology, Vila Nova de Gaia/Espinho Hospital Center, Vila Nova de Gaia, Portugal
| | - Silvio Danese
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy.,IBD center, Humanitas Research Hospital, IRCCS, Rozzano, Milan, Italy
| | - Fernando Magro
- Department of Biomedicine, Unit of Pharmacology and Therapeutics, Faculty of Medicine, University of Porto, Rua Dr. Plácido Costa, 3, Porto, 4200-450, Portugal.,Department of Gastroenterology, São João Hospital University Centre, Porto, Portugal.,Center for Health Technology and Services Research (CINTESIS), Porto, Portugal.,Unidade de Farmacologia Clínica, São João Hospital University Centre, Porto, Portugal.,Portuguese Inflammatory Bowel Disease group (GEDII)
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Xu YH, Zhu WM, Guo Z. Current status of novel biologics and small molecule drugs in the individualized treatment of inflammatory bowel disease. World J Gastroenterol 2022; 28:6888-6899. [PMID: 36632311 PMCID: PMC9827580 DOI: 10.3748/wjg.v28.i48.6888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/11/2022] [Accepted: 12/01/2022] [Indexed: 12/26/2022] Open
Abstract
Treatment strategies for inflammatory bowel disease (IBD) are rapidly evolving with the development of biologics and small molecule drugs (SMDs). However, these drugs are not guaranteed to be effective in all patients, and a “ceiling effect” of biologic monotherapy may occur. This issue highlights an unmet need for optimizing the use of biologics and predicting therapeutic responses. Thus, the development of new drugs with novel mechanisms of action is urgently needed for patients with primary nonresponse and secondary loss of response to conventional biologics and SMDs. In addition, combining different biologics or SMDs has been proposed as a novel strategy to enhance treatment efficacy in IBD, which theoretically has multidimensional anti-inflammatory potential. Based on the current evidence available for IBD, dual targeted therapy may be a promising strategy for refractory IBD patients who have failed in multiple biologic trea-tments or who have extraintestinal manifestation. Additionally, identifying the subgroup of IBD patients who are responding to biological combination therapies is also equally important in stable disease remission. In this review, we sum-marize the newly developed biologics and SMDs and the current status of bio-logics/SMDs to highlight the development of individualized treatment in IBD.
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Affiliation(s)
- Yi-Han Xu
- Department of General Surgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, Jiangsu Province, China
| | - Wei-Ming Zhu
- Department of General Surgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, Jiangsu Province, China
| | - Zhen Guo
- Department of General Surgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, Jiangsu Province, China
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Wang J, Macoritto M, Guay H, Davis JW, Levesque MC, Cao X. The Clinical Response of Upadacitinib and Risankizumab Is Associated With Reduced Inflammatory Bowel Disease Anti-TNF-α Inadequate Response Mechanisms. Inflamm Bowel Dis 2022; 29:771-782. [PMID: 36515243 DOI: 10.1093/ibd/izac246] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND Janus kinase (JAK) 1 inhibitor upadacitinib and IL-23 inhibitor risankizumab are efficacious in inflammatory bowel disease (IBD) patients who are antitumor necrosis factor (anti-TNF)-α inadequate responders (TNF-IRs). We aimed to understand the mechanisms mediating the response of upadacitinib and risankizumab. METHODS Eight tissue transcriptomic data sets from IBD patients treated with anti-TNF-α therapies along with single-cell RNAseq data from ulcerative colitis were integrated to identify TNF-IR mechanisms. The RNAseq colon tissue data from clinical studies of TNF-IR Crohn's disease patients treated with upadacitinib or risankizumab were used to identify TNF-IR mechanisms that were favorably modified by upadacitinib and risankizumab. RESULTS We found 7 TNF-IR upregulated modules related to innate/adaptive immune responses, interferon signaling, and tissue remodeling and 6 TNF-IR upregulated cell types related to inflammatory fibroblasts, postcapillary venules, inflammatory monocytes, macrophages, dendritic cells, and cycling B cells. Upadacitinib was associated with a significant decrease in the expression of most TNF-IR upregulated modules in JAK1 responders (JAK1-R); in contrast, there was no change in these modules among TNF-IR patients treated with a placebo or among JAK1 inadequate responders (JAK1-IR). In addition, 4 of the 6 TNF-IR upregulated cell types were significantly decreased after upadacitinib treatment in JAK1-R but not among subjects treated with a placebo or among JAK1-IR patients. We observed similar findings from colon biopsy samples from TNF-IR patients treated with risankizumab. CONCLUSIONS Collectively, these data suggest that upadacitinib and risankizumab affect TNF-IR upregulated mechanisms, which may account for their clinical response among TNF-IR IBD patients.
