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Xiao Y, Chen J, Li S, Zhang Q, Liu Y, Chen L, Sun Y, Gu M, Xie X, Nan F. Discovery of GPR84 Fluorogenic Probes Based on a Novel Antagonist for GPR84 Bioimaging. J Med Chem 2024; 67:10875-10890. [PMID: 38946306 DOI: 10.1021/acs.jmedchem.4c00359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
GPR84 is a promising therapeutic target and biomarker for a range of diseases. In this study, we reported the discovery of BINOL phosphate (BINOP) derivatives as GPR84 antagonists. By investigating the structure-activity relationship, we identified 15S as a novel GPR84 antagonist. 15S exhibits low nanomolar potency and high selectivity for GPR84, while its enantiomer 15R is less active. Next, we rationally designed and synthesized a series of GPR84 fluorogenic probes by conjugating Nile red and compound 15S. The leading hybrid, probe F8, not only retained GPR84 activity but also exhibited low nonspecific binding and a turn-on fluorescent signal in an apolar environment. F8 enabled visualization and detection of GPR84 in GPR84-overexpressing HEK293 cells and lipopolysaccharide-stimulated neutrophils. Furthermore, we demonstrated that F8 can detect upregulated GPR84 protein levels in mice models of inflammatory bowel disease and acute lung injury. Thus, compound F8 represents a promising tool for studying GPR84 functions.
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Affiliation(s)
- Yufeng Xiao
- State Key Laboratory of Drug Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Chen
- State Key Laboratory of Drug Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shaoxian Li
- State Key Laboratory of Drug Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qing Zhang
- State Key Laboratory of Drug Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai 264117, Shandong, China
| | - Yin Liu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Linhai Chen
- State Key Laboratory of Drug Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai 264117, Shandong, China
| | - Yadi Sun
- State Key Laboratory of Drug Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Min Gu
- State Key Laboratory of Drug Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xin Xie
- State Key Laboratory of Drug Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai 264117, Shandong, China
| | - Fajun Nan
- State Key Laboratory of Drug Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai 264117, Shandong, China
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Gao H, Peng K, Shi Y, Zhu S, Sun R, Xu C, Liu P, Pang Z, Zhu L, Chen W, Feng B, Wu H, Zhou G, Li M, Li J, Ding B, Liu Z. Development and validation of a novel criterion of histologic healing in ulcerative colitis defined by inflammatory cell enumeration in lamina propria mucosa: A multicenter retrospective cohort in China. Chin Med J (Engl) 2024; 137:1316-1323. [PMID: 38738696 PMCID: PMC11191007 DOI: 10.1097/cm9.0000000000003154] [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: 12/12/2023] [Indexed: 05/14/2024] Open
Abstract
BACKGROUND Histological healing is closely associated with improved long-term clinical outcomes and lowered relapses in patients with ulcerative colitis (UC). Here, we developed a novel diagnostic criterion for assessing histological healing in UC patients. METHODS We conducted a retrospective cohort study in UC patients, whose treatment was iteratively optimized to achieve mucosal healing at Shanghai Tenth People's Hospital of Tongji University from January 2017 to May 2022. We identified an inflammatory cell enumeration index (ICEI) for assessing histological healing based on the proportions of eosinophils, CD177 + neutrophils, and CD40L + T cells in the colonic lamina propria under high power field (HPF), and the outcomes (risks of symptomatic relapses) of achieving histological remission vs . persistent histological inflammation using Kaplan-Meier curves. Intrareader reliability and inter-reader reliability were evaluated by each reader. The relationships to the changes in the Nancy index and the Geboes score were also assessed for responsiveness. The ICEI was further validated in a new cohort of UC patients from other nine university hospitals. RESULTS We developed an ICEI for clinical diagnosis of histological healing, i.e., Y = 1.701X 1 + 0.758X 2 + 1.347X 3 - 7.745 (X 1 , X 2 , and X 3 represent the proportions of CD177 + neutrophils, eosinophils, and CD40L + T cells, respectively, in the colonic lamina propria under HPF). The receiver operating characteristics curve (ROC) analysis revealed that Y <-0.391 was the cutoff value for the diagnosis of histological healing and that an area under the curve (AUC) was 0.942 (95% confidence interval [CI]: 0.905-0.979) with a sensitivity of 92.5% and a specificity of 83.6% ( P <0.001). The intraclass correlation coefficient (ICC) for the intrareader reliability was 0.855 (95% CI: 0.781-0.909), and ICEI had good inter-reader reliability of 0.832 (95% CI: 0.748-0.894). During an 18-month follow-up, patients with histological healing had a substantially better outcome compared with those with unachieved histological healing ( P <0.001) using ICEI. During a 12-month follow-up from other nine hospitals, patients with histological healing also had a lower risk of relapse than patients with unachieved histological healing. CONCLUSIONS ICEI can be used to predict histological healing and identify patients with a risk of relapse 12 months and 18 months after clinical therapy. Therefore, ICEI provides a promising, simplified approach to monitor histological healing and to predict the prognosis of UC. REGISTRATION Chinese Clinical Trial Registry, No. ChiCTR2300077792.
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Affiliation(s)
- Han Gao
- Center for IBD Research and Department of Gastroenterology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai 200085, China
| | - Kangsheng Peng
- Center for IBD Research and Department of Gastroenterology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai 200085, China
| | - Yadi Shi
- Clinical Medicine, Sanquan College of Xinxiang Medical University, Xinxiang, Henan 453003, China
| | - Shenshen Zhu
- Center for IBD Research and Department of Gastroenterology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai 200085, China
| | - Ruicong Sun
- Center for IBD Research and Department of Gastroenterology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai 200085, China
| | - Chunjin Xu
- Department of Gastroenterology, The First People’s Hospital of Shangqiu City Affiliated to Xinxiang Medical University, Shangqiu, Henan 476100, China
| | - Ping Liu
- Department of Gastroenterology, Wuhu First People’s Hospital, Wuhu, Anhui 241000, China
| | - Zhi Pang
- Department of Gastroenterology, Suzhou Municipal Hospital Affiliated to Nanjing Medical University, Suzhou, Jiangsu 215008, China
| | - Lanxiang Zhu
- Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 251006, China
| | - Weichang Chen
- Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 251006, China
| | - Baisui Feng
- Department of Gastroenterology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450014, China
| | - Huili Wu
- Department of Gastroenterology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan 450000, China
| | - Guangxi Zhou
- Department of Gastroenterology, The Affiliated Hospital of Jining Medical College, Jining, Shandong 272004, China
| | - Mingsong Li
- Department of Gastroenterology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510140, China
| | - Junxiang Li
- Department of Gastroenterology, Dongfang Hospital of Beijing University of Chinese Medicine, Beijing 100078, China
| | - Baijing Ding
- Department of Gastroenterology, Wuhu First People’s Hospital, Wuhu, Anhui 241000, China
| | - Zhanju Liu
- Center for IBD Research and Department of Gastroenterology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai 200085, China
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Aktar R, Rondinelli S, Peiris M. GPR84 in physiology-Many functions in many tissues. Br J Pharmacol 2024; 181:1524-1535. [PMID: 37533166 DOI: 10.1111/bph.16206] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/20/2023] [Accepted: 07/17/2023] [Indexed: 08/04/2023] Open
Abstract
Members of the GPCR superfamily have a wide variety of physiological roles and are therefore valuable targets for developing effective medicines. However, within this superfamily are receptors that are less well characterized and remain orphans, including GPR84. This receptor is stimulated by ligands derived from dietary nutrients, specifically medium chain fatty acids (C9-14), and novel synthetic agonists. There are data demonstrating the role of GPR84 in inflammatory pathways, in addition to emerging data suggesting a key role for GPR84 as a nutrient-sensing GPCR involved in metabolism by sensing energy load via nutrient exposure and subsequent signalling leading to modulation of food intake. Exploring GPR84 pharmacology, its localization and what drives its expression has revealed multiple roles for this receptor. Here, we will reflect on these various roles of GRP84 demonstrated thus far, primarily by exploring data from pre-clinical and clinical studies in various physiological systems, with a specific focus on the gastrointestinal tract. LINKED ARTICLES: This article is part of a themed issue GPR84 Pharmacology. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v181.10/issuetoc.
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Affiliation(s)
- Rubina Aktar
- Centre for Neuroscience, Surgery and Trauma, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Silvia Rondinelli
- Centre for Neuroscience, Surgery and Trauma, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Madusha Peiris
- Centre for Neuroscience, Surgery and Trauma, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
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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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Kumar M, Murugesan S, Ibrahim N, Elawad M, Al Khodor S. Predictive biomarkers for anti-TNF alpha therapy in IBD patients. J Transl Med 2024; 22:284. [PMID: 38493113 PMCID: PMC10943853 DOI: 10.1186/s12967-024-05058-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/04/2024] [Indexed: 03/18/2024] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic gastrointestinal condition characterized by severe gut inflammation, commonly presenting as Crohn's disease, ulcerative colitis or categorized as IBD- unclassified. While various treatments have demonstrated efficacy in adult IBD patients, the advent of anti-TNF therapies has significantly revolutionized treatment outcomes and clinical management. These therapies have played a pivotal role in achieving clinical and endoscopic remission, promoting mucosal healing, averting disease progression, and diminishing the necessity for surgery. Nevertheless, not all patients exhibit positive responses to these therapies, and some may experience a loss of responsiveness over time. This review aims to present a comprehensive examination of predictive biomarkers for monitoring the therapeutic response to anti-TNF therapy in IBD patients. It will explore their limitations and clinical utilities, paving the way for a more personalized and effective therapeutic approach.
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Affiliation(s)
- Manoj Kumar
- Research Department, Sidra Medicine, Doha, Qatar
| | | | - Nazira Ibrahim
- Division of Gastroenterology, Hepatology and Nutrition, Sidra Medicine, Doha, Qatar
| | - Mamoun Elawad
- Division of Gastroenterology, Hepatology and Nutrition, Sidra Medicine, Doha, Qatar
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Wacker EM, Uellendahl-Werth F, Bej S, Wolkenhauer O, Vesterhus M, Lieb W, Franke A, Karlsen TH, Folseraas T, Ellinghaus D. Whole blood RNA sequencing identifies transcriptional differences between primary sclerosing cholangitis and ulcerative colitis. JHEP Rep 2024; 6:100988. [PMID: 38304234 PMCID: PMC10832281 DOI: 10.1016/j.jhepr.2023.100988] [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: 05/10/2023] [Revised: 11/10/2023] [Accepted: 12/06/2023] [Indexed: 02/03/2024] Open
Abstract
Background & Aims Genetic and microbiome studies across patients with primary sclerosing cholangitis (PSC) and ulcerative colitis (UC) have indicated that UC in PSC is a separate disease entity to primary UC, but expression studies for PSC are lacking. Methods We conducted whole blood RNA sequencing experiments for 495 patients with UC, 220 patients with PSC (including 177 with UC), and 320 healthy controls from Germany and Norway. Differential expression analyses, gene ontology and coexpression analyses and random forest machine learning were performed to identify genes, ontologies and transcriptional features that discriminate diagnoses. Results The blood transcriptome in UC and PSC is dominated by neutrophil activation genes (e.g. S100A12). In UC, but not in PSC (neither PSC alone nor patients with an additional diagnosis of UC [PSC/UC]), ribosomal, mitochondrial, and energy metabolism genes are upregulated in conjunction with antibody transcript expression (MZB1, IGJ). In PSC, there is an increase in modules related to apoptosis and expression of genes of interferon-I-related ontologies. Random forest analysis could poorly discriminate PSC alone from PSC/UC (AUROC 0.56), but could discriminate PSC, UC, and controls with high accuracy (AUROC UC vs. controls 0.95, PSC vs. controls 0.88, UC vs. PSC 0.986). The main coexpression modules relevant for distinguishing PSC, UC, and controls are enriched in neutrophil degranulation and antibody production genes. Conclusions Supported by machine learning results, PSC and UC appear to be separate entities on a molecular level, while PSC/UC and PSC are indistinguishable. Impact and implications Clinical and genetic studies suggest that the colitis-like symptoms in primary sclerosing cholangitis (PSC) represent a different disease entity from primary ulcerative colitis (UC). The present study supports this assumption with transcriptomic data from whole blood and describes notable differences in gene expression between primary UC and PSC, providing insights into the still unclear pathophysiology of both diseases. These findings are of interest to scientists seeking to decipher the molecular pathophysiology of both diseases and provide evidence that a redefinition of the PSC-UC phenotype should be considered. The study practically supports future molecular research by providing a large transcriptomic whole blood reference cohort.
