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Toto F, Marangelo C, Scanu M, De Angelis P, Isoldi S, Abreu MT, Cucchiara S, Stronati L, Del Chierico F, Putignani L. A Novel Microbial Dysbiosis Index and Intestinal Microbiota-Associated Markers as Tools of Precision Medicine in Inflammatory Bowel Disease Paediatric Patients. Int J Mol Sci 2024; 25:9618. [PMID: 39273567 PMCID: PMC11395508 DOI: 10.3390/ijms25179618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Revised: 08/30/2024] [Accepted: 09/03/2024] [Indexed: 09/15/2024] Open
Abstract
Recent evidence indicates that the gut microbiota (GM) has a significant impact on the inflammatory bowel disease (IBD) progression. Our aim was to investigate the GM profiles, the Microbial Dysbiosis Index (MDI) and the intestinal microbiota-associated markers in relation to IBD clinical characteristics and disease state. We performed 16S rRNA metataxonomy on both stools and ileal biopsies, metabolic dysbiosis tests on urine and intestinal permeability and mucosal immunity activation tests on the stools of 35 IBD paediatric patients. On the GM profile, we assigned the MDI to each patient. In the statistical analyses, the MDI was correlated with clinical parameters and intestinal microbial-associated markers. In IBD patients with high MDI, Gemellaceae and Enterobacteriaceae were increased in stools, and Fusobacterium, Haemophilus and Veillonella were increased in ileal biopsies. Ruminococcaceae and WAL_1855D were enriched in active disease condition; the last one was also positively correlated to MDI. Furthermore, the MDI results correlated with PUCAI and Matts scores in ulcerative colitis patients (UC). Finally, in our patients, we detected metabolic dysbiosis, intestinal permeability and mucosal immunity activation. In conclusion, the MDI showed a strong association with both severity and activity of IBD and a positive correlation with clinical scores, especially in UC. Thus, this evidence could be a useful tool for the diagnosis and prognosis of IBD.
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Affiliation(s)
- Francesca Toto
- Immunology, Rheumatology and Infectious Diseases Research Area, Unit of Microbiome, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Chiara Marangelo
- Immunology, Rheumatology and Infectious Diseases Research Area, Unit of Microbiome, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Matteo Scanu
- Immunology, Rheumatology and Infectious Diseases Research Area, Unit of Microbiome, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Paola De Angelis
- Digestive Endoscopy and Surgery Unit, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Sara Isoldi
- Pediatric Gastroenterology and Hepatology Unit, Santobono-Pausilipon Children's Hospital, 80122 Naples, Italy
| | - Maria Teresa Abreu
- Crohn's and Colitis Center, Division of Digestive Health and Liver Diseases, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Salvatore Cucchiara
- Maternal Child Health Department, Pediatric Gastroenterology and Liver Unit, Sapienza University of Rome, 00185 Rome, Italy
| | - Laura Stronati
- Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Federica Del Chierico
- Immunology, Rheumatology and Infectious Diseases Research Area, Unit of Microbiome, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Lorenza Putignani
- Unit of Microbiology and Diagnostic Immunology, Unit of Microbiomics and Immunology, Rheumatology and Infectious Diseases Research Area, Unit of Microbiome, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
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Wang D, Chen W, Wang Y, Yu J, Bai Y, Luo S, Song C, Wang M, Yu Y, Li Z, Han Y, Zhen Q, Sun L. Genome-Wide Meta-Analysis Identifies 11 Susceptibility Variants of Vitiligo in the Chinese Han Population. J Invest Dermatol 2024; 144:1843-1849.e1. [PMID: 38286188 DOI: 10.1016/j.jid.2024.01.010] [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: 08/12/2023] [Revised: 01/10/2024] [Accepted: 01/18/2024] [Indexed: 01/31/2024]
Abstract
Vitiligo is an autoimmune disease involving loss of melanocytes. Although several genetic studies have confirmed that genetic factors play an important role, its pathogenesis remains incompletely characterized. In this study, a genome-wide meta-analysis was conducted to search for more susceptibility variants of vitiligo. Tang et al performed a GWAS for cohort I (1117 vitiligo cases and 1701 healthy controls) previously, and we conducted a GWAS for cohort II (3323 vitiligo cases and 7186 healthy controls) in this study, with the results subjected to a genome-wide meta-analysis and linkage disequilibrium analysis. We identify, to our knowledge, 11 previously unreported susceptibility variants, of which 6 variants are located in the intronic regions, and the remaining 5 variants are located within intergenic regions between genes. In addition, the results of polygenic risk score show that the best evaluated effect for target data is among significant SNVs of the base data. The susceptibility genes of vitiligo are mainly enriched in the immune-related functions and pathways. The susceptibility variants expand the role of genetic factors associated with vitiligo. The bioinformatics analysis for risk genes provides further insight into the pathogenesis of vitiligo.