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Affiliation(s)
- Jing Wang
- Genomic Research Center, AbbVie Inc, Cambridge, MA, 02139, USA
| | | | - Heath Guay
- AbbVie Bioresearch Center, Worcester, MA, 01605, USA
| | - Justin W Davis
- Genomic Research Center, AbbVie Inc, North Chicago, IL, 60064, USA
| | | | - Xiaohong Cao
- Genomic Research Center, AbbVie Inc, Cambridge, MA, 02139, USA
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Pavlidis P, Tsakmaki A, Pantazi E, Li K, Cozzetto D, Digby-Bell J, Yang F, Lo JW, Alberts E, Sa ACC, Niazi U, Friedman J, Long AK, Ding Y, Carey CD, Lamb C, Saqi M, Madgwick M, Gul L, Treveil A, Korcsmaros T, Macdonald TT, Lord GM, Bewick G, Powell N. Interleukin-22 regulates neutrophil recruitment in ulcerative colitis and is associated with resistance to ustekinumab therapy. Nat Commun 2022; 13:5820. [PMID: 36192482 PMCID: PMC9530232 DOI: 10.1038/s41467-022-33331-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 09/14/2022] [Indexed: 11/28/2022] Open
Abstract
The function of interleukin-22 (IL-22) in intestinal barrier homeostasis remains controversial. Here, we map the transcriptional landscape regulated by IL-22 in human colonic epithelial organoids and evaluate the biological, functional and clinical significance of the IL-22 mediated pathways in ulcerative colitis (UC). We show that IL-22 regulated pro-inflammatory pathways are involved in microbial recognition, cancer and immune cell chemotaxis; most prominently those involving CXCR2+ neutrophils. IL-22-mediated transcriptional regulation of CXC-family neutrophil-active chemokine expression is highly conserved across species, is dependent on STAT3 signaling, and is functionally and pathologically important in the recruitment of CXCR2+ neutrophils into colonic tissue. In UC patients, the magnitude of enrichment of the IL-22 regulated transcripts in colonic biopsies correlates with colonic neutrophil infiltration and is enriched in non-responders to ustekinumab therapy. Our data provide further insights into the biology of IL-22 in human disease and highlight its function in the regulation of pathogenic immune pathways, including neutrophil chemotaxis. The transcriptional networks regulated by IL-22 are functionally and clinically important in UC, impacting patient trajectories and responsiveness to biological intervention.