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Affiliation(s)
- Eike Matthias Wacker
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | | | - Saptarshi Bej
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
- Indian Institute of Science Education and Research, Thiruvananthapuram, India
| | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
- Leibniz-Institute for Food Systems Biology at the Technical University Munich, Munich, Germany
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
| | - Mette Vesterhus
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway
- Department of Medicine, Haraldsplass Deaconess Hospital, Bergen, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Wolfgang Lieb
- Institute of Epidemiology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Tom Hemming Karlsen
- Research Institute for Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway
| | - Trine Folseraas
- Research Institute for Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
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Gerassy-Vainberg S, Starosvetsky E, Gaujoux R, Blatt A, Maimon N, Gorelik Y, Pressman S, Alpert A, Bar-Yoseph H, Dubovik T, Perets B, Katz A, Milman N, Segev M, Chowers Y, Shen-Orr SS. A personalized network framework reveals predictive axis of anti-TNF response across diseases. Cell Rep Med 2024; 5:101300. [PMID: 38118442 PMCID: PMC10829759 DOI: 10.1016/j.xcrm.2023.101300] [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: 02/21/2023] [Revised: 08/20/2023] [Accepted: 10/31/2023] [Indexed: 12/22/2023]
Abstract
Personalized treatment of complex diseases has been mostly predicated on biomarker identification of one drug-disease combination at a time. Here, we use a computational approach termed Disruption Networks to generate a data type, contextualized by cell-centered individual-level networks, that captures biology otherwise overlooked when performing standard statistics. This data type extends beyond the "feature level space", to the "relations space", by quantifying individual-level breaking or rewiring of cross-feature relations. Applying Disruption Networks to dissect high-dimensional blood data, we discover and validate that the RAC1-PAK1 axis is predictive of anti-TNF response in inflammatory bowel disease. Intermediate monocytes, which correlate with the inflammatory state, play a key role in the RAC1-PAK1 responses, supporting their modulation as a therapeutic target. This axis also predicts response in rheumatoid arthritis, validated in three public cohorts. Our findings support blood-based drug response diagnostics across immune-mediated diseases, implicating common mechanisms of non-response.
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Affiliation(s)
- Shiran Gerassy-Vainberg
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 32000, Israel; Department of Gastroenterology, Rambam Health Care Campus, Haifa 3109601, Israel
| | - Elina Starosvetsky
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Renaud Gaujoux
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 32000, Israel; CytoReason, Tel Aviv 67012, Israel
| | - Alexandra Blatt
- Department of Gastroenterology, Rambam Health Care Campus, Haifa 3109601, Israel
| | - Naama Maimon
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 32000, Israel; Department of Gastroenterology, Rambam Health Care Campus, Haifa 3109601, Israel
| | - Yuri Gorelik
- Department of Gastroenterology, Rambam Health Care Campus, Haifa 3109601, Israel
| | - Sigal Pressman
- Department of Gastroenterology, Rambam Health Care Campus, Haifa 3109601, Israel; Clinical Research Institute, Rambam Health Care Campus, Haifa 3109601, Israel
| | - Ayelet Alpert
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Haggai Bar-Yoseph
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 32000, Israel; Department of Gastroenterology, Rambam Health Care Campus, Haifa 3109601, Israel
| | - Tania Dubovik
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Benny Perets
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | | | - Neta Milman
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Meital Segev
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Yehuda Chowers
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 32000, Israel; Department of Gastroenterology, Rambam Health Care Campus, Haifa 3109601, Israel; Clinical Research Institute, Rambam Health Care Campus, Haifa 3109601, Israel.
| | - Shai S Shen-Orr
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 32000, Israel.
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Wang Z, Wang Y, Yan J, Wei Y, Zhang Y, Wang X, Leng X. Analysis of cuproptosis-related genes in Ulcerative colitis and immunological characterization based on machine learning. Front Med (Lausanne) 2023; 10:1115500. [PMID: 37529244 PMCID: PMC10389668 DOI: 10.3389/fmed.2023.1115500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 07/03/2023] [Indexed: 08/03/2023] Open
Abstract
Cuproptosis is a novel form of cell death, mediated by protein lipid acylation and highly associated with mitochondrial metabolism, which is regulated in the cell. Ulcerative colitis (UC) is a chronic inflammatory bowel disease that recurs frequently, and its incidence is increasing worldwide every year. Currently, a growing number of studies have shown that cuproptosis-related genes (CRGs) play a crucial role in the development and progression of a variety of tumors. However, the regulatory role of CRGs in UC has not been fully elucidated. Firstly, we identified differentially expressed genes in UC, Likewise, CRGs expression profiles and immunological profiles were evaluated. Using 75 UC samples, we typed UC based on the expression profiles of CRGs, followed by correlative immune cell infiltration analysis. Using the weighted gene co-expression network analysis (WGCNA) methodology, the cluster's differentially expressed genes (DEGs) were produced. Then, the performances of extreme gradient boosting models (XGB), support vector machine models (SVM), random forest models (RF), and generalized linear models (GLM) were constructed and predicted. Finally, the effectiveness of the best machine learning model was evaluated using five external datasets, receiver operating characteristic curve (ROC), the area under the curve of ROC (AUC), a calibration curve, a nomogram, and a decision curve analysis (DCA). A total of 13 CRGs were identified as significantly different in UC and control samples. Two subtypes were identified in UC based on CRGs expression profiles. Immune cell infiltration analysis of subtypes showed significant differences between immune cells of different subtypes. WGCNA results showed a total of 8 modules with significant differences between subtypes, with the turquoise module being the most specific. The machine learning results showed satisfactory performance of the XGB model (AUC = 0.981). Finally, the construction of the final 5-gene-based XGB model, validated by the calibration curve, nomogram, decision curve analysis, and five external datasets (GSE11223: AUC = 0.987; GSE38713: AUC = 0.815; GSE53306: AUC = 0.946; GSE94648: AUC = 0.809; GSE87466: AUC = 0.981), also proved to predict subtypes of UC with accuracy. Our research presents a trustworthy model that can predict the likelihood of developing UC and methodically outlines the complex relationship between CRGs and UC.
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Affiliation(s)
- Zhengyan Wang
- Changchun University of Chinese Medicine, Changchun, China
| | - Ying Wang
- The Affiliated Hospital of Changchun University of Chinese Medicine, Changchun, China
| | - Jing Yan
- Changchun University of Chinese Medicine, Changchun, China
| | - Yuchi Wei
- Changchun University of Chinese Medicine, Changchun, China
| | - Yinzhen Zhang
- Changchun University of Chinese Medicine, Changchun, China
| | - Xukai Wang
- Department of Orthopedics, The Affiliated Hospital of Changchun University of Chinese Medicine, Changchun, China
| | - Xiangyang Leng
- Changchun University of Chinese Medicine, Changchun, China
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9
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Chen Q, Bei S, Zhang Z, Wang X, Zhu Y. Identification of diagnostic biomarks and immune cell infiltration in ulcerative colitis. Sci Rep 2023; 13:6081. [PMID: 37055577 PMCID: PMC10102327 DOI: 10.1038/s41598-023-33388-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/12/2023] [Indexed: 04/15/2023] Open
Abstract
We aimed to explore diagnostic biomarks and immune cell infiltration characteristics in ulcerative colitis (UC). We used the dataset GSE38713 as the training set and dataset GSE94648 as the test set. A total of 402 differentially expressed genes (DEGs) were obtained from GSE38713. Annotating, visualizing, and integrating discovery of these differential genes was performed using Gene Ontology (GO), Kyoto Gene and Genome Encyclopedia Pathway (KEGG), and Gene Set Enrichment Analysis (GSEA). Protein-protein interaction networks were constructed from the STRING database, and protein functional modules were identified using the CytoHubba plugin of Cytoscape. Random forest and LASSO regression were used to screen for UC-related diagnostic markers, and ROC curves were generated to validate their diagnostic value. The composition of 22 immune cells was analyzed, and the immune cell infiltration in UC was analyzed using CIBERSORT. Results: Seven diagnostic markers associated with UC were identified: TLCD3A, KLF9, EFNA1, NAAA,WDR4, CKAP4, and CHRNA1. Immune cell infiltration assessment revealed that macrophages M1, activated dendritic cells, and neutrophil cells infiltrated relatively more compared to normal control samples. Our results suggest a new functional feature of UC and suggest potential biomarkers for UC through comprehensive analysis of integrated gene expression data.
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Affiliation(s)
- Qin Chen
- Department of Anorectal, Kunming Municipal Hospital of Traditional Chinese Medicine, The Third Affiliated Hospital of Yunnan University of Chinese Medicine, No. 25 Dongfeng East Road, Panlong District, Kunming, 650011, Yunnan Province, China.
| | - Shaosheng Bei
- Department of Anorectal, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhiyun Zhang
- Department of Anorectal, Kunming Municipal Hospital of Traditional Chinese Medicine, The Third Affiliated Hospital of Yunnan University of Chinese Medicine, No. 25 Dongfeng East Road, Panlong District, Kunming, 650011, Yunnan Province, China
| | - Xiaofeng Wang
- Department of Colorectal Surgery, Guang'an Men Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yunying Zhu
- Department of Anorectal, Kunming Municipal Hospital of Traditional Chinese Medicine, The Third Affiliated Hospital of Yunnan University of Chinese Medicine, No. 25 Dongfeng East Road, Panlong District, Kunming, 650011, Yunnan Province, China
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10
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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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11
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Dovrolis N, Filidou E, Tarapatzi G, Kokkotis G, Spathakis M, Kandilogiannakis L, Drygiannakis I, Valatas V, Arvanitidis K, Karakasiliotis I, Vradelis S, Manolopoulos VG, Paspaliaris V, Bamias G, Kolios G. Co-expression of fibrotic genes in inflammatory bowel disease; A localized event? Front Immunol 2022; 13:1058237. [PMID: 36632136 PMCID: PMC9826764 DOI: 10.3389/fimmu.2022.1058237] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/08/2022] [Indexed: 12/27/2022] Open
Abstract
Introduction Extracellular matrix turnover, a ubiquitous dynamic biological process, can be diverted to fibrosis. The latter can affect the intestine as a serious complication of Inflammatory Bowel Diseases (IBD) and is resistant to current pharmacological interventions. It embosses the need for out-of-the-box approaches to identify and target molecular mechanisms of fibrosis. Methods and results In this study, a novel mRNA sequencing dataset of 22 pairs of intestinal biopsies from the terminal ileum (TI) and the sigmoid of 7 patients with Crohn's disease, 6 with ulcerative colitis and 9 control individuals (CI) served as a validation cohort of a core fibrotic transcriptomic signature (FIBSig), This signature, which was identified in publicly available data (839 samples from patients and healthy individuals) of 5 fibrotic disorders affecting different organs (GI tract, lung, skin, liver, kidney), encompasses 241 genes and the functional pathways which derive from their interactome. These genes were used in further bioinformatics co-expression analyses to elucidate the site-specific molecular background of intestinal fibrosis highlighting their involvement, particularly in the terminal ileum. We also confirmed different transcriptomic profiles of the sigmoid and terminal ileum in our validation cohort. Combining the results of these analyses we highlight 21 core hub genes within a larger single co-expression module, highly enriched in the terminal ileum of CD patients. Further pathway analysis revealed known and novel inflammation-regulated, fibrogenic pathways operating in the TI, such as IL-13 signaling and pyroptosis, respectively. Discussion These findings provide a rationale for the increased incidence of fibrosis at the terminal ileum of CD patients and highlight operating pathways in intestinal fibrosis for future evaluation with mechanistic and translational studies.
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Affiliation(s)
- Nikolas Dovrolis
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece,Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece,Individualised Medicine & Pharmacological Research Solutions Center (IMPReS), Alexandroupolis, Greece,*Correspondence: George Kolios, ; Nikolas Dovrolis,
| | - Eirini Filidou
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece,Individualised Medicine & Pharmacological Research Solutions Center (IMPReS), Alexandroupolis, Greece
| | - Gesthimani Tarapatzi
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece,Individualised Medicine & Pharmacological Research Solutions Center (IMPReS), Alexandroupolis, Greece
| | - Georgios Kokkotis
- Gastrointestinal (GI) Unit, 3 Department of Internal Medicine, Sotiria Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Michail Spathakis
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece,Individualised Medicine & Pharmacological Research Solutions Center (IMPReS), Alexandroupolis, Greece
| | - Leonidas Kandilogiannakis
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece,Individualised Medicine & Pharmacological Research Solutions Center (IMPReS), Alexandroupolis, Greece
| | - Ioannis Drygiannakis
- Gastroenterology and Hepatology Research Laboratory, Medical School, University of Crete, Heraklion, Greece
| | - Vassilis Valatas
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece,Gastroenterology and Hepatology Research Laboratory, Medical School, University of Crete, Heraklion, Greece
| | - Konstantinos Arvanitidis
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece,Individualised Medicine & Pharmacological Research Solutions Center (IMPReS), Alexandroupolis, Greece
| | - Ioannis Karakasiliotis
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Stergios Vradelis
- Second Department of Internal Medicine, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
| | - Vangelis G. Manolopoulos
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece,Individualised Medicine & Pharmacological Research Solutions Center (IMPReS), Alexandroupolis, Greece
| | | | - Giorgos Bamias
- Gastrointestinal (GI) Unit, 3 Department of Internal Medicine, Sotiria Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - George Kolios
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece,Individualised Medicine & Pharmacological Research Solutions Center (IMPReS), Alexandroupolis, Greece,*Correspondence: George Kolios, ; Nikolas Dovrolis,
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12
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Li X, Yan L, Wang X, Ouyang C, Wang C, Chao J, Zhang J, Lian G. Predictive models for endoscopic disease activity in patients with ulcerative colitis: Practical machine learning-based modeling and interpretation. Front Med (Lausanne) 2022; 9:1043412. [PMID: 36619650 PMCID: PMC9810755 DOI: 10.3389/fmed.2022.1043412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Background Endoscopic disease activity monitoring is important for the long-term management of patients with ulcerative colitis (UC), there is currently no widely accepted non-invasive method that can effectively predict endoscopic disease activity. We aimed to develop and validate machine learning (ML) models for predicting it, which are desired to reduce the frequency of endoscopic examinations and related costs. Methods The patients with a diagnosis of UC in two hospitals from January 2016 to January 2021 were enrolled in this study. Thirty nine clinical and laboratory variables were collected. All patients were divided into four groups based on MES or UCEIS scores. Logistic regression (LR) and four ML algorithms were applied to construct the prediction models. The performance of models was evaluated in terms of accuracy, sensitivity, precision, F1 score, and area under the receiver-operating characteristic curve (AUC). Then Shapley additive explanations (SHAP) was applied to determine the importance of the selected variables and interpret the ML models. Results A total of 420 patients were entered into the study. Twenty four variables showed statistical differences among the groups. After synthetic minority oversampling technique (SMOTE) oversampling and RFE variables selection, the random forests (RF) model with 23 variables in MES and the extreme gradient boosting (XGBoost) model with 21 variables in USEIS, had the greatest discriminatory ability (AUC = 0.8192 in MES and 0.8006 in UCEIS in the test set). The results obtained from SHAP showed that albumin, rectal bleeding, and CRP/ALB contributed the most to the overall model. In addition, the above three variables had a more balanced contribution to each classification under the MES than the UCEIS according to the SHAP values. Conclusion This proof-of-concept study demonstrated that the ML model could serve as an effective non-invasive approach to predicting endoscopic disease activity for patients with UC. RF and XGBoost, which were first introduced into data-based endoscopic disease activity prediction, are suitable for the present prediction modeling.