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Affiliation(s)
- Daiyue Wang
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Weiwei Chen
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Yirui Wang
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Jing Yu
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Yuanming Bai
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Sihan Luo
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Can Song
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Minhao Wang
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Yanxia Yu
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Zhuo Li
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Yang Han
- Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China; School of Public Health, North China University of Science and Technology, Tangshan, China; Health Science Center, North China University of Science and Technology, Tangshan, China
| | - Qi Zhen
- Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China; School of Public Health, North China University of Science and Technology, Tangshan, China; Health Science Center, North China University of Science and Technology, Tangshan, China.
| | - Liangdan Sun
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China; School of Public Health, North China University of Science and Technology, Tangshan, China; Health Science Center, North China University of Science and Technology, Tangshan, China; Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China; Inflammation and Immune Diseases Laboratory, North China University of Science and Technology, Tangshan, China.
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Diez-Martin E, Hernandez-Suarez L, Muñoz-Villafranca C, Martin-Souto L, Astigarraga E, Ramirez-Garcia A, Barreda-Gómez G. Inflammatory Bowel Disease: A Comprehensive Analysis of Molecular Bases, Predictive Biomarkers, Diagnostic Methods, and Therapeutic Options. Int J Mol Sci 2024; 25:7062. [PMID: 39000169 PMCID: PMC11241012 DOI: 10.3390/ijms25137062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 06/15/2024] [Accepted: 06/25/2024] [Indexed: 07/16/2024] Open
Abstract
In inflammatory bowel diseases (IBDs), such as Crohn's disease (CD) and ulcerative colitis (UC), the immune system relentlessly attacks intestinal cells, causing recurrent tissue damage over the lifetime of patients. The etiology of IBD is complex and multifactorial, involving environmental, microbiota, genetic, and immunological factors that alter the molecular basis of the organism. Among these, the microbiota and immune cells play pivotal roles; the microbiota generates antigens recognized by immune cells and antibodies, while autoantibodies target and attack the intestinal membrane, exacerbating inflammation and tissue damage. Given the altered molecular framework, the analysis of multiple molecular biomarkers in patients proves exceedingly valuable for diagnosing and prognosing IBD, including markers like C reactive protein and fecal calprotectin. Upon detection and classification of patients, specific treatments are administered, ranging from conventional drugs to new biological therapies, such as antibodies to neutralize inflammatory molecules like tumor necrosis factor (TNF) and integrin. This review delves into the molecular basis and targets, biomarkers, treatment options, monitoring techniques, and, ultimately, current challenges in IBD management.