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Affiliation(s)
| | - Anastasia Tsakmaki
- Diabetes Research Group, School of Life Course Sciences, Faculty of Life Science and Medicine, King's College London, London, UK
| | - Eirini Pantazi
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Katherine Li
- Janssen Research & Development, 1400 McKean Rd, Spring House, PA, 19477, USA
| | - Domenico Cozzetto
- Translational Bioinformatics, National Institute for Health Research Biomedical Centre, Guy's and St Thomas' NHS Foundation Trust and King's College London, London, UK
| | - Jonathan Digby-Bell
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Feifei Yang
- Janssen Research & Development, 1400 McKean Rd, Spring House, PA, 19477, USA
| | - Jonathan W Lo
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Elena Alberts
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | | | - Umar Niazi
- Translational Bioinformatics, National Institute for Health Research Biomedical Centre, Guy's and St Thomas' NHS Foundation Trust and King's College London, London, UK
| | - Joshua Friedman
- Janssen Research & Development, 1400 McKean Rd, Spring House, PA, 19477, USA
| | - Anna K Long
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Yuchun Ding
- Translational and Clinical Research Institute, Newcastle University, Framlington Place, Newcastle upon Tyne, UK
| | - Christopher D Carey
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Translational and Clinical Research Institute, Newcastle University, Framlington Place, Newcastle upon Tyne, UK
| | - Christopher Lamb
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Translational and Clinical Research Institute, Newcastle University, Framlington Place, Newcastle upon Tyne, UK
| | - Mansoor Saqi
- Translational Bioinformatics, National Institute for Health Research Biomedical Centre, Guy's and St Thomas' NHS Foundation Trust and King's College London, London, UK
| | - Matthew Madgwick
- Earlham Institute, Norwich Research Park, Norwich, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Leila Gul
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Agatha Treveil
- Earlham Institute, Norwich Research Park, Norwich, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Tamas Korcsmaros
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Thomas T Macdonald
- Centre for Immunobiology, Barts and the London School of Medicine and Dentistry, QMUL, London, UK
| | - Graham M Lord
- School of Immunology and Microbial Sciences, King's College London, London, UK
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Gavin Bewick
- Diabetes Research Group, School of Life Course Sciences, Faculty of Life Science and Medicine, King's College London, London, UK
| | - Nick Powell
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, UK.
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Rankouhi TR, Keulen DV, Tempel D, Venhorst J. Oncostatin M: Risks and Benefits of a Novel Therapeutic Target for Atherosclerosis. Curr Drug Targets 2022; 23:1345-1369. [PMID: 35959619 DOI: 10.2174/1389450123666220811101032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/30/2022] [Accepted: 06/03/2022] [Indexed: 01/25/2023]
Abstract
BACKGROUND Cardiovascular disease (CVD) is a leading cause of death worldwide. It is predicted that approximately 23.6 million people will die from CVDs annually by 2030. Therefore, there is a great need for an effective therapeutic approach to combat this disease. The European Cardiovascular Target Discovery (CarTarDis) consortium identified Oncostatin M (OSM) as a potential therapeutic target for atherosclerosis. The benefits of modulating OSM - an interleukin (IL)-6 family cytokine - have since been studied for multiple indications. However, as decades of high attrition rates have stressed, the success of a drug target is determined by the fine balance between benefits and the risk of adverse events. Safety issues should therefore not be overlooked. OBJECTIVE In this review, a risk/benefit analysis is performed on OSM inhibition in the context of atherosclerosis treatment. First, OSM signaling characteristics and its role in atherosclerosis are described. Next, an overview of in vitro, in vivo, and clinical findings relating to both the benefits and risks of modulating OSM in major organ systems is provided. Based on OSM's biological function and expression profile as well as drug intervention studies, safety concerns of inhibiting this target have been identified, assessed, and ranked for the target population. CONCLUSION While OSM may be of therapeutic value in atherosclerosis, drug development should also focus on de-risking the herein identified major safety concerns: tissue remodeling, angiogenesis, bleeding, anemia, and NMDA- and glutamate-induced neurotoxicity. Close monitoring and/or exclusion of patients with various comorbidities may be required for optimal therapeutic benefit.