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Affiliation(s)
- Xiaojun Li
- Department of Gastroenterology, The Second Xiangya Hospital of Central South University, Research Center of Digestive Disease, Central South University, Changsha, China
| | - Lamei Yan
- Department of Gastroenterology, The Second Xiangya Hospital of Central South University, Research Center of Digestive Disease, Central South University, Changsha, China,Department of Gastroenterology, The First Affiliated Hospital of Shaoyang College, Shaoyang, Hunan, China
| | - Xuehong Wang
- Department of Gastroenterology, The Second Xiangya Hospital of Central South University, Research Center of Digestive Disease, Central South University, Changsha, China
| | - Chunhui Ouyang
- Department of Gastroenterology, The Second Xiangya Hospital of Central South University, Research Center of Digestive Disease, Central South University, Changsha, China
| | - Chunlian Wang
- Department of Gastroenterology, The Second Xiangya Hospital of Central South University, Research Center of Digestive Disease, Central South University, Changsha, China
| | - Jun Chao
- Department of Gastroenterology, The Second Xiangya Hospital of Central South University, Research Center of Digestive Disease, Central South University, Changsha, China,Hunan Aicortech Intelligent Research Institute Co., Changsha, Hunan, China
| | - Jie Zhang
- Department of Gastroenterology, The Second Xiangya Hospital of Central South University, Research Center of Digestive Disease, Central South University, Changsha, China,*Correspondence: Jie Zhang,
| | - Guanghui Lian
- Department of Gastroenterology, Xiangya Hospital of Central South University, Changsha, Hunan, China,Guanghui Lian,
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13
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Välikangas T, Junttila S, Rytkönen KT, Kukkonen-Macchi A, Suomi T, Elo LL. COVID-19-specific transcriptomic signature detectable in blood across multiple cohorts. Front Genet 2022; 13:929887. [PMID: 35991542 PMCID: PMC9388772 DOI: 10.3389/fgene.2022.929887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/27/2022] [Indexed: 01/08/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is spreading across the world despite vast global vaccination efforts. Consequently, many studies have looked for potential human host factors and immune mechanisms associated with the disease. However, most studies have focused on comparing COVID-19 patients to healthy controls, while fewer have elucidated the specific host factors distinguishing COVID-19 from other infections. To discover genes specifically related to COVID-19, we reanalyzed transcriptome data from nine independent cohort studies, covering multiple infections, including COVID-19, influenza, seasonal coronaviruses, and bacterial pneumonia. The identified COVID-19-specific signature consisted of 149 genes, involving many signals previously associated with the disease, such as induction of a strong immunoglobulin response and hemostasis, as well as dysregulation of cell cycle-related processes. Additionally, potential new gene candidates related to COVID-19 were discovered. To facilitate exploration of the signature with respect to disease severity, disease progression, and different cell types, we also offer an online tool for easy visualization of the selected genes across multiple datasets at both bulk and single-cell levels.
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Affiliation(s)
- Tommi Välikangas
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Sini Junttila
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Kalle T. Rytkönen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Anu Kukkonen-Macchi
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Tomi Suomi
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- *Correspondence: Tomi Suomi, ; Laura L. Elo,
| | - Laura L. Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
- *Correspondence: Tomi Suomi, ; Laura L. Elo,
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14
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Cao P, Yang M, Chang C, Wu H, Lu Q. Germinal Center-Related G Protein-Coupled Receptors in Antibody-Mediated Autoimmune Skin Diseases: from Basic Research to Clinical Trials. Clin Rev Allergy Immunol 2022; 63:357-370. [PMID: 35674978 DOI: 10.1007/s12016-022-08936-y] [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] [Accepted: 03/23/2022] [Indexed: 11/30/2022]
Abstract
Germinal center (GC) reaction greatly contributes to the humoral immune response, which begins in lymph nodes or other secondary lymphoid organs after follicular B cells are activated by T-dependent antigens. The GCs then serve as a platform for follicular B cells to complete clonal expansion and somatic hypermutation and then interact with follicular dendritic cells (FDC) and follicular helper T cells (Tfh). Through the interaction between the immune cells, significant processes of the humoral immune response are accomplished, such as antibody affinity maturation, class switching, and production of memory B cells and plasma cells. Cell positioning during the GC reaction is mainly mediated by the chemokine receptors and lipid receptors, which both belong to G protein-coupled receptors (GPCRs) family. There are some orphan GPCRs whose endogenous ligands are unclear yet contribute to the regulation of GC reaction as well. This review will give an introduction on the ligands and functions of two types of GC-relating GPCRs-chemokine receptors like CXCR4 and CXCR5, as well as emerging de-orphanized GPCRs like GPR183, GPR174, and P2RY8. The roles these GPCRs play in several antibody-mediated autoimmune skin diseases will be also discussed, including systemic lupus erythematosus (SLE), pemphigus, scleroderma, and dermatomyositis. Besides, GPCRs are excellent drug targets due to the unique structure and vital functions. Therefore, this review is aimed at providing readers with a focused knowledge about the role that GPCRs play in GC reaction, as well as in provoking the development of GPCR-targeting agents for immune-mediated diseases besides autoimmune diseases.
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Affiliation(s)
- Pengpeng Cao
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Ming Yang
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Christopher Chang
- Division of Pediatric Immunology and Allergy, Joe DiMaggio Children's Hospital, Hollywood, FL, 33021, USA.,Division of Rheumatology, Allergy and Clinical Immunology, University of California Davis, Davis, CA, 95616, USA
| | - Haijing Wu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China.
| | - Qianjin Lu
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, 12 Jiangwangmiao Street, Nanjing, 210042, China. .,Key Laboratory of Basic and Translational Research On Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China. .,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China. .,Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, China.
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15
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Elfiky AMI, Ghiboub M, Li Yim AYF, Hageman IL, Verhoeff J, de Krijger M, van Hamersveld PHP, Welting O, Admiraal I, Rahman S, Garcia-Vallejo JJ, Wildenberg ME, Tomlinson L, Gregory R, Rioja I, Prinjha RK, Furze RC, Lewis HD, Mander PK, Heinsbroek SEM, Bell MJ, de Jonge WJ. Carboxylesterase-1 Assisted Targeting of HDAC Inhibitors to Mononuclear Myeloid Cells in Inflammatory Bowel Disease. J Crohns Colitis 2022; 16:668-681. [PMID: 34633041 PMCID: PMC9089418 DOI: 10.1093/ecco-jcc/jjab176] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND AND AIMS Histone deacetylase inhibitors [HDACi] exert potent anti-inflammatory effects. Because of the ubiquitous expression of HDACs, clinical utility of HDACi is limited by off-target effects. Esterase-sensitive motif [ESM] technology aims to deliver ESM-conjugated compounds to human mononuclear myeloid cells, based on their expression of carboxylesterase 1 [CES1]. This study aims to investigate utility of an ESM-tagged HDACi in inflammatory bowel disease [IBD]. METHODS CES1 expression was assessed in human blood, in vitro differentiated macrophage and dendritic cells, and Crohn's disease [CD] colon mucosa, by mass cytometry, quantitative polymerase chain reaction [PCR], and immunofluorescence staining, respectively. ESM-HDAC528 intracellular retention was evaluated by mass spectrometry. Clinical efficacy of ESM-HDAC528 was tested in dextran sulphate sodium [DSS]-induced colitis and T cell transfer colitis models using transgenic mice expressing human CES1 under the CD68 promoter. RESULTS CES1 mRNA was highly expressed in human blood CD14+ monocytes, in vitro differentiated and lipopolysaccharide [LPS]-stimulated macrophages, and dendritic cells. Specific hydrolysis and intracellular retention of ESM-HDAC528 in CES1+ cells was demonstrated. ESM-HDAC528 inhibited LPS-stimulated IL-6 and TNF-α production 1000 times more potently than its control, HDAC800, in CES1high monocytes. In healthy donor peripheral blood, CES1 expression was significantly higher in CD14++CD16- monocytes compared with CD14+CD16++ monocytes. In CD-inflamed colon, a higher number of mucosal CD68+ macrophages expressed CES1 compared with non-inflamed mucosa. In vivo, ESM-HDAC528 reduced monocyte differentiation in the colon and significantly improved colitis in a T cell transfer model, while having limited potential in ameliorating DSS-induced colitis. CONCLUSIONS We demonstrate that monocytes and inflammatory macrophages specifically express CES1, and can be preferentially targeted by ESM-HDAC528 to achieve therapeutic benefit in IBD.
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Affiliation(s)
- Ahmed M I Elfiky
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology & Metabolism, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Immunology Research Unit, GSK Medicines Research Centre, Stevenage, UK
| | - Mohammed Ghiboub
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology & Metabolism, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Immunology Research Unit, GSK Medicines Research Centre, Stevenage, UK
| | - Andrew Y F Li Yim
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology & Metabolism, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Immunology Research Unit, GSK Medicines Research Centre, Stevenage, UK
- Department of Clinical Genetics, Amsterdam Reproduction & Development, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Ishtu L Hageman
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology & Metabolism, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Jan Verhoeff
- Department of Molecular Cell Biology & Immunology, Amsterdam Infection & Immunity Institute and Cancer Center Amsterdam, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Manon de Krijger
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology & Metabolism, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Patricia H P van Hamersveld
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology & Metabolism, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Olaf Welting
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology & Metabolism, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Iris Admiraal
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology & Metabolism, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Shafaque Rahman
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology & Metabolism, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Juan J Garcia-Vallejo
- Department of Molecular Cell Biology & Immunology, Amsterdam Infection & Immunity Institute and Cancer Center Amsterdam, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Manon E Wildenberg
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology & Metabolism, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Laura Tomlinson
- Discovery DMPK, IVIVT, GSK Medicines Research Centre, Stevenage, UK
| | - Richard Gregory
- Discovery DMPK, IVIVT, GSK Medicines Research Centre, Stevenage, UK
| | - Inmaculada Rioja
- Immunology Research Unit, GSK Medicines Research Centre, Stevenage, UK
| | - Rab K Prinjha
- Immunology Research Unit, GSK Medicines Research Centre, Stevenage, UK
| | - Rebecca C Furze
- Immunology Research Unit, GSK Medicines Research Centre, Stevenage, UK
| | - Huw D Lewis
- Immunology Research Unit, GSK Medicines Research Centre, Stevenage, UK
| | | | - Sigrid E M Heinsbroek
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology & Metabolism, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Matthew J Bell
- Immunology Research Unit, GSK Medicines Research Centre, Stevenage, UK
| | - Wouter J de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology & Metabolism, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Department of Surgery, University of Bonn, Bonn, Germany
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16
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Fu X, Wei S, Wang T, Fan H, Zhang Y, Costa CD, Brandner S, Yang G, Pan Y, He Y, Li N. Research Status of the Orphan G Protein Coupled Receptor 158 and Future Perspectives. Cells 2022; 11:cells11081334. [PMID: 35456013 PMCID: PMC9027133 DOI: 10.3390/cells11081334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/10/2022] [Accepted: 04/11/2022] [Indexed: 02/01/2023] Open
Abstract
G-protein-coupled receptors (GPCRs) remain one of the most successful targets for therapeutic drugs approved by the US Food and Drug Administration (FDA). Many novel orphan GPCRs have been identified by human genome sequencing and considered as putative targets for refractory diseases. Of note, a series of studies have been carried out involving GPCR 158 (or GPR158) since its identification in 2005, predominantly focusing on the characterization of its roles in the progression of cancer and mental illness. However, advances towards an in-depth understanding of the biological mechanism(s) involved for clinical application of GPR158 are lacking. In this paper, we clarify the origin of the GPR158 evolution in different species and summarize the relationship between GPR158 and different diseases towards potential drug target identification, through an analysis of the sequences and substructures of GPR158. Further, we discuss how recent studies set about unraveling the fundamental features and principles, followed by future perspectives and thoughts, which may lead to prospective therapies involving GPR158.