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Affiliation(s)
- Eguzkiñe Diez-Martin
- Research and Development Department, IMG Pharma Biotech S.L., 48170 Zamudio, Spain
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Leidi Hernandez-Suarez
- Research and Development Department, IMG Pharma Biotech S.L., 48170 Zamudio, Spain
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Carmen Muñoz-Villafranca
- Department of Gastroenterology, University Hospital of Basurto, Avda Montevideo 18, 48013 Bilbao, Spain
| | - Leire Martin-Souto
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Egoitz Astigarraga
- Research and Development Department, IMG Pharma Biotech S.L., 48170 Zamudio, Spain
| | - Andoni Ramirez-Garcia
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
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Kim K, Oh SJ, Lee J, Kwon A, Yu CY, Kim S, Choi CH, Kang SB, Kim TO, Park DI, Lee CK. Regulatory Variants on the Leukocyte Immunoglobulin-Like Receptor Gene Cluster are Associated with Crohn's Disease and Interact with Regulatory Variants for TAP2. J Crohns Colitis 2024; 18:47-53. [PMID: 37523193 DOI: 10.1093/ecco-jcc/jjad127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Indexed: 08/01/2023]
Abstract
BACKGROUND AND AIMS Crohn's disease [CD] has a complex polygenic aetiology with high heritability. There is ongoing effort to identify novel variants associated with susceptibility to CD through a genome-wide association study [GWAS] in large Korean populations. METHODS Genome-wide variant data from 902 Korean patients with CD and 72 179 controls were used to assess the genetic associations in a meta-analysis with previous Korean GWAS results from 1621 patients with CD and 4419 controls. Epistatic interactions between CD-risk variants of interest were tested using a multivariate logistic regression model with an interaction term. RESULTS We identified two novel genetic associations with the risk of CD near ZBTB38 and within the leukocyte immunoglobulin-like receptor [LILR] gene cluster [p < 5 × 10-8], with highly consistent effect sizes between the two independent Korean cohorts. CD-risk variants in the LILR locus are known quantitative trait loci [QTL] for multiple LILR genes, of which LILRB2 directly interacts with various ligands including MHC class I molecules. The LILR lead variant exhibited a significant epistatic interaction with CD-associated regulatory variants for TAP2 involved in the antigen presentation of MHC class I molecules [p = 4.11 × 10-4], showing higher CD-risk effects of the TAP2 variant in individuals carrying more risk alleles of the LILR lead variant (odds ratio [OR] = 0.941, p = 0.686 in non-carriers; OR = 1.45, p = 2.51 × 10-4 in single-copy carriers; OR = 2.38, p = 2.76 × 10-6 in two-copy carriers). CONCLUSIONS This study demonstrated that genetic variants at two novel susceptibility loci and the epistatic interaction between variants in LILR and TAP2 loci confer a risk of CD.
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Affiliation(s)
- Kwangwoo Kim
- Department of Biology, Kyung Hee University, Seoul, Republic of Korea
- Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - Shin Ju Oh
- Department of Gastroenterology, Center for Crohn's and Colitis, Kyung Hee University College of Medicine, Seoul, Republic of Korea
| | - Junho Lee
- Department of Biology, Kyung Hee University, Seoul, Republic of Korea
- Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - Ayeong Kwon
- Department of Biology, Kyung Hee University, Seoul, Republic of Korea
| | - Chae-Yeon Yu
- Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - Sangsoo Kim
- Department of Bioinformatics, Soongsil University, Seoul, Republic of Korea
| | - Chang Hwan Choi
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Sang-Bum Kang
- Department of Internal Medicine, College of Medicine, Daejeon St. Mary's Hospital, The Catholic University of Korea, Daejeon, Republic of Korea
| | - Tae Oh Kim
- Department of Internal Medicine, Haeundae Paik Hospital, Inje University College of Medicine, Busan, Republic of Korea
| | - Dong Il Park
- Division of Gastroenterology, Department of Internal Medicine and Inflammatory Bowel Disease Center, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Chang Kyun Lee
- Department of Gastroenterology, Center for Crohn's and Colitis, Kyung Hee University College of Medicine, Seoul, Republic of Korea
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Tyebally R, Xue A, Powell JE. The potential clinical impact of cell type-specific genetic regulation: Crohn's disease. Clin Transl Med 2023; 13:e1474. [PMID: 37983917 PMCID: PMC10659767 DOI: 10.1002/ctm2.1474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023] Open
Abstract
Complex diseases are heterogenous due to variation in their genetic and environmental underpinnings, leading to varied treatment responses. Genome-wide association studies (GWAS) integrated with single-cell expression quantitative trait loci analyses (eQTL) can pinpoint cell-type specific candidate disease-relevant genes and pathways. This knowledge can be applied to patient stratification and novel therapeutic target identification. Here, we describe the translational potential of cell-type specific genetic regulation, using Crohn's disease as an example.