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Affiliation(s)
- Tanja Rouhani Rankouhi
- Department of Risk Analysis for Products in Development, TNO, Utrechtseweg 48, 3704 HE, Zeist, The Netherlands
| | - Daniëlle van Keulen
- SkylineDx BV, Science and Clinical Development, 3062 ME Rotterdam, The Netherlands
| | - Dennie Tempel
- SkylineDx BV, Science and Clinical Development, 3062 ME Rotterdam, The Netherlands
| | - Jennifer Venhorst
- Department of Risk Analysis for Products in Development, TNO, Utrechtseweg 48, 3704 HE, Zeist, The Netherlands
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45
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Bertani L, Barberio B, Fornili M, Antonioli L, Zanzi F, Casadei C, Benvenuti L, Facchin S, D'Antongiovanni V, Lorenzon G, Ceccarelli L, Baglietto L, de Bortoli N, Bellini M, Costa F, Savarino EV, Fornai M. Serum oncostatin M predicts mucosal healing in patients with inflammatory bowel diseases treated with anti-TNF, but not vedolizumab. Dig Liver Dis 2022; 54:1367-1373. [PMID: 35393259 DOI: 10.1016/j.dld.2022.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 03/09/2022] [Accepted: 03/13/2022] [Indexed: 12/29/2022]
Abstract
BACKGROUND Oncostatin M was recently highlighted as a promising biomarker for therapeutic effectiveness in inflammatory bowel diseases (IBD), with particular regard for infliximab. The primary aim was to evaluate the ability of serum oncostatin M to predict endoscopic response to different drugs in IBD. METHODS We selected two different cohorts of patients with IBD, treated with anti-TNF (infliximab and adalimumab) or with vedolizumab. Therapeutic response was evaluated at week 54 in terms of mucosal healing. Serum oncostatin M and C-reactive protein were measured at baseline; fecal calprotectin was measured at baseline and after 14 weeks of treatment. We evaluated the association of these biomarkers with mucosal healing at week 54. RESULTS Among 66 patients treated with anti-TNFs and 68 treated with vedolizumab, 35 and 31 attained mucosal healing, respectively. Mucosal healing at 54 weeks was significantly associated with low oncostatin M levels at baseline in the anti-TNF cohort; the diagnostic accuracy of oncostatin M at baseline in predicting mucosal healing was 0.91 (95% CI 0.84 to 0.99) in the anti-TNF cohort and 0.56 (95% CI 0.43 to 0.70, P < 0.001) in the vedolizumab cohort. Mucosal healing was also associated with low fecal calprotectin levels at week 14 in both cohorts. CONCLUSION Our study suggests that serum oncostatin M is a drug-specific biomarker, since it could be used to predict therapeutic effectiveness to anti-TNFs but not to vedolizumab. Moreover, these results emphasize the utility of serum oncostatin M measurement in patients treated with anti-TNF.
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Affiliation(s)
- Lorenzo Bertani
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, via Roma, 67, Pisa 56100, Italy.
| | - Brigida Barberio
- Department of Department of Surgery, Oncology and Gastroenterology -DiSCOG, University of Padua, Padua, Italy
| | - Marco Fornili
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Luca Antonioli
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Federico Zanzi
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, via Roma, 67, Pisa 56100, Italy
| | - Cesare Casadei
- Department of Department of Surgery, Oncology and Gastroenterology -DiSCOG, University of Padua, Padua, Italy
| | - Laura Benvenuti
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Sonia Facchin
- Department of Department of Surgery, Oncology and Gastroenterology -DiSCOG, University of Padua, Padua, Italy
| | | | - Greta Lorenzon
- Department of Department of Surgery, Oncology and Gastroenterology -DiSCOG, University of Padua, Padua, Italy
| | - Linda Ceccarelli
- Department of General Surgery and Gastroenterology, IBD Unit, Pisa University Hospital, Pisa, Italy
| | - Laura Baglietto
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Nicola de Bortoli
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, via Roma, 67, Pisa 56100, Italy
| | - Massimo Bellini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, via Roma, 67, Pisa 56100, Italy
| | - Francesco Costa
- Department of General Surgery and Gastroenterology, IBD Unit, Pisa University Hospital, Pisa, Italy
| | - Edoardo Vincenzo Savarino
- Department of Department of Surgery, Oncology and Gastroenterology -DiSCOG, University of Padua, Padua, Italy
| | - Matteo Fornai
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
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Ashton JJ, Cheng G, Stafford IS, Kellermann M, Seaby EG, Cummings JRF, Coelho TAF, Batra A, Afzal NA, Beattie RM, Ennis S. Prediction of Crohn's Disease Stricturing Phenotype Using a NOD2-derived Genomic Biomarker. Inflamm Bowel Dis 2022; 29:511-521. [PMID: 36161322 PMCID: PMC10069659 DOI: 10.1093/ibd/izac205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Indexed: 12/09/2022]
Abstract