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Affiliation(s)
- Xianan Fu
- Tomas Lindhal Nobel Laureate Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University (SYSU), No.628, Zhenyuan Rd., Guangming Dist., Shenzhen 518107, China; (X.F.); (S.W.); (T.W.); (H.F.); (Y.Z.); (Y.P.)
| | - Shoupeng Wei
- Tomas Lindhal Nobel Laureate Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University (SYSU), No.628, Zhenyuan Rd., Guangming Dist., Shenzhen 518107, China; (X.F.); (S.W.); (T.W.); (H.F.); (Y.Z.); (Y.P.)
| | - Tao Wang
- Tomas Lindhal Nobel Laureate Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University (SYSU), No.628, Zhenyuan Rd., Guangming Dist., Shenzhen 518107, China; (X.F.); (S.W.); (T.W.); (H.F.); (Y.Z.); (Y.P.)
| | - Hengxin Fan
- Tomas Lindhal Nobel Laureate Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University (SYSU), No.628, Zhenyuan Rd., Guangming Dist., Shenzhen 518107, China; (X.F.); (S.W.); (T.W.); (H.F.); (Y.Z.); (Y.P.)
| | - Ying Zhang
- Tomas Lindhal Nobel Laureate Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University (SYSU), No.628, Zhenyuan Rd., Guangming Dist., Shenzhen 518107, China; (X.F.); (S.W.); (T.W.); (H.F.); (Y.Z.); (Y.P.)
| | - Clive Da Costa
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK;
| | - Sebastian Brandner
- Department of Neurodegenerative Disease, Institute of Neurology, University College London, Queen Square, London WC1N 3BG, UK;
| | - Guang Yang
- Department of Burn and Plastic Surgery, Institute of Translational Medicine, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen 518039, China;
| | - Yihang Pan
- Tomas Lindhal Nobel Laureate Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University (SYSU), No.628, Zhenyuan Rd., Guangming Dist., Shenzhen 518107, China; (X.F.); (S.W.); (T.W.); (H.F.); (Y.Z.); (Y.P.)
| | - Yulong He
- Tomas Lindhal Nobel Laureate Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University (SYSU), No.628, Zhenyuan Rd., Guangming Dist., Shenzhen 518107, China; (X.F.); (S.W.); (T.W.); (H.F.); (Y.Z.); (Y.P.)
- Center for Digestive Disease, The Seventh Affiliated Hospital of Sun Yat-sen University (SYSU), No.628, Zhenyuan Rd., Guangming Dist., Shenzhen 518107, China
- Correspondence: (Y.H.); (N.L.)
| | - Ningning Li
- Tomas Lindhal Nobel Laureate Laboratory, The Seventh Affiliated Hospital of Sun Yat-sen University (SYSU), No.628, Zhenyuan Rd., Guangming Dist., Shenzhen 518107, China; (X.F.); (S.W.); (T.W.); (H.F.); (Y.Z.); (Y.P.)
- China-UK Institute for Frontier Science, Shenzhen 518107, China
- Correspondence: (Y.H.); (N.L.)
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17
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Chen LH, Zhang Q, Xiao YF, Fang YC, Xie X, Nan FJ. Phosphodiesters as GPR84 Antagonists for the Treatment of Ulcerative Colitis. J Med Chem 2022; 65:3991-4006. [PMID: 35195005 DOI: 10.1021/acs.jmedchem.1c01813] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
GPR84 is a proinflammatory G protein-coupled receptor associated with several inflammatory and fibrotic diseases. GPR84 antagonists have been evaluated in clinical trials to treat ulcerative colitis, idiopathic pulmonary fibrosis, and nonalcoholic steatohepatitis. However, the variety of potent and selective GPR84 antagonists is still limited. Through high-throughput screening, a novel phosphodiester compound hit 1 was identified as a GPR84 antagonist. The subsequent structural optimization led to the identification of compound 33 with improved potency in the calcium mobilization assay and the ability to inhibit the chemotaxis of neutrophils and macrophages upon GPR84 activation. In a DSS-induced mouse model of ulcerative colitis, compound 33 significantly alleviated colitis symptoms and reduced the disease activity index score at oral doses of 25 mg/kg qd, with an efficacy similar to that of positive control 5-aminosalicylic acid (200 mg/kg, qd, po), suggesting that compound 33 is a promising candidate for further drug development.
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Affiliation(s)
- Lin-Hai Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Qing Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,CAS Key Laboratory of Receptor Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Yu-Feng Xiao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - You-Chen Fang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,CAS Key Laboratory of Receptor Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xin Xie
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,CAS Key Laboratory of Receptor Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Fa-Jun Nan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.,Yantai Institute of Materia Medica, Shandong 264000, China
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18
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Kou F, Cheng Y, Shi L, Liu J, Liu Y, Shi R, Peng G, Li J. LCN2 as a Potential Diagnostic Biomarker for Ulcerative Colitis-Associated Carcinogenesis Related to Disease Duration. Front Oncol 2022; 11:793760. [PMID: 35111677 PMCID: PMC8801604 DOI: 10.3389/fonc.2021.793760] [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] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/20/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Patients with long-duration ulcerative colitis (UC) had a higher risk of developing ulcerative colitis-associated carcinogenesis (UCAC) when compared to those with short-duration UC. This study aimed to discover the biomarker for cancer surveillance related to disease duration. METHODS The microarrays were divided into short-duration (<10 years) UC, long-duration (≥10 years) UC, UCAC, and normal groups in the Gene Expression Omnibus (GEO) datasets. Differentially expressed genes (DEGs) of GEO and the hub genes of the selected weighted gene co-expression network analysis (WGCNA) were intersected to obtain the overlapping genes. Among these genes, the key gene was identified by using the protein-protein interaction (PPI) network, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, the cytoHubba of Cytoscape, and the expression levels. Also, immunofluorescence of human colonic mucosa and animal experiment were used to validate the expression trend of the key gene in the progress of UC developing into UCAC. RESULTS Lipocalin-2 (LCN2) was more relevant with disease duration of UC and significantly negatively correlated with the risk of UCAC. The expression level of LCN2 in short-duration UC was higher than that of long-duration UC (P < 0.01), long-duration UC was higher than that of UCAC (P = 0.001), and UC and UCAC were all higher than that of the normal (P < 0.001). We then discovered that the expression trend of LCN2 in blood and stool samples was consistent with that in colorectal mucosa. CONCLUSION The research indicates that LCN2 could be a novel biomarker to evaluate cancer surveillance related to disease duration of developing UC into UCAC. Compared with that of blood samples, stool detection of LCN2 may have more advantages for diagnosis value of early stage of UCAC as a complement to colonoscopy surveillance.
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Affiliation(s)
- Fushun Kou
- Graduate School, Beijing University of Chinese Medicine, Beijing, China
- Gastroenterology Department, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Yuan Cheng
- Graduate School, Beijing University of Chinese Medicine, Beijing, China
- Gastroenterology Department, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Lei Shi
- Gastroenterology Department, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Jiajing Liu
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Yuyue Liu
- Gastroenterology Department, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Rui Shi
- Gastroenterology Department, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Guiying Peng
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Junxiang Li
- Gastroenterology Department, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
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19
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Jacobsen GE, Fernández I, Quintero MA, Santander AM, Pignac-Kobinger J, Damas OM, Deshpande AR, Kerman DH, Ban Y, Gao Z, Silva TC, Wang L, Beecham AH, McCauley JL, Burgueño JF, Abreu MT. Lamina Propria Phagocyte Profiling Reveals Targetable Signaling Pathways in Refractory Inflammatory Bowel Disease. GASTRO HEP ADVANCES 2022; 1:380-392. [PMID: 36061955 PMCID: PMC9438737 DOI: 10.1016/j.gastha.2022.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Gillian E. Jacobsen
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, Florida
- Division of Gastroenterology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida
- Medical Scientist Training Program, Miller School of Medicine, University of Miami, Miami, Florida
| | - Irina Fernández
- Division of Gastroenterology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida
| | - Maria A. Quintero
- Division of Gastroenterology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida
| | - Ana M. Santander
- Division of Gastroenterology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida
| | - Judith Pignac-Kobinger
- Division of Gastroenterology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida
| | - Oriana M. Damas
- Division of Gastroenterology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida
| | - Amar R. Deshpande
- Division of Gastroenterology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida
| | - David H. Kerman
- Division of Gastroenterology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida
| | - Yuguang Ban
- Biostatistics and Bioinformatics Shared Resource, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - Zhen Gao
- Biostatistics and Bioinformatics Shared Resource, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - Tiago C. Silva
- Division of Biostatistics, Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, Florida
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, Florida
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida
| | - Ashley H. Beecham
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida
| | - Jacob L. McCauley
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida
| | - Juan F. Burgueño
- Division of Gastroenterology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida
| | - Maria T. Abreu
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, Florida
- Division of Gastroenterology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida
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20
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Lu J, Wang Z, Maimaiti M, Hui W, Abudourexiti A, Gao F. Identification of diagnostic signatures in ulcerative colitis patients via bioinformatic analysis integrated with machine learning. Hum Cell 2022; 35:179-188. [PMID: 34731452 DOI: 10.1007/s13577-021-00641-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/28/2021] [Indexed: 02/07/2023]
Abstract
Ulcerative colitis (UC) is an immune-related disorder with enhanced prevalence globally. Early diagnosis is critical for the effective treatment of UC. However, it still lacks specific diagnostic signatures. The aim of our study was to explore efficient signatures and construct the diagnostic model for UC. Microarray data of GSE87473 and GSE48634, which were obtained from tissue biopsy samples, were downloaded from the Gene Expression Omnibus (GEO), and differently expressed genes (DEGs), GO, and KEGG analyses were performed. We constructed the PPI network via STRING database. The immune infiltration of the samples was evaluated using CIBERSORT methods combined with the LM22 feature matrix. The logistic regression model was constructed, with the expression of selected genes as the predictor variable, and the UC occurrence as the responsive variable. As a result, a total of 126 DEGs between the UC patients and normal counterparts were identified. The GO and KEGG analysis revealed that multiple biological processes, such as antimicrobial humoral immune response mediated by antimicrobial peptide and IL-17 signaling pathway, were enriched. The infiltration of eight immune cell types (B cells naive, Dendritic.cells.activated, Macrophages.M0, Macrophages.M2, Mast.cells.resting, Neutrophils, Plasma.cells, and T.cells.follicular.helper) was significantly different between patients with UC and normal counterparts. The top 50 most significant DEGs were selected for the construction of the PPI network. The average AUC of the logistic regression model in the fivefold cross-validation was 0.8497 in the training set, GSE87473. The AUC of another independent verification set of GSE48634 from the GEO database was 0.7208. In conclusion, we identified potential hub genes, including REG3A, REG1A, DEFA6, REG1B, and DEFA5, which might be significantly associated with UC progression. The logistic regression model based on the five genes could reliably diagnose UC patients.
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Affiliation(s)
- Jiajie Lu
- Xinjiang Medical University, Urumqi, 830001, Xinjiang Uygur Autonomous Region, China
| | - Zhiyuan Wang
- Department of Gastroenterology, People's Hospital of Xinjiang Uygur Autonomous Region, No. 91, Tianchi Road, Urumqi, 830001, Xinjiang Uygur Autonomous Region, China
| | - Munila Maimaiti
- Department of Gastroenterology, People's Hospital of Xinjiang Uygur Autonomous Region, No. 91, Tianchi Road, Urumqi, 830001, Xinjiang Uygur Autonomous Region, China
| | - Wenjia Hui
- Department of Gastroenterology, People's Hospital of Xinjiang Uygur Autonomous Region, No. 91, Tianchi Road, Urumqi, 830001, Xinjiang Uygur Autonomous Region, China
| | - Adilai Abudourexiti
- Department of Gastroenterology, People's Hospital of Xinjiang Uygur Autonomous Region, No. 91, Tianchi Road, Urumqi, 830001, Xinjiang Uygur Autonomous Region, China
| | - Feng Gao
- Department of Gastroenterology, People's Hospital of Xinjiang Uygur Autonomous Region, No. 91, Tianchi Road, Urumqi, 830001, Xinjiang Uygur Autonomous Region, China.
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21
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Caballol B, Gudiño V, Panes J, Salas A. Ulcerative colitis: shedding light on emerging agents and strategies in preclinical and early clinical development. Expert Opin Investig Drugs 2021; 30:931-946. [PMID: 34365869 DOI: 10.1080/13543784.2021.1965122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Ulcerative colitis (UC) is an inflammatory disease of the large intestine. Progress in preclinical therapeutic target discovery and clinical trial design has resulted in the approval of new therapies. Nonetheless, remission rates remain below 30% thus underlining the need for novel, more effective therapies. AREAS COVERED This paper reviews current experimental techniques available for drug testing in intestinal inflammation and examines new therapies in clinical development for the treatment of UC. The authors searched the literature for 'ulcerative colitis' AND 'preclinical' OR 'drug target/drug name' (i.e. infliximab, vedolizumab, IL-12, IL-23, JAK, etc.). Studies that included preclinical in vivo or in vitro experiments are discussed. The clinicaltrial.gov site was searched for 'ulcerative colitis' AND 'Recruiting' OR 'Active, not recruiting' AND 'Interventional (Clinical Trial)' AND 'early phase 1' OR 'phase 1' OR 'phase 2' OR 'phase 3.' EXPERT OPINION Using in vivo, ex vivo, and/or in vitro models could increase the success rates of drugs moving to clinical trials, and hence increase the efficiency of this costly process. Selective JAK1 inhibitors, S1P modulators, and anti-p19 antibodies are the most promising options to improve treatment effectiveness. The development of drugs with gut-restricted exposure may provide increased efficacy and an improved safety.