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Affiliation(s)
- Rika Tyebally
- Translational GenomicsGarvan Institute of Medical Research, DarlinghurstSydneyNew South WalesAustralia
- UNSW Cellular Genomics Futures InstituteUniversity of New South Wales, KingstonSydneyNew South WalesAustralia
| | - Angli Xue
- Translational GenomicsGarvan Institute of Medical Research, DarlinghurstSydneyNew South WalesAustralia
- School of Biomedical SciencesUniversity of New South WalesSydneyNew South WalesAustralia
| | - Joseph E. Powell
- Translational GenomicsGarvan Institute of Medical Research, DarlinghurstSydneyNew South WalesAustralia
- UNSW Cellular Genomics Futures InstituteUniversity of New South Wales, KingstonSydneyNew South WalesAustralia
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Gao H, Liu Z. The latest breakthrough on genetic characteristics of inflammatory bowel disease in Chinese and other East Asian ancestries. PRECISION CLINICAL MEDICINE 2023; 6:pbad017. [PMID: 37456986 PMCID: PMC10346401 DOI: 10.1093/pcmedi/pbad017] [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: 06/04/2023] [Accepted: 06/24/2023] [Indexed: 07/18/2023] Open
Abstract
Inflammatory bowel diseases (IBDs) are complex chronic disorders of the gastrointestinal tract with the following two subtypes: Crohn's disease and ulcerative colitis. Disease presentation and progression within and across IBDs, especially Crohn's disease, are highly heterogeneous in the location, severity of inflammation, intestinal stenosis and obstruction, and extraintestinal manifestations. Clinical classifications fail to accurately predict the disease course and response to therapies. To date, most IBD genetic associations are derived from individuals of European ancestries, leading to a limitation of the discovery and application of IBD genetics in the rest of the world populations. In this mini-review, we summarize the latest progress of genome-wide association studies of IBD across global ancestries especially the Chinese population, the similarities and differences in genetic architecture between European and East Asian ancestries, as well as, the clinical significances relevant to IBD genetic study.
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Affiliation(s)
- Han Gao
- Center for Inflammatory Bowel Disease Research and Department of Gastroenterology, The Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
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Song EM, Na SY, Hong SN, Ng SC, Hisamatsu T, Ye BD. Treatment of inflammatory bowel disease-Asian perspectives: the results of a multinational web-based survey in the 8th Asian Organization for Crohn's and Colitis meeting. Intest Res 2023; 21:339-352. [PMID: 37533265 PMCID: PMC10397553 DOI: 10.5217/ir.2022.00135] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 03/16/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND/AIMS As the characteristics of inflammatory bowel disease (IBD) differ between Asians and Westerners, it is necessary to determine adequate therapeutic strategy for Asian IBD patients. We evaluated the current treatment of IBD in Asian countries/regions using a web-based survey. METHODS The Korean Association for the Study of Intestinal Diseases conducted a multinational web-based survey for current IBD care in Asia between September 16, 2020, and November 13, 2020. RESULTS A total of 384 doctors treating IBD patients from 24 Asian countries/regions responded to the survey. Anti-tumor necrosis factor (TNF) agents, anti-integrins, and anti-interleukin-12/23 agents were available for use by 93.8%, 72.1%, and 70.1% of respondents in Asian countries/regions. Compared with a previous survey performed in 2014, an increased tendency for treatment with biologics, including anti-TNF agents, was observed. In the treatment of corticosteroid-refractory acute severe ulcerative colitis, 72.1% of respondents chose anti-TNF agents, followed by tacrolimus (11.7%). In the treatment of corticosteroid-refractory Crohn's disease, 90.4% chose anti-TNF agents, followed by thiopurines (53.1%), anti-interleukin-12/23 agents (39.3%), and anti-integrin agents (35.7%). In the treatment of Crohn's disease patients refractory to anti-TNF agents, the most preferred strategy was to measure serum levels of anti-TNF and anti-drug antibodies (40.9%), followed by empiric dose escalation or shortening of dosing intervals (25.3%). CONCLUSIONS Although there were some differences, treatment strategies for patients with IBD were mostly similar among Asian doctors. Based on the therapeutic outcomes, it is necessary to identify the most appropriate therapeutic strategy for Asian IBD patients.