BACKGROUND Crohn's disease (CD) is highly heterogenous and may be complicated by stricturing behavior. Personalized prediction of stricturing will inform management. We aimed to create a stricturing risk stratification model using genomic/clinical data. METHODS Exome sequencing was performed on CD patients, and phenotype data retrieved. Biallelic variants in NOD2 were identified. NOD2 was converted into a per-patient deleteriousness metric ("GenePy"). Using training data, patients were stratified into risk groups for fibrotic stricturing using NOD2. Findings were validated in a testing data set. Models were modified to include disease location at diagnosis. Cox proportional hazards assessed performance. RESULTS Six hundred forty-five patients were included (373 children and 272 adults); 48 patients fulfilled criteria for monogenic NOD2-related disease (7.4%), 24 of whom had strictures. NOD2 GenePy scores stratified patients in training data into 2 risk groups. Within testing data, 30 of 161 patients (18.6%) were classified as high-risk based on the NOD2 biomarker, with stricturing in 17 of 30 (56.7%). In the low-risk group, 28 of 131 (21.4%) had stricturing behavior. Cox proportional hazards using the NOD2 risk groups demonstrated a hazard ratio (HR) of 2.092 (P = 2.4 × 10-5), between risk groups. Limiting analysis to patients diagnosed aged < 18-years improved performance (HR-3.164, P = 1 × 10-6). Models were modified to include disease location, such as terminal ileal (TI) disease or not. Inclusion of NOD2 risk groups added significant additional utility to prediction models. High-risk group pediatric patients presenting with TI disease had a HR of 4.89 (P = 2.3 × 10-5) compared with the low-risk group patients without TI disease. CONCLUSIONS A NOD2 genomic biomarker predicts stricturing risk, with prognostic power improved in pediatric-onset CD. Implementation into a clinical setting can help personalize management.
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Affiliation(s)
- James J Ashton
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK.,Department of Paediatric Gastroenterology, Southampton Children's Hospital, Southampton, UK
| | - Guo Cheng
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
| | - Imogen S Stafford
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK.,Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Melina Kellermann
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
| | - Eleanor G Seaby
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
| | - J R Fraser Cummings
- Department of Gastroenterology, University Hospital Southampton, Southampton, UK
| | - Tracy A F Coelho
- Department of Paediatric Gastroenterology, Southampton Children's Hospital, Southampton, UK
| | - Akshay Batra
- Department of Paediatric Gastroenterology, Southampton Children's Hospital, Southampton, UK
| | - Nadeem A Afzal
- Department of Paediatric Gastroenterology, Southampton Children's Hospital, Southampton, UK
| | - R Mark Beattie
- Department of Paediatric Gastroenterology, Southampton Children's Hospital, Southampton, UK
| | - Sarah Ennis
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
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Longitudinal multi-omics analysis identifies early blood-based predictors of anti-TNF therapy response in inflammatory bowel disease. Genome Med 2022; 14:110. [PMID: 36153599 PMCID: PMC9509553 DOI: 10.1186/s13073-022-01112-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 09/02/2022] [Indexed: 11/10/2022] Open
Abstract
Background and aims Treatment with tumor necrosis factor α (TNFα) antagonists in IBD patients suffers from primary non-response rates of up to 40%. Biomarkers for early prediction of therapy success are missing. We investigated the dynamics of gene expression and DNA methylation in blood samples of IBD patients treated with the TNF antagonist infliximab and analyzed the predictive potential regarding therapy outcome. Methods We performed a longitudinal, blood-based multi-omics study in two prospective IBD patient cohorts receiving first-time infliximab therapy (discovery: 14 patients, replication: 23 patients). Samples were collected at up to 7 time points (from baseline to 14 weeks after therapy induction). RNA-sequencing and genome-wide DNA methylation data were analyzed and correlated with clinical remission at week 14 as a primary endpoint. Results We found no consistent ex ante predictive signature across the two cohorts. Longitudinally upregulated transcripts in the non-remitter group comprised TH2- and eosinophil-related genes including ALOX15, FCER1A, and OLIG2. Network construction identified transcript modules that were coherently expressed at baseline and in non-remitting patients but were disrupted at early time points in remitting patients. These modules reflected processes such as interferon signaling, erythropoiesis, and platelet aggregation. DNA methylation analysis identified remission-specific temporal changes, which partially overlapped with transcriptomic signals. Machine learning approaches identified features from differentially expressed genes cis-linked to DNA methylation changes at week 2 as a robust predictor of therapy outcome at week 14, which was validated in a publicly available dataset of 20 infliximab-treated CD patients. Conclusions Integrative multi-omics analysis reveals early shifts of gene expression and DNA methylation as predictors for efficient response to anti-TNF treatment. Lack of such signatures might be used to identify patients with IBD unlikely to benefit from TNF antagonists at an early time point. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01112-z.