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Affiliation(s)
- Berta Caballol
- Inflammatory Bowel Disease Unit, Department of Gastroenterology, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigaciones Biomédicas en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Victoria Gudiño
- Inflammatory Bowel Disease Unit, Department of Gastroenterology, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigaciones Biomédicas en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Julian Panes
- Inflammatory Bowel Disease Unit, Department of Gastroenterology, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigaciones Biomédicas en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Azucena Salas
- Inflammatory Bowel Disease Unit, Department of Gastroenterology, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigaciones Biomédicas en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
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22
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Wang J, Lv M, He L, Wang X, Lan Y, Chen J, Chen M, Zhang C, Tang R, Zhou D, Deng X, Li J, Guo T, Price M, Yue B, Fan Z. Transcriptomic landscape of persistent diarrhoea in rhesus macaques and comparison with humans and mouse models with inflammatory bowel disease. Gene 2021; 800:145837. [PMID: 34274469 DOI: 10.1016/j.gene.2021.145837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 05/26/2021] [Accepted: 07/13/2021] [Indexed: 12/19/2022]
Abstract
Diarrhoea is a widespread disease in captive rhesus macaques (Macaca mulatta) and a small proportion of individuals may experience persistent diarrhoea. Persistent diarrhoea can lead to a compromised immune system, intestinal inflammation and malnutrition. We analyzed the blood transcriptomes of 10 persistent diarrhoeal and 12 healthy rhesus macaques to investigate the gene expression differences between the two groups. We identified 330 DEGs between persistent diarrhoeal and healthy rhesus macaques. The 211 up-regulated DEGs in the diarrhoeal group were mainly enriched in immune-related and interleukin-related categories. Among them, three interleukin (IL) 18 related DEGs (IL18, IL18R1, and IL18BP) played important roles in actively regulating pro-inflammatory responses. Interestingly, the up- and down-regulated DEGs were both enriched in the same immune-related categories. Thus, we applied a new method to examine the distribution of DEGs in all child categories. We found that interleukin and T cell related categories were mainly occupied by up-regulated DEGs, while immunoglobulin production and B cell related categories were enriched by down-regulated DEGs. We also compared rhesus macaque DEGs with the DEGs of inflammatory bowel disease (IBD) humans and IBD mouse models and found that 30-40% of macaque DEGs were shared with IBD humans and mouse models. In conclusion, our results showed that there were significant immune differences between persistent diarrhoeal rhesus macaques and healthy macaques, which was similar to the expression differences in IBD patients and mouse models.
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Affiliation(s)
- Jiao Wang
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Mingyi Lv
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Lewei He
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Xinqi Wang
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Yue Lan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China
| | - Jieyun Chen
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Minghui Chen
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Chunhui Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China
| | - Ruixiang Tang
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Dan Zhou
- The First People's Hospital of Neijiang, Neijiang 641000, Sichuan, China
| | - Xiaoyang Deng
- Lasa Sunshine Maternity Hospital, Lasa 850000, Xizang, China
| | - Jing Li
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Tao Guo
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Megan Price
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China
| | - Zhenxin Fan
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China.
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23
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Aschenbrenner D, Quaranta M, Banerjee S, Ilott N, Jansen J, Steere B, Chen YH, Ho S, Cox K, Arancibia-Cárcamo CV, Coles M, Gaffney E, Travis SP, Denson L, Kugathasan S, Schmitz J, Powrie F, Sansom SN, Uhlig HH. Deconvolution of monocyte responses in inflammatory bowel disease reveals an IL-1 cytokine network that regulates IL-23 in genetic and acquired IL-10 resistance. Gut 2021; 70:1023-1036. [PMID: 33037057 PMCID: PMC8108288 DOI: 10.1136/gutjnl-2020-321731] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/16/2020] [Accepted: 08/28/2020] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Dysregulated immune responses are the cause of IBDs. Studies in mice and humans suggest a central role of interleukin (IL)-23-producing mononuclear phagocytes in disease pathogenesis. Mechanistic insights into the regulation of IL-23 are prerequisite for selective IL-23 targeting therapies as part of personalised medicine. DESIGN We performed transcriptomic analysis to investigate IL-23 expression in human mononuclear phagocytes and peripheral blood mononuclear cells. We investigated the regulation of IL-23 expression and used single-cell RNA sequencing to derive a transcriptomic signature of hyperinflammatory monocytes. Using gene network correlation analysis, we deconvolved this signature into components associated with homeostasis and inflammation in patient biopsy samples. RESULTS We characterised monocyte subsets of healthy individuals and patients with IBD that express IL-23. We identified autosensing and paracrine sensing of IL-1α/IL-1β and IL-10 as key cytokines that control IL-23-producing monocytes. Whereas Mendelian genetic defects in IL-10 receptor signalling induced IL-23 secretion after lipopolysaccharide stimulation, whole bacteria exposure induced IL-23 production in controls via acquired IL-10 signalling resistance. We found a transcriptional signature of IL-23-producing inflammatory monocytes that predicted both disease and resistance to antitumour necrosis factor (TNF) therapy and differentiated that from an IL-23-associated lymphocyte differentiation signature that was present in homeostasis and in disease. CONCLUSION Our work identifies IL-10 and IL-1 as critical regulators of monocyte IL-23 production. We differentiate homeostatic IL-23 production from hyperinflammation-associated IL-23 production in patients with severe ulcerating active Crohn's disease and anti-TNF treatment non-responsiveness. Altogether, we identify subgroups of patients with IBD that might benefit from IL-23p19 and/or IL-1α/IL-1β-targeting therapies upstream of IL-23.
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Affiliation(s)
- Dominik Aschenbrenner
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Oxford, Oxfordshire, UK
| | - Maria Quaranta
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Oxford, Oxfordshire, UK
- IBD Center, Laboratory of Gastrointestinal Immunopathology, Humanitas Clinical and Research Center, Milan, Italy
| | - Soumya Banerjee
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Oxford, Oxfordshire, UK
- Department of Psychology, University of Cambridge, Cambridge, Cambridgeshire, UK
| | - Nicholas Ilott
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, Oxfordshire, UK
| | - Joanneke Jansen
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Oxford, Oxfordshire, UK
- Wolfson Centre for Mathematical Biology, University of Oxford, Oxford, Oxfordshire, UK
| | - Boyd Steere
- Immunology Translational Sciences, Eli Lilly and Company, Indianapolis, Indiana, USA
| | - Yin-Huai Chen
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Oxford, Oxfordshire, UK
| | - Stephen Ho
- Immunology Translational Sciences, Eli Lilly and Company, Indianapolis, Indiana, USA
| | - Karen Cox
- Immunology Translational Sciences, Eli Lilly and Company, Indianapolis, Indiana, USA
| | - Carolina V Arancibia-Cárcamo
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Oxford, Oxfordshire, UK
| | - Mark Coles
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, Oxfordshire, UK
| | - Eamonn Gaffney
- Wolfson Centre for Mathematical Biology, University of Oxford, Oxford, Oxfordshire, UK
| | - Simon Pl Travis
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Oxford, Oxfordshire, UK
| | - Lee Denson
- Pediatric Gastroenterology, Cincinnati Childrens Hospital Medical Center, Cincinnati, Ohio, USA
| | - Subra Kugathasan
- Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jochen Schmitz
- Immunology Translational Sciences, Eli Lilly and Company, Indianapolis, Indiana, USA
| | - Fiona Powrie
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, Oxfordshire, UK
| | - Stephen N Sansom
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, Oxfordshire, UK
| | - Holm H Uhlig
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Oxford, Oxfordshire, UK
- Department of Paediatrics, University of Oxford, Oxford, Oxfordshire, UK
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24
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State M, Negreanu L, Voiosu T, Voiosu A, Balanescu P, Mateescu RB. Surrogate markers of mucosal healing in inflammatory bowel disease: A systematic review. World J Gastroenterol 2021; 27:1828-1840. [PMID: 33967560 PMCID: PMC8072191 DOI: 10.3748/wjg.v27.i16.1828] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/02/2021] [Accepted: 04/07/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Mucosal healing (MH) has emerged as a key therapeutic target in inflammatory bowel disease (IBD), and achievement of this goal is documented by endoscopy with biopsy. However, colonoscopy is burdensome and invasive, and substitution with an accurate noninvasive biomarker is desirable.
AIM To summarize published data regarding the performance of noninvasive biomarkers in assessing MH in IBD patients.
METHODS We conducted a systematic review of studies that reported the performance of biomarkers in diagnosing MH in patients with IBD. The main outcome measure was to review the diagnostic accuracy of serum and fecal markers that showed promising utility in assessing MH.
RESULTS We screened 1301 articles, retrieved 46 manuscripts and included 23 articles for full-text analysis. The majority of the included manuscripts referred to fecal markers (12/23), followed by circulatory markers (8/23); only 3/23 of the included manuscripts investigated combined markers (serum and/or fecal markers). Fecal calprotectin (FC) was the most investigated fecal marker for assessing MH. In ulcerative colitis, for cutoff levels ranging between 58 mcg/g and 490 mcg/g, the sensitivity was 89.7%-100% and the specificity was 62%-93.3%. For Crohn’s disease, the cutoff levels of FC ranged from 71 mcg/g to 918 mcg/g (sensitivity 50%-95.9% and specificity 52.3%-100%). The best performance for a serum marker was observed for the endoscopic healing index, which showed a comparable accuracy to the measurement of FC and a higher accuracy than the measurement of serum C-reactive protein.
CONCLUSION Several promising biomarkers of MH are emerging but cannot yet substitute for endoscopy with biopsy due to issues with reproducibility and standardization.
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Affiliation(s)
- Monica State
- Department of Gastroenterology, Colentina Clinical Hospital, Bucharest 020125, Romania
| | - Lucian Negreanu
- Department of Gastroenterology, Emergency University Hospital, Bucharest 050098, Romania
- Carol Davila University of Medicine and Pharmacy, Bucharest 020021, Romania
| | - Theodor Voiosu
- Department of Gastroenterology, Colentina Clinical Hospital, Bucharest 020125, Romania
- Carol Davila University of Medicine and Pharmacy, Bucharest 020021, Romania
| | - Andrei Voiosu
- Department of Gastroenterology, Colentina Clinical Hospital, Bucharest 020125, Romania
- Carol Davila University of Medicine and Pharmacy, Bucharest 020021, Romania
| | - Paul Balanescu
- Carol Davila University of Medicine and Pharmacy, Bucharest 020021, Romania
- Department of Internal Medicine and Research Methodology, Colentina Clinical Hospital, Bucharest 020125, Romania
| | - Radu Bogdan Mateescu
- Department of Gastroenterology, Colentina Clinical Hospital, Bucharest 020125, Romania
- Carol Davila University of Medicine and Pharmacy, Bucharest 020021, Romania
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25
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Omics data integration identifies ELOVL7 and MMD gene regions as novel loci for adalimumab response in patients with Crohn's disease. Sci Rep 2021; 11:5449. [PMID: 33750834 PMCID: PMC7970911 DOI: 10.1038/s41598-021-84909-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 02/22/2021] [Indexed: 12/13/2022] Open
Abstract
Response to anti-TNF therapy is of pivotal importance in patients with Crohn’s disease (CD). Here we integrated our and previously reported PBMC derived transcriptomic and genomic data for identification of biomarkers for discrimination between responders and non-responders to anti-TNF therapy. CD patients, who were naïve with respect to the treatment with biologicals, were enrolled in the study. DNA and RNA were extracted from peripheral blood mononuclear cells. RNA-seq was performed using BGISEQ-500. Genotyping was performed using Infinium Global Screening Array. Association regressions were carried out with 12 week response to adalimumab as an outcome variable. RNA-seq analysis confirmed 7 out of 65 previously suggested genes involved in anti-TNF response. Subsequently, analysis of single nucleotide variants in regions of confirmed genes identified 5 variants near MMD and two in ELOVL7 intronic regions associated with treatment response to anti-TNF. Functional analysis has shown that rs1465352, rs4422035 and rs78620886 are listed at H3K9ac_Pro histone modification epigenetic mark. The present study confirmed MMD and ELOVL7 involvement in anti-TNF response and revealed that the regulation of MMD and ELOVL7 gene regions in ADA response may be a part of a complex interplay extending from genetic to epigenetic and to transcriptomic level.