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Affiliation(s)
- Eun Mi Song
- Department of Internal Medicine, Ewha Womans University College of Medicine, Seoul, Korea
| | - Soo-Young Na
- Department of Internal Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Incheon, Korea
| | - Sung Noh Hong
- Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Siew Chien Ng
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Tadakazu Hisamatsu
- Department of Gastroenterology and Hepatology, Kyorin University School of Medicine, Tokyo, Japan
| | - Byong Duk Ye
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
- Inflammatory Bowel Disease Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
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Richard N, Savoye G, Leboutte M, Amamou A, Ghosh S, Marion-Letellier R. Crohn’s disease: Why the ileum? World J Gastroenterol 2023; 29:3222-3240. [PMID: 37377591 PMCID: PMC10292140 DOI: 10.3748/wjg.v29.i21.3222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/23/2023] [Accepted: 05/08/2023] [Indexed: 06/01/2023] Open
Abstract
Crohn’s disease (CD) is an inflammatory bowel disease characterized by immune-mediated flares affecting any region of the intestine alternating with remission periods. In CD, the ileum is frequently affected and about one third of patients presents with a pure ileal type. Moreover, the ileal type of CD presents epidemiological specificities like a younger age at onset and often a strong link with smoking and genetic susceptibility genes. Most of these genes are associated with Paneth cell dysfunction, a cell type found in the intestinal crypts of the ileum. Besides, a Western-type diet is associated in epidemiological studies with CD onset and increasing evidence shows that diet can modulate the composition of bile acids and gut microbiota, which in turn modulates the susceptibility of the ileum to inflammation. Thus, the interplay between environmental factors and the histological and anatomical features of the ileum is thought to explain the specific transcriptome profile observed in CD ileitis. Indeed, both immune response and cellular healing processes harbour differences between ileal and non-ileal CD. Taken together, these findings advocate for a dedicated therapeutic approach to managing ileal CD. Currently, interventional pharmacological studies have failed to clearly demonstrate distinct response profiles according to disease site. However, the high rate of stricturing disease in ileal CD requires the identification of new therapeutic targets to significantly change the natural history of this debilitating disease.