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48
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Bertani L. Treatment and Management of Chronic Inflammatory Bowel Diseases: Optimizing Present and Future Therapeutic Choices. J Clin Med 2022; 11:jcm11185267. [PMID: 36142914 PMCID: PMC9501929 DOI: 10.3390/jcm11185267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 08/31/2022] [Accepted: 09/03/2022] [Indexed: 11/16/2022] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic relapsing diseases of the gastrointestinal tract of unknown origin, resulting from an aberrant immune response to microbial and gut-specific antigens in genetically susceptible patients [...]
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Affiliation(s)
- Lorenzo Bertani
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy;
- Department of Surgery, Tuscany North-West ASL, Pontedera Hospital, 56025 Pontedera, Italy
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49
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Lin S, Chanchlani N, Carbery I, Janjua M, Nice R, McDonald TJ, Bewshea C, Kennedy NA, Ahmad T, Selinger CP, Goodhand JR. Understanding anti-TNF treatment failure: does serum triiodothyronine-to-thyroxine (T3/T4) ratio predict therapeutic outcome to anti-TNF therapies in biologic-naïve patients with active luminal Crohn's disease? Aliment Pharmacol Ther 2022; 56:783-793. [PMID: 35768996 PMCID: PMC9540440 DOI: 10.1111/apt.17089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/10/2022] [Accepted: 06/02/2022] [Indexed: 12/18/2022]
Abstract
BACKGROUND During illness, adaptations of the hypothalamic-pituitary-thyroid axis reduce energy expenditure, protein catabolism and modulate immune responses to promote survival. Lower serum free triiodothyronine-to-thyroxine (fT3/fT4) ratio has been linked to non-response to treatment in a range of diseases, including in biologic-treated patients with inflammatory bowel disease. AIM To assess whether baseline serum fT3/fT4 ratio predicted primary non-response (PNR) and non-remission to infliximab and adalimumab in patients with Crohn's disease METHODS: Thyroid function tests were undertaken in stored serum from biologic-naïve adult patients with active luminal Crohn's disease immediately prior to treatment with infliximab (427 originator; 122 biosimilar) or adalimumab (448) in the Personalised Anti-TNF Therapy in Crohn's Disease study (PANTS). RESULTS Baseline median [IQR] fT3/fT4 ratios were lower in women than men (0.30 [0.27-0.34] vs 0.32 [0.28-0.36], p < 0.001), in patients with more severe inflammatory disease, and in patients receiving corticosteroids (0.28 [0.25-0.33] vs. 0.32 [0.29-0.36], p < 0.001). Multivariable logistic regression analysis demonstrated that fT3/fT4 ratio was independently associated with PNR at week 14 (odds ratio [OR] 0.51, 95% confidence interval [CI] 0.31-0.85, p = 0.009), but not non-remission or changes in faecal calprotectin concentrations at week 54. The optimal threshold to determine PNR was 0.31 (area under the curve 0.57 [95% CI 0.54-0.61], sensitivity 0.62 [95% CI 0.41-0.74], and specificity 0.53 [95% CI 0.42-0.73]). CONCLUSIONS Lower baseline serum fT3/fT4 ratio was associated with female sex, corticosteroid use and disease activity. It predicted PNR to anti-TNF treatment at week 14, but not non-remission at week 54.