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26
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Rodrigues BL, Mazzaro MC, Nagasako CK, Ayrizono MDLS, Fagundes JJ, Leal RF. Assessment of disease activity in inflammatory bowel diseases: Non-invasive biomarkers and endoscopic scores. World J Gastrointest Endosc 2020; 12:504-520. [PMID: 33362904 PMCID: PMC7739141 DOI: 10.4253/wjge.v12.i12.504] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/06/2020] [Accepted: 11/05/2020] [Indexed: 02/05/2023] Open
Abstract
Inflammatory bowel diseases (IBD) comprise two major forms: Crohn's disease and ulcerative colitis. The diagnosis of IBD is based on clinical symptoms combined with results found in endoscopic and radiological examinations. In addition, the discovery of biomarkers has significantly improved the diagnosis and management of IBD. Several potential genetic, serological, fecal, microbial, histological and immunological biomarkers have been proposed for IBD, and they have been evaluated for clinical routine and clinical trials. Ileocolonoscopy, especially with biopsy collection, has been considered the standard method to diagnose IBD and to assess clinical activity of the disease, but it is limited to the colon and terminal ileum and is considered invasive. For this reason, non-invasive biomarkers are necessary for this type of chronic inflammatory disease, which affects mostly young individuals, as they are expected to have a long follow-up.
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Affiliation(s)
- Bruno Lima Rodrigues
- Inflammatory Bowel Disease Research Laboratory, Gastrocenter, Colorectal Surgery Unit, Department of Surgery, School of Medical Sciences, University of Campinas (UNICAMP), Campinas 13083-878, São Paulo, Brazil
| | - Márcia Carolina Mazzaro
- Inflammatory Bowel Disease Research Laboratory, Gastrocenter, Colorectal Surgery Unit, Department of Surgery, School of Medical Sciences, University of Campinas (UNICAMP), Campinas 13083-878, São Paulo, Brazil
| | - Cristiane Kibune Nagasako
- Department of Gastroenterology, Gastrocenter, School of Medical Sciences, University of Campinas (UNICAMP), Campinas 13083-878, São Paulo, Brazil
| | - Maria de Lourdes Setsuko Ayrizono
- Inflammatory Bowel Disease Research Laboratory, Gastrocenter, Colorectal Surgery Unit, Department of Surgery, School of Medical Sciences, University of Campinas (UNICAMP), Campinas 13083-878, São Paulo, Brazil
| | - João José Fagundes
- Inflammatory Bowel Disease Research Laboratory, Gastrocenter, Colorectal Surgery Unit, Department of Surgery, School of Medical Sciences, University of Campinas (UNICAMP), Campinas 13083-878, São Paulo, Brazil
| | - Raquel Franco Leal
- Inflammatory Bowel Disease Research Laboratory, Gastrocenter, Colorectal Surgery Unit, Department of Surgery, School of Medical Sciences, University of Campinas (UNICAMP), Campinas 13083-878, São Paulo, Brazil
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27
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Luscombe VB, Lucy D, Bataille CJR, Russell AJ, Greaves DR. 20 Years an Orphan: Is GPR84 a Plausible Medium-Chain Fatty Acid-Sensing Receptor? DNA Cell Biol 2020; 39:1926-1937. [PMID: 33001759 DOI: 10.1089/dna.2020.5846] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
GPR84 is an inflammation-induced receptor highly expressed on immune cells, yet its endogenous ligand is still unknown. This makes any interpretation of its physiological activity in vivo difficult. However, experiments with potent synthetic agonists have highlighted what the receptor can do, namely, enhance proinflammatory signaling and macrophage effector functions such as phagocytosis. Developing drugs to block these effects has attracted interest from the scientific community with the aim of decreasing disease activity in inflammatory disorders or enhancing inflammation resolution. In this review, we critically reassess the widely held belief that the major role of GPR84 is that of being a medium-chain fatty acid (MCFA) receptor. While MCFAs have been shown to activate GPR84, it remains to be demonstrated that they are present in relevant tissues at appropriate concentrations. In contrast to four other "full-time" free fatty acid receptor subtypes, GPR84 is not expressed by enteroendocrine cells and has limited expression in the gastrointestinal tract. Across multiple tissues and cell types, the highest expression levels of GPR84 are observed hours after exposure to an inflammatory stimulus. These factors obscure the relationship between ligand and receptor in the human body and do not support the exclusive physiological pairing of MCFAs with GPR84. To maximize the chances of developing efficacious drugs for inflammatory diseases, we must advance our understanding of GPR84 and what it does in vivo.
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Affiliation(s)
- Vincent B Luscombe
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Daniel Lucy
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom.,Department of Chemistry and University of Oxford, Oxford, United Kingdom
| | | | - Angela J Russell
- Department of Chemistry and University of Oxford, Oxford, United Kingdom.,Department of Pharmacology, University of Oxford, Oxford, United Kingdom
| | - David R Greaves
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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28
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Marsango S, Barki N, Jenkins L, Tobin AB, Milligan G. Therapeutic validation of an orphan G protein-coupled receptor: The case of GPR84. Br J Pharmacol 2020; 179:3529-3541. [PMID: 32869860 PMCID: PMC9361006 DOI: 10.1111/bph.15248] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/04/2020] [Accepted: 08/24/2020] [Indexed: 12/12/2022] Open
Abstract
Despite the importance of members of the GPCR superfamily as targets of a broad range of effective medicines many GPCRs remain poorly characterised. GPR84 is an example. Expression of GPR84 is strongly up regulated in immune cells in a range of pro-inflammatory settings and clinical trials to treat idiopathic pulmonary fibrosis are currently ongoing using ligands with differing levels of selectivity and affinity as GPR84 antagonists. Although blockade of GPR84 may potentially prove effective also in diseases associated with inflammation of the lower gut there is emerging interest in defining if agonists of GPR84 might find utility in conditions in which regulation of metabolism or energy sensing is compromised. Here, we consider the physiological and pathological expression profile of GPR84 and, in the absence of direct structural information, recent developments and use of GPR84 pharmacological tool compounds to study its broader role and biology.
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Affiliation(s)
- Sara Marsango
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Natasja Barki
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Laura Jenkins
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Andrew B Tobin
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Graeme Milligan
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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29
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Integrated Bioinformatics Analysis Identifies ELAVL1 and APP as Candidate Crucial Genes for Crohn's Disease. J Immunol Res 2020; 2020:3067273. [PMID: 32724827 PMCID: PMC7382743 DOI: 10.1155/2020/3067273] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 06/12/2020] [Indexed: 12/14/2022] Open
Abstract
Immune imbalance and barrier destruction of intestinal mucosa are the central pathogenic factors of Crohn's disease (CD). In this study, three independent microarray studies of CD were integrated and 9912 differentially expressed genes (DEGs) were analysed by NetworkAnalyst to screen candidate crucial genes. NetworkAnalyst identified ELAV-like RNA binding protein 1 (ELAVL1) as the most crucial upregulated gene and amyloid-β precursor protein (APP) as the most crucial downregulated gene in peripheral blood of CD patients. By computing significance with hypergeometric test based on the KEGG pathway database, upregulated DEGs highlight the pathways of T cell receptor signaling and the differentiation of T helpers. Downregulated DEGs were found enriched in pathways in multiple cancers, MAPK signaling, Rap1 signaling, and PI3K-AKT signaling. Further taking all DEGs together, Gene Set Enrichment Analysis (GSEA) brought out the NOD-like receptor (NLR) signaling pathway which could be regulated by ELAVL1. xCell found decreased naïve and differentiated T cell proportions in the peripheral blood of CD patients suggesting T cell migration to the intestinal tissue and/or exhaustion. Further, ELAVL1 expression correlating with multiple T cell proportions suggests that ELAVL1 may regulate T cell activation. These findings illustrated that ELAVL1 and APP were candidate crucial genes in the peripheral blood of CD patients. ELAVL1 possibly acts as a key regulator of T cell activation via the NLR signaling pathway. APP might be a downstream effector of infliximab treatment connecting with MAPK signaling.
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30
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Wang H, Zhang M, Zhang M, Wang F, Liu J, Zhao Q. Carboxypeptidase A6 was identified and validated as a novel potential biomarker for predicting the occurrence of active ulcerative colitis. J Cell Mol Med 2020; 24:8803-8813. [PMID: 32570281 PMCID: PMC7412415 DOI: 10.1111/jcmm.15517] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/24/2020] [Accepted: 05/28/2020] [Indexed: 12/18/2022] Open
Abstract
Ulcerative colitis (UC) is a chronic, highly heterogeneous intestinal inflammation with changes in epithelial function and tissue damage. However, the pathogenesis is still unclear between active UC and inactive UC. Herein, weighted gene co‐expression network analysis was applied to explore the gene modules related to active UC. Gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA) were used to further investigate the underlying mechanism of selected genes. We found that in the blue module (r = −.72), carboxypeptidase A6 (CPA6) was chosen to validate because of its high intra‐modular connectivity and module membership. In the test sets, the expression level of CPA6 was down‐regulated in active UC compared with inactive UC and normal colon. Furthermore, CPA6 expression was decreased primarily in the descending colon and only in mucosa affected by active UC. The receiver operating characteristic curve indicated that CPA6 expression had a performed well in diagnosing active UC from inactive UC (area under the curve = 0.99). Importantly, anti‐tumour necrosis factor (TNF) treatment (infliximab and golimumab) significantly increased the CPA6 expression. Finally, GSEA and GSVA found that extracellular matrix receptor, inflammatory response and epithelial‐mesenchymal transition were highly enriched in active UC with low CPA6 expression. In conclusion, CPA6 was identified and validated as a novel potential biomarker for predicting the occurrence of active UC, probably through regulating extracellular matrix or immune response.
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Affiliation(s)
- Haizhou Wang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Meng Zhang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Mengna Zhang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Fan Wang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Jing Liu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Qiu Zhao
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
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31
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Remote ischemic conditioning in active ulcerative colitis: An explorative randomized clinical trial. Sci Rep 2020; 10:9537. [PMID: 32533085 PMCID: PMC7293253 DOI: 10.1038/s41598-020-65692-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 05/06/2020] [Indexed: 02/08/2023] Open
Abstract
Remote ischemic conditioning (RIC) by repetitive brief periods of limb ischemia and reperfusion renders organs more resistant to ischemic injury. The protection is partly through down-regulation of the inflammatory response. Our aim was to investigate the clinical and anti-inflammatory effects of RIC in patients with active ulcerative colitis (UC). We included 22 patients with active UC in this explorative, randomized, sham-controlled clinical trial. The patients were randomly assigned 1:1 to RIC (induced in the arm through four cycles of 5-min inflation and 5-min deflation of a blood-pressure cuff) or sham (incomplete inflation of the blood-pressure cuff) once daily for 10 days. Outcome variables were measured at baseline and on day 11. When compared with sham, RIC did not affect inflammation in the UC patients measured by fecal calprotectin, plasma C-reactive protein, Mayo Score, Mayo Endoscopic Subscore, Nancy Histological Index or inflammatory cytokines involved in UC and RIC. The mRNA and miRNA expression profiles in the UC patients were measured by RNA sequencing and multiplexed hybridization, respectively, but were not significantly affected by RIC. We used the Langendorff heart model to assess activation of the organ protective mechanism induced by RIC, but could not confirm activation of the organ protective mechanism in the UC patients.
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32
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Nardone OM, Shivaji UN, Ferruzza V, Ghosh S, Iacucci M. Soluble Blood Markers of Mucosal Healing in Inflammatory Bowel Disease: The Future of Noninvasive Monitoring. Inflamm Bowel Dis 2020; 26:961-969. [PMID: 31587036 DOI: 10.1093/ibd/izz226] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Indexed: 12/13/2022]
Abstract
The traditional management of inflammatory bowel disease (IBD) based on symptom control is not considered valid anymore by most specialists in this field, and a new paradigm called "treat to target" has been introduced. This is based on the assessment of disease activity using objective measures. The identification of noninvasive biomarkers is crucial to diagnosis and monitor IBD because frequent endoscopic examinations are costly and uncomfortable for the patient. In this review, we focus on blood markers that may be able to assess mucosal healing (MH) in IBD and recent advances in this area. Introduction of commercial panel to predict MH opens the way for further developments so that colonoscopy or fecal markers may be avoided in some patients. This may also permit frequent monitoring for therapeutic response and achieve MH. It is a challenging area of research to identify a panel of biomarkers that may reflect inflammation and healing to serve as a surrogate of MH.