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Affiliation(s)
- Nicolas Richard
- University of Rouen Normandie, INSERM, ADEN UMR 1073, Nutrition, Inflammation and Microbiota-Gut-Brain Axis, Rouen F-76000, France
- CHU Rouen, Department of Gastroenterology, Rouen University Hospital-Charles Nicolle, Rouen F-76000, France
- Institute for Research and Innovation in Biomedicine, University of Rouen Normandie, Rouen F-76000, France
| | - Guillaume Savoye
- University of Rouen Normandie, INSERM, ADEN UMR 1073, Nutrition, Inflammation and Microbiota-Gut-Brain Axis, Rouen F-76000, France
- CHU Rouen, Department of Gastroenterology, Rouen University Hospital-Charles Nicolle, Rouen F-76000, France
- Institute for Research and Innovation in Biomedicine, University of Rouen Normandie, Rouen F-76000, France
| | - Mathilde Leboutte
- University of Rouen Normandie, INSERM, ADEN UMR 1073, Nutrition, Inflammation and Microbiota-Gut-Brain Axis, Rouen F-76000, France
- Institute for Research and Innovation in Biomedicine, University of Rouen Normandie, Rouen F-76000, France
| | - Asma Amamou
- APC Microbiome Ireland, Biosciences Building, University College Cork, Cork T12 YT20, Ireland
| | - Subrata Ghosh
- APC Microbiome Ireland, Biosciences Building, University College Cork, Cork T12 YT20, Ireland
| | - Rachel Marion-Letellier
- University of Rouen Normandie, INSERM, ADEN UMR 1073, Nutrition, Inflammation and Microbiota-Gut-Brain Axis, Rouen F-76000, France
- Institute for Research and Innovation in Biomedicine, University of Rouen Normandie, Rouen F-76000, France
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Mu C, Zhao Q, Zhao Q, Yang L, Pang X, Liu T, Li X, Wang B, Fung SY, Cao H. Multi-omics in Crohn's disease: New insights from inside. Comput Struct Biotechnol J 2023; 21:3054-3072. [PMID: 37273853 PMCID: PMC10238466 DOI: 10.1016/j.csbj.2023.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 06/06/2023] Open
Abstract
Crohn's disease (CD) is an inflammatory bowel disease (IBD) with complex clinical manifestations such as chronic diarrhea, weight loss and hematochezia. Despite the increasing incidence worldwide, cure of CD remains extremely difficult. The rapid development of high-throughput sequencing technology with integrated-omics analyses in recent years has provided a new means for exploring the pathogenesis, mining the biomarkers and designing targeted personalized therapeutics of CD. Host genomics and epigenomics unveil heredity-related mechanisms of susceptible individuals, while microbiome and metabolomics map host-microbe interactions in CD patients. Proteomics shows great potential in searching for promising biomarkers. Nonetheless, single omics technology cannot holistically connect the mechanisms with heterogeneity of pathological behavior in CD. The rise of multi-omics analysis integrates genetic/epigenetic profiles with protein/microbial metabolite functionality, providing new hope for comprehensive and in-depth exploration of CD. Herein, we emphasized the different omics features and applications of CD and discussed the current research and limitations of multi-omics in CD. This review will update and deepen our understanding of CD from integration of broad omics spectra and will provide new evidence for targeted individualized therapeutics.
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Affiliation(s)
- Chenlu Mu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Qianjing Zhao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Qing Zhao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Lijiao Yang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xiaoqi Pang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Tianyu Liu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xiaomeng Li
- Department of Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Science, Tianjin Medical University, Tianjin, China
| | - Bangmao Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Shan-Yu Fung
- Department of Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Science, Tianjin Medical University, Tianjin, China
| | - Hailong Cao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
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Liu Z, Liu R, Gao H, Jung S, Gao X, Sun R, Liu X, Kim Y, Lee HS, Kawai Y, Nagasaki M, Umeno J, Tokunaga K, Kinouchi Y, Masamune A, Shi W, Shen C, Guo Z, Yuan K, Zhu S, Li D, Liu J, Ge T, Cho J, Daly MJ, McGovern DPB, Ye BD, Song K, Kakuta Y, Li M, Huang H. Genetic architecture of the inflammatory bowel diseases across East Asian and European ancestries. Nat Genet 2023; 55:796-806. [PMID: 37156999 PMCID: PMC10290755 DOI: 10.1038/s41588-023-01384-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 03/27/2023] [Indexed: 05/10/2023]
Abstract
Inflammatory bowel diseases (IBDs) are chronic disorders of the gastrointestinal tract with the following two subtypes: Crohn's disease (CD) and ulcerative colitis (UC). To date, most IBD genetic associations were derived from individuals of European (EUR) ancestries. Here we report the largest IBD study of individuals of East Asian (EAS) ancestries, including 14,393 cases and 15,456 controls. We found 80 IBD loci in EAS alone and 320 when meta-analyzed with ~370,000 EUR individuals (~30,000 cases), among which 81 are new. EAS-enriched coding variants implicate many new IBD genes, including ADAP1 and GIT2. Although IBD genetic effects are generally consistent across ancestries, genetics underlying CD appears more ancestry dependent than UC, driven by allele frequency (NOD2) and effect (TNFSF15). We extended the IBD polygenic risk score (PRS) by incorporating both ancestries, greatly improving its accuracy and highlighting the importance of diversity for the equitable deployment of PRS.