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Affiliation(s)
- Simeng Lin
- GastroenterologyRoyal Devon and Exeter NHS Foundation TrustExeterUK,Exeter Inflammatory Bowel Disease and Pharmacogenetics Research GroupUniversity of ExeterExeterUK
| | - Neil Chanchlani
- GastroenterologyRoyal Devon and Exeter NHS Foundation TrustExeterUK,Exeter Inflammatory Bowel Disease and Pharmacogenetics Research GroupUniversity of ExeterExeterUK
| | - Isabel Carbery
- Leeds Gastroenterology Institute, Leeds Teaching Hospitals NHS TrustLeedsUK,The Leeds Institute of Research at St James'University of LeedsLeedsUK
| | - Malik Janjua
- GastroenterologyRoyal Devon and Exeter NHS Foundation TrustExeterUK,Exeter Inflammatory Bowel Disease and Pharmacogenetics Research GroupUniversity of ExeterExeterUK
| | - Rachel Nice
- Biochemistry, Exeter Clinical Laboratory InternationalRoyal Devon and Exeter NHS Foundation TrustExeterUK
| | - Timothy J. McDonald
- Biochemistry, Exeter Clinical Laboratory InternationalRoyal Devon and Exeter NHS Foundation TrustExeterUK
| | - Claire Bewshea
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research GroupUniversity of ExeterExeterUK
| | - Nicholas A. Kennedy
- GastroenterologyRoyal Devon and Exeter NHS Foundation TrustExeterUK,Exeter Inflammatory Bowel Disease and Pharmacogenetics Research GroupUniversity of ExeterExeterUK
| | - Tariq Ahmad
- GastroenterologyRoyal Devon and Exeter NHS Foundation TrustExeterUK,Exeter Inflammatory Bowel Disease and Pharmacogenetics Research GroupUniversity of ExeterExeterUK
| | - Christian P. Selinger
- Leeds Gastroenterology Institute, Leeds Teaching Hospitals NHS TrustLeedsUK,The Leeds Institute of Research at St James'University of LeedsLeedsUK
| | - James R. Goodhand
- GastroenterologyRoyal Devon and Exeter NHS Foundation TrustExeterUK,Exeter Inflammatory Bowel Disease and Pharmacogenetics Research GroupUniversity of ExeterExeterUK
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50
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Noor NM, Sousa P, Paul S, Roblin X. Early Diagnosis, Early Stratification, and Early Intervention to Deliver Precision Medicine in IBD. Inflamm Bowel Dis 2022; 28:1254-1264. [PMID: 34480558 PMCID: PMC9340521 DOI: 10.1093/ibd/izab228] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Indexed: 12/15/2022]
Abstract
Despite huge advances in understanding the molecular basis of IBD, clinical management has continued to rely on a "trial and error" approach. In addition, a therapeutic ceiling has emerged whereby even the most effective interventions are only beneficial for approximately 30% of patients. Consequently, several tools have been developed to aid stratification and guide treatment-decisions. We review the potential application for many of these precision medicine approaches, which are now almost within reach. We highlight the importance of early action (and avoiding inaction) to ensure the best outcomes for patients and how combining early action with precision tools will likely ensure the right treatment is delivered at the right time and place for each individual person living with IBD. The lack of clinical impact to date from precision medicine, despite much hype and investment, should be tempered with the knowledge that clinical translation can take a long time, and many promising breakthroughs might be ready for clinical implementation in the near future. We discuss some of the remaining challenges and barriers to overcome for clinical adoption. We also highlight that early recognition, early diagnosis, early stratification, and early intervention go hand in hand with precision medicine tools. It is the combination of these approaches that offer the greatest opportunity to finally deliver on the promise of precision medicine in IBD.
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Affiliation(s)
- Nurulamin M Noor
- Department of Gastroenterology, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Trust, Cambridge, United Kingdom
- Medical Research Council Clinical Trials Unit, University College London, London, United Kingdom
| | - Paula Sousa
- Department of Gastroenterology, Viseu Unit, Tondela-Viseu Hospital Centre, 3504–509 Viseu, Portugal
| | - Stéphane Paul
- Faculty of Medicine of Saint-Etienne, Immunology Unit University Hospital of Saint-Etienne, CIC INSERM 1408, Saint-Etienne, France
| | - Xavier Roblin
- Department of Gastroenterology, University Hospital of Sain- Etienne, Saint-Etienne, France
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