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Affiliation(s)
- Olga Maria Nardone
- Institute of Translational Medicine and Institute of Immunology and Immunotherapy, University of Birmingham, UK
| | - Uday Nagesh Shivaji
- Institute of Translational Medicine and Institute of Immunology and Immunotherapy, University of Birmingham, UK
| | - Vittoria Ferruzza
- Institute of Translational Medicine and Institute of Immunology and Immunotherapy, University of Birmingham, UK
| | - Subrata Ghosh
- Institute of Translational Medicine and Institute of Immunology and Immunotherapy, University of Birmingham, UK.,University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital Birmingham, UK.,NIHR Biomedical Research Centre, University of Birmingham and University Hospitals NHS Foundation Trust Birmingham, UK.,Department of Gastroenterology and Hepatology, University of Calgary, Alberta, Canada
| | - Marietta Iacucci
- Institute of Translational Medicine and Institute of Immunology and Immunotherapy, University of Birmingham, UK.,University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital Birmingham, UK.,NIHR Biomedical Research Centre, University of Birmingham and University Hospitals NHS Foundation Trust Birmingham, UK.,Department of Gastroenterology and Hepatology, University of Calgary, Alberta, Canada
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33
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Vennou KE, Piovani D, Kontou PI, Bonovas S, Bagos PG. Multiple outcome meta-analysis of gene-expression data in inflammatory bowel disease. Genomics 2020; 112:1761-1767. [DOI: 10.1016/j.ygeno.2019.09.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 09/26/2019] [Accepted: 09/27/2019] [Indexed: 01/02/2023]
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34
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S100A12 in Digestive Diseases and Health: A Scoping Review. Gastroenterol Res Pract 2020; 2020:2868373. [PMID: 32184815 PMCID: PMC7061133 DOI: 10.1155/2020/2868373] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 01/05/2020] [Accepted: 01/22/2020] [Indexed: 02/07/2023] Open
Abstract
Calgranulin proteins are an important class of molecules involved in innate immunity. These members of the S100 class of the EF-hand family of calcium-binding proteins have numerous cellular and antimicrobial functions. One protein in particular, S100A12 (also called EN-RAGE or calgranulin C), is highly abundant in neutrophils during acute inflammation and has been implicated in immune regulation. Structure-function analyses reveal that S100A12 has the capacity to bind calcium, zinc, and copper, processes that contribute to nutritional immunity against invading microbial pathogens. S100A12 is a ligand for the receptor for advanced glycation end products (RAGE), toll-like receptor 4 (TLR4), and CD36, which promote cellular and immunological pathways to alter inflammation. We conducted a scoping review of the existing literature to define what is known about the association of S100A12 with digestive disease and health. Results suggest that S100A12 is implicated in gastroenteritis, necrotizing enterocolitis, gastritis, gastric cancer, Crohn's disease, irritable bowel syndrome, inflammatory bowel disease, and digestive tract cancers. Together, these results reveal S100A12 is an important molecule broadly associated with the pathogenesis of digestive diseases.
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35
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Borg-Bartolo SP, Boyapati RK, Satsangi J, Kalla R. Precision medicine in inflammatory bowel disease: concept, progress and challenges. F1000Res 2020; 9:F1000 Faculty Rev-54. [PMID: 32047622 PMCID: PMC6993839 DOI: 10.12688/f1000research.20928.1] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/16/2020] [Indexed: 12/12/2022] Open
Abstract
Crohn's disease and ulcerative colitis are increasingly prevalent, relapsing and remitting inflammatory bowel diseases (IBDs) with variable disease courses and complications. Their aetiology remains unclear but current evidence shows an increasingly complex pathophysiology broadly centring on the genome, exposome, microbiome and immunome. Our increased understanding of disease pathogenesis is providing an ever-expanding arsenal of therapeutic options, but these can be expensive and patients can lose response or never respond to certain therapies. Therefore, there is now a growing need to personalise therapies on the basis of the underlying disease biology and a desire to shift our approach from "reactive" management driven by disease complications to "proactive" care with an aim to prevent disease sequelae. Precision medicine is the tailoring of medical treatment to the individual patient, encompassing a multitude of data-driven (and multi-omic) approaches to foster accurate clinical decision-making. In IBD, precision medicine would have significant benefits, enabling timely therapy that is both effective and appropriate for the individual. In this review, we summarise some of the key areas of progress towards precision medicine, including predicting disease susceptibility and its course, personalising therapies in IBD and monitoring response to therapy. We also highlight some of the challenges to be overcome in order to deliver this approach.
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Affiliation(s)
- Simon P. Borg-Bartolo
- Department of Gastroenterology, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Southmoor Road, Wythenshawe, Manchester, M23 9LT, UK
| | - Ray Kiran Boyapati
- Department of Gastroenterology, Monash Health, Clayton, Victoria, Australia
- Faculty of Medicine, Nursing & Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Jack Satsangi
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Rahul Kalla
- Department of Gastroenterology, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh, EH16 4SA, UK
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Palmer NP, Silvester JA, Lee JJ, Beam AL, Fried I, Valtchinov VI, Rahimov F, Kong SW, Ghodoussipour S, Hood HC, Bousvaros A, Grand RJ, Kunkel LM, Kohane IS. Concordance between gene expression in peripheral whole blood and colonic tissue in children with inflammatory bowel disease. PLoS One 2019; 14:e0222952. [PMID: 31618209 PMCID: PMC6795427 DOI: 10.1371/journal.pone.0222952] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/10/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Presenting features of inflammatory bowel disease (IBD) are non-specific. We hypothesized that mRNA profiles could (1) identify genes and pathways involved in disease pathogenesis; (2) identify a molecular signature that differentiates IBD from other conditions; (3) provide insight into systemic and colon-specific dysregulation through study of the concordance of the gene expression. METHODS Children (8-18 years) were prospectively recruited at the time of diagnostic colonoscopy for possible IBD. We used transcriptome-wide mRNA profiling to study gene expression in colon biopsies and paired whole blood samples. Using blood mRNA measurements, we fit a regression model for disease state prediction that was validated in an independent test set of adult subjects (GSE3365). RESULTS Ninety-eight children were recruited [39 Crohn's disease, 18 ulcerative colitis, 2 IBDU, 39 non-IBD]. There were 1,118 significantly differentially (IBD vs non-IBD) expressed genes in colon tissue, and 880 in blood. The direction of relative change in expression was concordant for 106/112 genes differentially expressed in both tissue types. The regression model from the blood mRNA measurements distinguished IBD vs non-IBD disease status in the independent test set with 80% accuracy using only 6 genes. The overlap of 5 immune and metabolic pathways in the two tissue types was significant (p<0.001). CONCLUSIONS Blood and colon tissue from patients with IBD share a common transcriptional profile dominated by immune and metabolic pathways. Our results suggest that peripheral blood expression levels of as few as 6 genes (IL7R, UBB, TXNIP, S100A8, ALAS2, and SLC2A3) may distinguish patients with IBD from non-IBD.
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Affiliation(s)
- Nathan P Palmer
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jocelyn A Silvester
- Division of Gastroenterology and Nutrition, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jessica J Lee
- Division of Gastroenterology and Nutrition, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Andrew L Beam
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Inbar Fried
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Vladimir I Valtchinov
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Evidence Based Imaging, Brigham and Women's Hospital, Harvard Medical School, Massachusetts, United States of America
| | - Fedik Rahimov
- Division of Genetics and Genomics, Boston Children's Hospital, Departments of Genetics and Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sek Won Kong
- Computational Health Informatics Program, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Saum Ghodoussipour
- Division of Gastroenterology and Nutrition, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Helen C Hood
- Division of Gastroenterology and Nutrition, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Athos Bousvaros
- Division of Gastroenterology and Nutrition, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Richard J Grand
- Division of Gastroenterology and Nutrition, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Louis M Kunkel
- Division of Genetics and Genomics, Boston Children's Hospital, Departments of Genetics and Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Isaac S Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
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Yang L, Bian Y, Li Z, Yan Y, Li J, Li W, Zeng L. Identification of potential biomarkers and pathways in ulcerative colitis with combined public mRNA and miRNA expression microarray data analysis. J Gastrointest Oncol 2019; 10:847-858. [PMID: 31602322 DOI: 10.21037/jgo.2019.06.06] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Background Ulcerative colitis (UC) is a chronic, relapsing and non-specific inflammatory disease, involving various genes and pathways in their pathogenesis. Increasing evidences have showed that microRNAs (miRNAs) act as key post-transcriptional regulators of gene expression in UC. This current study aimed to identify key miRNAs, potential target genes, and relevant pathways involved in UC to uncover their underlying molecular mechanisms by using bioinformatics analysis. Methods The mRNA and miRNA expression profiles were retrieved and downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) and miRNAs (DEMIs) were obtained by using the R software package. Results A total of 79 DEGs and 47 DEMIs were obtained. And a panel of miRNAs and their target mRNAs were identified. It showed that miR-1231 may be a key regulator for DUOX2 and TFF1. CCL11 may be potentially targeted by miR-625. MMP1 may play vital roles in the development of UC by regulating the miR-1228/PPAR signaling pathway. In addition, we validated the most significantly up/down-expressed miRNAs (miR-92b, miR-625) and two of their corresponding target mRNAs (AQP8 and TAGAP, CCL11 and CHI3L1) in colon tissues of UC models preliminarily. The results were consistent with the microarray analysis. Conclusions These findings may provide new insights into representing key mechanisms associated with the development of UC.
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Affiliation(s)
- Lili Yang
- School of First Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.,Jingwen Library, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yaoyao Bian
- School of Nursing, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Zhengjun Li
- Management School, Lancaster University, Lancaster, LA1 4YW, UK
| | - Yan Yan
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, China
| | - Junyi Li
- School of First Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Wenlin Li
- Jingwen Library, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Li Zeng
- School of First Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.,Jingwen Library, Nanjing University of Chinese Medicine, Nanjing 210023, China
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Scaioli E, Belluzzi A, Ricciardiello L, Del Rio D, Rotondo E, Mena P, Derlindati E, Danesi F. Pomegranate juice to reduce fecal calprotectin levels in inflammatory bowel disease patients with a high risk of clinical relapse: Study protocol for a randomized controlled trial. Trials 2019; 20:327. [PMID: 31171016 PMCID: PMC6554985 DOI: 10.1186/s13063-019-3321-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 03/25/2019] [Indexed: 12/12/2022] Open
Abstract
Background Inflammatory bowel disease (IBD) is a chronic condition characterized by recurrent episodes of intestinal inflammation and is thought to be related to an autoimmune reaction to genetic and environmental factors. Although evidence indicates that a polyphenolic-rich diet plays an important role in modulating aspects of chronic inflammation, few studies have focused on the effect of ellagitannin (ET)-rich food consumption on long-term remission maintenance in IBD patients with a high risk of clinical relapse. Therefore, we hypothesize that supplementation with a pomegranate juice, a naturally rich source of ETs, could significantly modulate the markers of mucosal and systemic inflammation relative to a control group receiving a placebo. Methods/design This double-blind, randomized controlled trial includes patients with IBD involving the colorectum who have been in stable therapy for at least the three previous months and have a high risk of clinical relapse. Participants are randomly allocated to one of two groups: active supplementation (125 mL of cv. Wonderful pomegranate juice) or placebo (125 mL) taken twice daily for 12 weeks. The primary outcome is changes in the fecal neutrophil-derived protein calprotectin, a surrogate marker of mucosal improvement, between the two groups from baseline to 12 weeks later. The secondary outcomes include transcriptomic changes in peripheral blood mononuclear cells and intestinal biopsies and changes in circulating inflammatory markers and trimethylamine-N-oxide levels. Pomegranate ET-derived metabolites are identified and quantified in plasma and urine samples. Discussion The results will provide information on the possible reduction of fecal calprotectin levels following the consumption of pomegranate juice. The findings will also show the in vivo metabolism of pomegranate ETs. Finally, the effect of 12-week pomegranate juice consumption on local and systemic inflammatory markers will be elucidated, which will likely provide additional insights into the maintenance of remission in IBD patients. Trial registration ClinicalTrials.gov, NCT03000101. Registered on 21 December 2016. Electronic supplementary material The online version of this article (10.1186/s13063-019-3321-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eleonora Scaioli
- Gastroenterological Unit, Department of Medical and Surgical Sciences, University of Bologna, Via Massarenti 9, 40138, Bologna, Italy
| | - Andrea Belluzzi
- Gastroenterological Unit, St. Orsola-Malpighi Hospital, Via Massarenti 9, 40138, Bologna, Italy
| | - Luigi Ricciardiello
- Gastroenterological Unit, Department of Medical and Surgical Sciences, University of Bologna, Via Massarenti 9, 40138, Bologna, Italy
| | - Daniele Del Rio
- Department of Veterinary Science, University of Parma, Strada del Taglio, 10, 43126, Parma, Italy
| | - Enrica Rotondo
- Human Nutrition Unit, Department of Agricultural and Food Sciences, Campus of Food Science, University of Bologna, Piazza Goidanich, 60, 47521, Cesena, FC, Italy
| | - Pedro Mena
- Human Nutrition Unit, Department of Food and Drug, University of Parma, Medical School, Building C, Via Volturno 39, 43125, Parma, Italy
| | - Eleonora Derlindati
- Human Nutrition Unit, Department of Agricultural and Food Sciences, Campus of Food Science, University of Bologna, Piazza Goidanich, 60, 47521, Cesena, FC, Italy.,Endocrinology and Metabolism Unit, Department of Medicine and Surgery, University of Parma, Via Gramsci 14, 43126, Parma, Italy
| | - Francesca Danesi
- Human Nutrition Unit, Department of Agricultural and Food Sciences, Campus of Food Science, University of Bologna, Piazza Goidanich, 60, 47521, Cesena, FC, Italy.
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Abstract
OBJECTIVES In 2015, the Selecting Therapeutic Targets in Inflammatory Bowel Disease (STRIDE) program proposed shifting the therapeutic focus on ulcerative colitis (UC) toward altering the natural history of the disease course by regularly monitoring objective measurements of disease activity and tailoring treatment accordingly. The therapeutic paradigm shift was well received in the research community and is often cited. However, new evidence on optimal UC treatment targets continues to accumulate since the time of the STRIDE guidelines. This systematic review summarizes the evidence accrued since the STRIDE UC recommendations, discusses the barriers for adoption of treat-to-target approaches in clinical practice in UC, and suggests directions for future research. METHODS We systematically reviewed MEDLINE for studies from the time of the STRIDE systematic review up to March 31, 2018, that assessed the potential treatment targets identified by the STRIDE recommendations. RESULTS Each potential treatment target literature search returned > 200 articles, which were then reviewed by 2 independent investigators for relevant studies. Selected studies of clinical factors, patient-reported outcomes, endoscopy, histology, imaging, and biomarkers and implications on treatment targets are summarized. CONCLUSIONS It appears that the relative weight given to different therapeutic targets in the development and improvement of UC treatments could be optimized, with an increased emphasis on endoscopic and histological targets over clinical or symptomatic targets. For this evolution to occur, however, new research has to demonstrate that the treat-to-target approach will deliver on the promise of better long-term outcomes compared with current approaches.