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Affiliation(s)
- Zhanju Liu
- Center for IBD Research, Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Ruize Liu
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Han Gao
- Center for IBD Research, Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Seulgi Jung
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Xiang Gao
- Center for IBD Research, Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ruicong Sun
- Center for IBD Research, Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaoming Liu
- Inflammatory Bowel Diseases Research Center, Department of Gastroenterology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yongjae Kim
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Ho-Su Lee
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Masao Nagasaki
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junji Umeno
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yoshitaka Kinouchi
- Student Healthcare Center, Institute for Excellence in Higher Education, Tohoku University, Sendai, Japan
| | - Atsushi Masamune
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Wenzhao Shi
- Digital Health China Technologies Corp Ltd., Beijing, China
| | - Chengguo Shen
- Digital Health China Technologies Corp Ltd., Beijing, China
| | - Zhenglin Guo
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kai Yuan
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shu Zhu
- Institute of Immunology, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Dalin Li
- Widjaja Inflammatory Bowel Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jianjun Liu
- Genome Institute of Singapore, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Tian Ge
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Precision Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Judy Cho
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dermot P B McGovern
- Widjaja Inflammatory Bowel Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Byong Duk Ye
- Department of Gastroenterology and Inflammatory Bowel Disease Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Kyuyoung Song
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea.
| | - Yoichi Kakuta
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan.
| | - Mingsong Li
- Inflammatory Bowel Diseases Research Center, Department of Gastroenterology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Hailiang Huang
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
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Jung S, Kim Y, Park D, Lee Y, Park S, Baek J, Hwang SW, Park SH, Yang SK, Ye BD, Han B, Song K, Lee HS. Case-case genome-wide association analysis identifying genetic loci with divergent effects on Crohn's disease and ulcerative colitis. Hum Mol Genet 2023; 32:677-684. [PMID: 36164742 DOI: 10.1093/hmg/ddac241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/07/2022] [Accepted: 09/21/2022] [Indexed: 02/07/2023] Open
Abstract
Crohn's disease (CD) and ulcerative colitis (UC), two major subtypes of inflammatory bowel disease, show substantial differences in their clinical course and treatment response. To identify the genetic factors underlying the distinct characteristics of these two diseases, we performed a genome-wide association study (GWAS) between CD (n = 2359) and UC (n = 2175) in a Korean population, followed by replication in an independent sample of 772 CD and 619 UC cases. Two novel loci were identified with divergent effects on CD and UC: rs9842650 in CD200 and rs885026 in NCOR2. In addition, the seven established susceptibility loci [major histocompatibility complex (MHC), TNFSF15, OTUD3, USP12, IL23R, FCHSD2 and RIPK2] reached genome-wide significance. Of the nine loci, six (MHC, TNFSF15, OTUD3, USP12, IL23R and CD200) were replicated in the case-case GWAS of European populations. The proportion of variance explained in CD-UC status by polygenic risk score analysis was up to 22.6%. The area under the receiver-operating characteristic curve value was 0.74, suggesting acceptable discrimination between CD and UC. This CD-UC GWAS provides new insights into genetic differences between the two diseases with similar symptoms and might be useful in improving their diagnosis and treatment.
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Affiliation(s)
- Seulgi Jung
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Yongjae Kim
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Dohoon Park
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Yoonho Lee
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Sojung Park
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Jiwon Baek
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Sung Wook Hwang
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Sang Hyoung Park
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Suk-Kyun Yang
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Byong Duk Ye
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Buhm Han
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Kyuyoung Song
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Ho-Su Lee
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul 05505, Korea
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Oh K, Hong HS, Ham NS, Lee J, Park SH, Yang SK, Yoon H, Kim YS, Choi CH, Ye BD. Real-world effectiveness and safety of ustekinumab induction therapy for Korean patients with Crohn's disease: a KASID prospective multicenter study. Intest Res 2023; 21:137-147. [PMID: 36751044 PMCID: PMC9911275 DOI: 10.5217/ir.2021.00173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/14/2022] [Indexed: 02/09/2023] Open
Abstract
BACKGROUND/AIMS We investigated the real-world effectiveness and safety of ustekinumab (UST) as induction treatment for Koreans with Crohn's disease (CD). METHODS CD patients who started UST were prospectively enrolled from 4 hospitals in Korea. All enrolled patients received intravenous UST infusion at week 0 and subcutaneous UST injection at week 8. Clinical outcomes were assessed using Crohn's Disease Activity Index (CDAI) scores at weeks 8 and 20 among patients with active disease (CDAI ≥150) at baseline. Clinical remission was defined as a CDAI <150, and clinical response was defined as a reduction in CDAI ≥70 points from baseline. Safety and factors associated with clinical remission at week 20 were also analyzed. RESULTS Sixty-five patients were enrolled between January 2019 and December 2020. Among 49 patients with active disease at baseline (CDAI ≥150), clinical remission and clinical response at week 8 were achieved in 26 (53.1%) and 30 (61.2%) patients, respectively. At week 20, 27 (55.1%) and 35 (71.4%) patients achieved clinical remission and clinical response, respectively. Twenty-seven patients (41.5%) experienced adverse events, with serious adverse events in 3 patients (4.6%). One patient (1.5%) stopped UST therapy due to poor response. Underweight (body mass index <18.5 kg/m2) (odds ratio [OR], 0.085; 95% confidence interval [CI], 0.014-0.498; P=0.006) and elevated C-reactive protein at baseline (OR, 0.133; 95% CI, 0.022-0.823; P=0.030) were inversely associated with clinical remission at week 20. CONCLUSIONS UST was effective and well-tolerated as induction therapy for Korean patients with CD.
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Affiliation(s)
- Kyunghwan Oh
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hee Seung Hong
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Nam Seok Ham
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jungbok Lee
- Department of Clinical Epidemiology and Biostatistics, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sang Hyoung Park
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea,Inflammatory Bowel Disease Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea,Digestive Diseases Research Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Suk-Kyun Yang
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea,Inflammatory Bowel Disease Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea,Digestive Diseases Research Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hyuk Yoon
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - You Sun Kim
- Department of Internal Medicine, Seoul Paik Hospital, Inje University College of Medicine, Seoul, Korea
| | - Chang Hwan Choi
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul, Korea
| | - Byong Duk Ye
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea,Inflammatory Bowel Disease Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea,Digestive Diseases Research Center, University of Ulsan College of Medicine, Seoul, Korea,Correspondence to Byong Duk Ye, Department of Gastroenterology and Inflammatory Bowel Disease Center, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul 05505, Korea. Tel: +82-2-3010-3181, Fax: +82-2-476-0824, E-mail:
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13
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OUP accepted manuscript. Hum Mol Genet 2022; 31:3934-3944. [DOI: 10.1093/hmg/ddac101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 11/14/2022] Open
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