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Gole B, Potočnik U. Pre-Treatment Biomarkers of Anti-Tumour Necrosis Factor Therapy Response in Crohn's Disease-A Systematic Review and Gene Ontology Analysis. Cells 2019; 8:cells8060515. [PMID: 31141991 PMCID: PMC6628089 DOI: 10.3390/cells8060515] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/24/2019] [Accepted: 05/25/2019] [Indexed: 12/15/2022] Open
Abstract
The most prominent treatment for the serious cases of Crohn’s disease (CD) are biological tumour necrosis factor (TNF) inhibitors. Unfortunately, therapy nonresponse is still a serious issue in ~1/3 of CD patients. Accurate prediction of responsiveness prior to therapy start would therefore be of great value. Clinical predictors have, however, proved insufficient. Here, we integrate genomic and expression data on potential pre-treatment biomarkers of anti-TNF nonresponse. We show that there is almost no overlap between genomic (annotated with tissue-specific expression quantitative trait loci data) and transcription (RNA and protein data) biomarkers. Furthermore, using interaction networks we demonstrate there is little direct interaction between the proposed biomarkers, though a majority do have common interactors connecting them into networks. Our gene ontology analysis shows that these networks have roles in apoptotic signalling, response to oxidative stress and inflammation pathways. We conclude that a more systematic approach with genome-wide search of genomic and expression biomarkers in the same patients is needed in future studies.
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Affiliation(s)
- Boris Gole
- Centre for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska ulica 8, SI-2000 Maribor, Slovenia.
| | - Uroš Potočnik
- Centre for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska ulica 8, SI-2000 Maribor, Slovenia.
- Laboratory for Biochemistry, Molecular biology and Genomics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia.
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41
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Common functional alterations identified in blood transcriptome of autoimmune cholestatic liver and inflammatory bowel diseases. Sci Rep 2019; 9:7190. [PMID: 31076612 PMCID: PMC6510750 DOI: 10.1038/s41598-019-43699-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 04/29/2019] [Indexed: 02/07/2023] Open
Abstract
Primary biliary cholangitis (PBC), primary sclerosing cholangitis (PSC), and inflammatory bowel diseases (IBDs), including Crohn’s disease (CD) and ulcerative colitis (UC), are heterogeneous chronic autoimmune diseases that may share underlying pathogenic mechanisms. Herein, we compared simultaneously analyzed blood transcriptomes from patients with PBC, PSC, and IBD. Microarray-based measurements were conducted using RNA isolated from whole blood samples from 90, 45, 95 and 93 patients with PBC, PSC, CD, and UC, respectively, and 47 healthy controls. Expression levels of selected transcripts were analyzed by quantitative reverse-transcribed PCR using an independent cohort of 292, 71 and 727 patients with PBC, PSC, and IBD, respectively. Of 4026, 2650 and 4967 probe sets differentially expressed (adjusted p-value < 0.05) in samples from patients with PBC, PSC, and IBD, respectively, compared with healthy controls, 1946 were common to all three comparisons. Functional analyses indicated that most terms enriched for genes differentially expressed in PBC, PSC, and IBD patients compared with healthy controls were related to mitochondrial function, the vesicle endomembrane system, and GTPase-mediated processes. This study indicates that microarray-based profiling of blood gene expression supports research into the molecular mechanisms underlying disease, rather than being useful for selection of diagnostic biomarkers for use in clinical practice.
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Ostrowski J, Dabrowska M, Lazowska I, Paziewska A, Balabas A, Kluska A, Kulecka M, Karczmarski J, Ambrozkiewicz F, Piatkowska M, Goryca K, Zeber-Lubecka N, Kierkus J, Socha P, Lodyga M, Klopocka M, Iwanczak B, Bak-Drabik K, Walkowiak J, Radwan P, Grzybowska-Chlebowczyk U, Korczowski B, Starzynska T, Mikula M. Redefining the Practical Utility of Blood Transcriptome Biomarkers in Inflammatory Bowel Diseases. J Crohns Colitis 2019; 13:626-633. [PMID: 30541017 PMCID: PMC6486489 DOI: 10.1093/ecco-jcc/jjy205] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND AND AIMS The study investigates the practical utility of whole-blood gene expression profiling to diagnose inflammatory bowel diseases [IBDs]. METHODS The discovery cohorts included 102 and 51 paediatric IBD patients and controls, and 95 and 46 adult IBD patients and controls, respectively. The replication cohorts included 447 and 76 paediatric IBD patients and controls, and 271 and 108 adult IBD patients and controls, respectively. In the discovery phase, RNA samples extracted from whole peripheral blood were analysed using RNA-Seq, and the predictive values of selected biomarkers were validated using quantitative polymerase chain reaction [qPCR]. RESULTS In all, 15 differentially expressed transcripts [adjusted p ≤0.05] were selected from the discovery sequencing datasets. The receiver operating characteristic curves and area under the curve [ROC-AUC] in replication analyses showed high discriminative power [AUC range, 0.91-0.98] for 11 mRNAs in paediatric patients with active IBD. By contrast, the AUC-ROC values ranged from 0.63 to 0.75 in comparison among inactive paediatric IBDs and active/inactive adult IBDs, indicating a lack of discriminative power. The best multi-mRNA diagnostic classifier showed moderate discriminative power [AUC = 0.81] for paediatric inactive IBD, but was not able to discriminate active or inactive adult IBD patients from controls. The AUC-ROC values did not confirm an ability of the mRNAs abundances to discriminate between active ulcerative colitis and active Crohn's disease in paediatric or adult populations. CONCLUSIONS This study identifies and validates blood transcriptional biomarkers that could be used in clinical settings as diagnostic predictors of IBD clinical activity in paediatric, but not adult, IBD patients.
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Affiliation(s)
- Jerzy Ostrowski
- Department of Genetics, Maria Sklodowska-Curie Institute – Oncology Centre, Warsaw, Poland,Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw, Poland,Corresponding author: Jerzy Ostrowski, MD, PhD; Cancer Center-Institute, Roentgena 5, 02-781 Warsaw, Poland. Tel.: +48 225462575; e-mail:
| | - Michalina Dabrowska
- Department of Genetics, Maria Sklodowska-Curie Institute – Oncology Centre, Warsaw, Poland
| | - Izabella Lazowska
- Department of Pediatric Gastroenterology and Nutrition, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Aneta Balabas
- Department of Genetics, Maria Sklodowska-Curie Institute – Oncology Centre, Warsaw, Poland
| | - Anna Kluska
- Department of Genetics, Maria Sklodowska-Curie Institute – Oncology Centre, Warsaw, Poland
| | - Maria Kulecka
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Jakub Karczmarski
- Department of Genetics, Maria Sklodowska-Curie Institute – Oncology Centre, Warsaw, Poland
| | - Filip Ambrozkiewicz
- Department of Genetics, Maria Sklodowska-Curie Institute – Oncology Centre, Warsaw, Poland
| | - Magdalena Piatkowska
- Department of Genetics, Maria Sklodowska-Curie Institute – Oncology Centre, Warsaw, Poland
| | - Krzysztof Goryca
- Department of Genetics, Maria Sklodowska-Curie Institute – Oncology Centre, Warsaw, Poland
| | - Natalia Zeber-Lubecka
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Jaroslaw Kierkus
- Department of Gastroenterology, Hepatology and Feeding Disorders, Children’s Memorial Health Institute, Warsaw, Poland
| | - Piotr Socha
- Department of Gastroenterology, Hepatology and Feeding Disorders, Children’s Memorial Health Institute, Warsaw, Poland
| | - Michal Lodyga
- Department of Internal Medicine and Gastroenterology with IBD Subdivision, Central Clinical Hospital of the Ministry of the Interior, Warsaw, Poland
| | - Maria Klopocka
- Vascular Diseases and Internal Medicine, Nicolaus Copernicus University in Torun, Collegium Medicum, Bydgoszcz, Poland
| | - Barbara Iwanczak
- Department of Pediatrics, Gastroenterology and Nutrition, Wroclaw Medical University, Wroclaw, Poland
| | - Katarzyna Bak-Drabik
- Department of Pediatrics, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia, Katowice, Poland
| | - Jaroslaw Walkowiak
- Department of Pediatric Gastroenterology & Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Piotr Radwan
- Department of Gastroenterology, Medical University of Lublin, Lublin, Poland
| | | | | | - Teresa Starzynska
- Department of Gastroenterology, Pomeranian Medical University, Szczecin, Poland
| | - Michal Mikula
- Department of Genetics, Maria Sklodowska-Curie Institute – Oncology Centre, Warsaw, Poland
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Gaujoux R, Starosvetsky E, Maimon N, Vallania F, Bar-Yoseph H, Pressman S, Weisshof R, Goren I, Rabinowitz K, Waterman M, Yanai H, Dotan I, Sabo E, Chowers Y, Khatri P, Shen-Orr SS. Cell-centred meta-analysis reveals baseline predictors of anti-TNFα non-response in biopsy and blood of patients with IBD. Gut 2019; 68:604-614. [PMID: 29618496 PMCID: PMC6580771 DOI: 10.1136/gutjnl-2017-315494] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 12/19/2017] [Accepted: 01/16/2018] [Indexed: 12/16/2022]
Abstract
OBJECTIVE Although anti-tumour necrosis factor alpha (anti-TNFα) therapies represent a major breakthrough in IBD therapy, their cost-benefit ratio is hampered by an overall 30% non-response rate, adverse side effects and high costs. Thus, finding predictive biomarkers of non-response prior to commencing anti-TNFα therapy is of high value. DESIGN We analysed publicly available whole-genome expression profiles of colon biopsies obtained from multiple cohorts of patients with IBD using a combined computational deconvolution-meta-analysis paradigm which allows to estimate immune cell contribution to the measured expression and capture differential regulatory programmes otherwise masked due to variation in cellular composition. Insights from this in silico approach were experimentally validated in biopsies and blood samples of three independent test cohorts. RESULTS We found the proportion of plasma cells as a robust pretreatment biomarker of non-response to therapy, which we validated in two independent cohorts of immune-stained colon biopsies, where a plasma cellular score from inflamed biopsies was predictive of non-response with an area under the curve (AUC) of 82%. Meta-analysis of the cell proportion-adjusted gene expression data suggested that an increase in inflammatory macrophages in anti-TNFα non-responding individuals is associated with the upregulation of the triggering receptor expressed on myeloid cells 1 (TREM-1) and chemokine receptor type 2 (CCR2)-chemokine ligand 7 (CCL7) -axes. Blood gene expression analysis of an independent cohort, identified TREM-1 downregulation in non-responders at baseline, which was predictive of response with an AUC of 94%. CONCLUSIONS Our study proposes two clinically feasible assays, one in biopsy and one in blood, for predicting non-response to anti-TNFα therapy prior to initiation of treatment. Moreover, it suggests that mechanism-driven novel drugs for non-responders should be developed.
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Affiliation(s)
- Renaud Gaujoux
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel,CytoReason
| | - Elina Starosvetsky
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Naama Maimon
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel,Department of Gastroenterology, Rambam Health Care Campus, Haifa, Israel
| | - Francesco Vallania
- Division of Biomedical Informatics Research, Department of Medicine, Stanford University, Palo Alto, California, USA,Stanford Institute for Immunity Transplantation and Infection, Department of Medicine, Stanford University, Palo Alto, California, USA
| | - Haggai Bar-Yoseph
- Department of Gastroenterology, Rambam Health Care Campus, Haifa, Israel
| | - Sigal Pressman
- Department of Gastroenterology, Rambam Health Care Campus, Haifa, Israel
| | - Roni Weisshof
- Department of Gastroenterology, Rambam Health Care Campus, Haifa, Israel
| | - Idan Goren
- Department of Gastroenterology and Liver Diseases, IBD Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Keren Rabinowitz
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel,Division of Gastroenterology, Rabin Medical Center, Petah Tikva, Israel
| | - Matti Waterman
- Department of Gastroenterology, Rambam Health Care Campus, Haifa, Israel
| | - Henit Yanai
- Department of Gastroenterology and Liver Diseases, IBD Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel,Division of Gastroenterology, Rabin Medical Center, Petah Tikva, Israel
| | - Iris Dotan
- Department of Gastroenterology and Liver Diseases, IBD Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel,Division of Gastroenterology, Rabin Medical Center, Petah Tikva, Israel
| | - Edmond Sabo
- Department of Pathology, Rambam Health Care Campus, Haifa, Israel
| | - Yehuda Chowers
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel,Department of Gastroenterology, Rambam Health Care Campus, Haifa, Israel
| | - Purvesh Khatri
- Division of Biomedical Informatics Research, Department of Medicine, Stanford University, Palo Alto, California, USA,Stanford Institute for Immunity Transplantation and Infection, Department of Medicine, Stanford University, Palo Alto, California, USA
| | - Shai S Shen-Orr
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
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